sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | bedtools 2.31.0+dfsg-2 (ppc64el) Sun, 19 Nov 2023 18:46:02 +0000 | +==============================================================================+ Package: bedtools Version: 2.31.0+dfsg-2 Source Version: 2.31.0+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: ppc64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-961b3836-b004-49d4-972b-9a556004eb2f' with '<>' I: NOTICE: Log filtering will replace 'build/bedtools-CNY5GR/resolver-3duFBx' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [198 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-11-19-1403.48-F-2023-11-19-0203.35.pdiff [21.5 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-11-19-1403.48-F-2023-11-19-0203.35.pdiff [25.3 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-11-19-1403.48-F-2023-11-19-0203.35.pdiff [21.5 kB] Get:6 http://localhost:3142/debian sid/main ppc64el Packages [9412 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-11-19-1403.48-F-2023-11-19-0203.35.pdiff [25.3 kB] Fetched 9784 kB in 3s (3560 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libsystemd0 libudev1 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 480 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://localhost:3142/debian sid/main amd64 libsystemd0 amd64 255~rc2-2 [359 kB] Get:2 http://localhost:3142/debian sid/main amd64 libudev1 amd64 255~rc2-2 [121 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 480 kB in 0s (4820 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14615 files and directories currently installed.) Preparing to unpack .../libsystemd0_255~rc2-2_amd64.deb ... Unpacking libsystemd0:amd64 (255~rc2-2) over (255~rc2-1) ... Setting up libsystemd0:amd64 (255~rc2-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14615 files and directories currently installed.) Preparing to unpack .../libudev1_255~rc2-2_amd64.deb ... Unpacking libudev1:amd64 (255~rc2-2) over (255~rc2-1) ... Setting up libudev1:amd64 (255~rc2-2) ... Processing triggers for libc-bin (2.37-12) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bedtools.git Please use: git clone https://salsa.debian.org/med-team/bedtools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 14.5 MB of source archives. Get:1 http://localhost:3142/debian sid/main bedtools 2.31.0+dfsg-2 (dsc) [2230 B] Get:2 http://localhost:3142/debian sid/main bedtools 2.31.0+dfsg-2 (tar) [14.5 MB] Get:3 http://localhost:3142/debian sid/main bedtools 2.31.0+dfsg-2 (diff) [14.6 kB] Fetched 14.5 MB in 0s (186 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedtools-CNY5GR/bedtools-2.31.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedtools-CNY5GR' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64, libc-dev:ppc64el, libstdc++-dev:ppc64el Filtered Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64, libc-dev:ppc64el, libstdc++-dev:ppc64el dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [770 B] Get:5 copy:/<>/apt_archive ./ Packages [815 B] Fetched 2194 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-powerpc64le-linux-gnu bsdextrautils cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-11-base:ppc64el gcc-13-base:ppc64el gcc-13-cross-base gcc-13-powerpc64le-linux-gnu gcc-13-powerpc64le-linux-gnu-base gcc-powerpc64le-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:ppc64el libasan8-ppc64el-cross libatomic1:ppc64el libatomic1-ppc64el-cross libbz2-1.0:ppc64el libbz2-dev:ppc64el libc6:ppc64el libc6-dev:ppc64el libc6-dev-ppc64el-cross libc6-ppc64el-cross libcom-err2:ppc64el libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:ppc64el libcrypt1:ppc64el libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:ppc64el libgcc-13-dev-ppc64el-cross libgcc-s1:ppc64el libgcc-s1-ppc64el-cross libgomp1:ppc64el libgomp1-ppc64el-cross libgssapi-krb5-2:ppc64el libicu72 libio-string-perl libitm1:ppc64el libitm1-ppc64el-cross libk5crypto3:ppc64el libkeyutils1:ppc64el libkrb5-3:ppc64el libkrb5support0:ppc64el liblocale-gettext-perl liblsan0:ppc64el liblsan0-ppc64el-cross liblzma-dev:ppc64el liblzma5:ppc64el libmagic-mgc libmagic1 libncursesw6 libnsl-dev:ppc64el libnsl2:ppc64el libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0:ppc64el libquadmath0-ppc64el-cross libreadline8 libsqlite3-0 libssl3:ppc64el libstdc++-11-dev:ppc64el libstdc++-13-dev-ppc64el-cross libstdc++6:ppc64el libstdc++6-ppc64el-cross libsub-override-perl libtirpc-dev:ppc64el libtirpc3:ppc64el libtool libtsan0:ppc64el libtsan2-ppc64el-cross libubsan1:ppc64el libubsan1-ppc64el-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:ppc64el linux-libc-dev-ppc64el-cross m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sensible-utils ucf zlib1g:ppc64el zlib1g-dev:ppc64el Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-13-locales cpp-13-doc cpp-doc dh-make binutils-multiarch gcc-13-doc manpages-dev flex bison gdb-powerpc64le-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:ppc64el libc-l10n:ppc64el locales:ppc64el libnss-nis:ppc64el libnss-nisplus:ppc64el manpages-dev:ppc64el krb5-doc:ppc64el krb5-user:ppc64el liblzma-doc:ppc64el libstdc++-11-doc:ppc64el libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx bzip2-doc:ppc64el libidn2-0:ppc64el libarchive-cpio-perl krb5-locales:ppc64el libgpm2 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-powerpc64le-linux-gnu bsdextrautils cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-11-base:ppc64el gcc-13-base:ppc64el gcc-13-cross-base gcc-13-powerpc64le-linux-gnu gcc-13-powerpc64le-linux-gnu-base gcc-powerpc64le-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:ppc64el libasan8-ppc64el-cross libatomic1:ppc64el libatomic1-ppc64el-cross libbz2-1.0:ppc64el libbz2-dev:ppc64el libc6:ppc64el libc6-dev:ppc64el libc6-dev-ppc64el-cross libc6-ppc64el-cross libcom-err2:ppc64el libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:ppc64el libcrypt1:ppc64el libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:ppc64el libgcc-13-dev-ppc64el-cross libgcc-s1:ppc64el libgcc-s1-ppc64el-cross libgomp1:ppc64el libgomp1-ppc64el-cross libgssapi-krb5-2:ppc64el libicu72 libio-string-perl libitm1:ppc64el libitm1-ppc64el-cross libk5crypto3:ppc64el libkeyutils1:ppc64el libkrb5-3:ppc64el libkrb5support0:ppc64el liblocale-gettext-perl liblsan0:ppc64el liblsan0-ppc64el-cross liblzma-dev:ppc64el liblzma5:ppc64el libmagic-mgc libmagic1 libncursesw6 libnsl-dev:ppc64el libnsl2:ppc64el libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0:ppc64el libquadmath0-ppc64el-cross libreadline8 libsqlite3-0 libssl3:ppc64el libstdc++-11-dev:ppc64el libstdc++-13-dev-ppc64el-cross libstdc++6:ppc64el libstdc++6-ppc64el-cross libsub-override-perl libtirpc-dev:ppc64el libtirpc3:ppc64el libtool libtsan0:ppc64el libtsan2-ppc64el-cross libubsan1:ppc64el libubsan1-ppc64el-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:ppc64el linux-libc-dev-ppc64el-cross m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sbuild-build-depends-main-dummy:ppc64el sensible-utils ucf zlib1g:ppc64el zlib1g-dev:ppc64el 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 106 MB of archives. After this operation, 435 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-6 [15.3 kB] Get:3 http://localhost:3142/debian sid/main amd64 libpython3.11-minimal amd64 3.11.6-3 [815 kB] Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-2 [99.0 kB] Get:5 http://localhost:3142/debian sid/main amd64 python3.11-minimal amd64 3.11.6-3 [2030 kB] Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.11.4-5+b1 [26.5 kB] Get:7 http://localhost:3142/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:8 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.4+20231016-1 [135 kB] Get:9 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:10 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:11 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.44.0-1 [881 kB] Get:12 http://localhost:3142/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.6-3 [1812 kB] Get:13 http://localhost:3142/debian sid/main amd64 python3.11 amd64 3.11.6-3 [586 kB] Get:14 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.11.4-5+b1 [9492 B] Get:15 http://localhost:3142/debian sid/main amd64 python3 amd64 3.11.4-5+b1 [26.5 kB] Get:16 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:17 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-2 [314 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.45-2 [105 kB] Get:19 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-2 [42.8 kB] Get:20 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-13+b1 [161 kB] Get:21 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:22 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-3 [1180 kB] Get:23 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.39.2-6 [89.1 kB] Get:24 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:25 http://localhost:3142/debian sid/main amd64 man-db amd64 2.12.0-1 [1402 kB] Get:26 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:27 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:28 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:29 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:30 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:31 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-13 [496 kB] Get:32 http://localhost:3142/debian sid/main amd64 binutils-powerpc64le-linux-gnu amd64 2.41-6 [2773 kB] Get:33 http://localhost:3142/debian sid/main amd64 gcc-13-powerpc64le-linux-gnu-base amd64 13.2.0-6cross1 [40.8 kB] Get:34 http://localhost:3142/debian sid/main amd64 cpp-13-powerpc64le-linux-gnu amd64 13.2.0-6cross1 [9188 kB] Get:35 http://localhost:3142/debian sid/main amd64 cpp-powerpc64le-linux-gnu amd64 4:13.2.0-1 [4124 B] Get:36 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:37 http://localhost:3142/debian sid/main amd64 gcc-13-cross-base all 13.2.0-6cross1 [36.3 kB] Get:38 http://localhost:3142/debian sid/main amd64 libc6-ppc64el-cross all 2.37-12cross1 [1352 kB] Get:39 http://localhost:3142/debian sid/main amd64 libgcc-s1-ppc64el-cross all 13.2.0-6cross1 [35.0 kB] Get:40 http://localhost:3142/debian sid/main amd64 libgomp1-ppc64el-cross all 13.2.0-6cross1 [134 kB] Get:41 http://localhost:3142/debian sid/main amd64 libitm1-ppc64el-cross all 13.2.0-6cross1 [28.3 kB] Get:42 http://localhost:3142/debian sid/main amd64 libatomic1-ppc64el-cross all 13.2.0-6cross1 [9484 B] Get:43 http://localhost:3142/debian sid/main amd64 libasan8-ppc64el-cross all 13.2.0-6cross1 [2516 kB] Get:44 http://localhost:3142/debian sid/main amd64 liblsan0-ppc64el-cross all 13.2.0-6cross1 [1113 kB] Get:45 http://localhost:3142/debian sid/main amd64 libtsan2-ppc64el-cross all 13.2.0-6cross1 [2352 kB] Get:46 http://localhost:3142/debian sid/main amd64 libstdc++6-ppc64el-cross all 13.2.0-6cross1 [729 kB] Get:47 http://localhost:3142/debian sid/main amd64 libubsan1-ppc64el-cross all 13.2.0-6cross1 [1022 kB] Get:48 http://localhost:3142/debian sid/main amd64 libquadmath0-ppc64el-cross all 13.2.0-6cross1 [149 kB] Get:49 http://localhost:3142/debian sid/main amd64 libgcc-13-dev-ppc64el-cross all 13.2.0-6cross1 [1378 kB] Get:50 http://localhost:3142/debian sid/main amd64 gcc-13-powerpc64le-linux-gnu amd64 13.2.0-6cross1 [18.1 MB] Get:51 http://localhost:3142/debian sid/main amd64 gcc-powerpc64le-linux-gnu amd64 4:13.2.0-1 [1480 B] Get:52 http://localhost:3142/debian sid/main amd64 linux-libc-dev-ppc64el-cross all 6.5.8-1cross1 [2004 kB] Get:53 http://localhost:3142/debian sid/main amd64 libc6-dev-ppc64el-cross all 2.37-12cross1 [1811 kB] Get:54 http://localhost:3142/debian sid/main amd64 libstdc++-13-dev-ppc64el-cross all 13.2.0-6cross1 [2290 kB] Get:55 http://localhost:3142/debian sid/main amd64 g++-13-powerpc64le-linux-gnu amd64 13.2.0-6cross1 [10.2 MB] Get:56 http://localhost:3142/debian sid/main amd64 g++-powerpc64le-linux-gnu amd64 4:13.2.0-1 [1184 B] Get:57 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:58 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:59 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:60 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [686 kB] Get:61 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:62 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:63 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:64 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:65 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:66 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:67 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:68 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:69 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:70 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:71 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:72 http://localhost:3142/debian sid/main amd64 crossbuild-essential-ppc64el all 12.10 [3492 B] Get:73 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.8 [82.1 kB] Get:74 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB] Get:75 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:76 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:77 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get:78 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:79 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:80 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.190-1 [176 kB] Get:81 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:82 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-13+b1 [1301 kB] Get:83 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:84 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:85 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.8 [956 kB] Get:86 http://localhost:3142/debian sid/main ppc64el gcc-11-base ppc64el 11.4.0-5 [40.1 kB] Get:87 http://localhost:3142/debian sid/main ppc64el gcc-13-base ppc64el 13.2.0-6 [40.5 kB] Get:88 http://localhost:3142/debian sid/main ppc64el libgcc-s1 ppc64el 13.2.0-6 [35.0 kB] Get:89 http://localhost:3142/debian sid/main ppc64el libc6 ppc64el 2.37-12 [2683 kB] Get:90 http://localhost:3142/debian sid/main ppc64el libasan6 ppc64el 11.4.0-5 [2037 kB] Get:91 http://localhost:3142/debian sid/main ppc64el libatomic1 ppc64el 13.2.0-6 [9772 B] Get:92 http://localhost:3142/debian sid/main ppc64el libbz2-1.0 ppc64el 1.0.8-5+b1 [51.8 kB] Get:93 http://localhost:3142/debian sid/main ppc64el linux-libc-dev ppc64el 6.5.10-1 [2006 kB] Get:94 http://localhost:3142/debian sid/main ppc64el libcrypt1 ppc64el 1:4.4.36-2 [98.0 kB] Get:95 http://localhost:3142/debian sid/main ppc64el libcrypt-dev ppc64el 1:4.4.36-2 [132 kB] Get:96 http://localhost:3142/debian sid/main ppc64el libkrb5support0 ppc64el 1.20.1-5 [36.2 kB] Get:97 http://localhost:3142/debian sid/main ppc64el libcom-err2 ppc64el 1.47.0-2+b1 [20.5 kB] Get:98 http://localhost:3142/debian sid/main ppc64el libk5crypto3 ppc64el 1.20.1-5 [89.8 kB] Get:99 http://localhost:3142/debian sid/main ppc64el libkeyutils1 ppc64el 1.6.3-2 [10.0 kB] Get:100 http://localhost:3142/debian sid/main ppc64el libssl3 ppc64el 3.0.12-2 [2030 kB] Get:101 http://localhost:3142/debian sid/main ppc64el libkrb5-3 ppc64el 1.20.1-5 [364 kB] Get:102 http://localhost:3142/debian sid/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-5 [149 kB] Get:103 http://localhost:3142/debian sid/main ppc64el libtirpc3 ppc64el 1.3.4+ds-1 [93.3 kB] Get:104 http://localhost:3142/debian sid/main ppc64el libnsl2 ppc64el 1.3.0-3 [44.3 kB] Get:105 http://localhost:3142/debian sid/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1 [206 kB] Get:106 http://localhost:3142/debian sid/main ppc64el libnsl-dev ppc64el 1.3.0-3 [72.7 kB] Get:107 http://localhost:3142/debian sid/main ppc64el libc6-dev ppc64el 2.37-12 [1815 kB] Get:108 http://localhost:3142/debian sid/main ppc64el libbz2-dev ppc64el 1.0.8-5+b1 [36.1 kB] Get:109 http://localhost:3142/debian sid/main ppc64el libgomp1 ppc64el 13.2.0-6 [137 kB] Get:110 http://localhost:3142/debian sid/main ppc64el libitm1 ppc64el 13.2.0-6 [28.8 kB] Get:111 http://localhost:3142/debian sid/main ppc64el liblsan0 ppc64el 13.2.0-6 [1114 kB] Get:112 http://localhost:3142/debian sid/main ppc64el libtsan0 ppc64el 11.4.0-5 [2023 kB] Get:113 http://localhost:3142/debian sid/main ppc64el libstdc++6 ppc64el 13.2.0-6 [777 kB] Get:114 http://localhost:3142/debian sid/main ppc64el libubsan1 ppc64el 13.2.0-6 [1023 kB] Get:115 http://localhost:3142/debian sid/main ppc64el libquadmath0 ppc64el 13.2.0-6 [150 kB] Get:116 http://localhost:3142/debian sid/main ppc64el libgcc-11-dev ppc64el 11.4.0-5 [1269 kB] Get:117 http://localhost:3142/debian sid/main ppc64el liblzma5 ppc64el 5.4.4-0.1 [237 kB] Get:118 http://localhost:3142/debian sid/main ppc64el liblzma-dev ppc64el 5.4.4-0.1 [293 kB] Get:119 http://localhost:3142/debian sid/main ppc64el libstdc++-11-dev ppc64el 11.4.0-5 [2071 kB] Get:120 http://localhost:3142/debian sid/main ppc64el zlib1g ppc64el 1:1.3.dfsg-2 [86.0 kB] Get:121 http://localhost:3142/debian sid/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-2 [917 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 106 MB in 1s (175 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14615 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-6) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.6-3_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.6-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.6-3_amd64.deb ... Unpacking python3.11-minimal (3.11.6-3) ... Setting up libpython3.11-minimal:amd64 (3.11.6-3) ... Setting up libexpat1:amd64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.6-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 14945 files and directories currently installed.) 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Setting up libconfig-inifiles-perl (3.000003-2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up gcc-11-base:ppc64el (11.4.0-5) ... Setting up libfile-which-perl (1.27-2) ... Setting up libicu72:amd64 (72.1-4) ... Setting up bsdextrautils (2.39.2-6) ... Setting up libmagic-mgc (1:5.45-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libc6-ppc64el-cross (2.37-12cross1) ... Setting up libdebhelper-perl (13.11.8) ... Setting up libsqlite3-0:amd64 (3.44.0-1) ... Setting up libmagic1:amd64 (1:5.45-2) ... Setting up linux-libc-dev:ppc64el (6.5.10-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-13+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2) ... Setting up gcc-13-powerpc64le-linux-gnu-base:amd64 (13.2.0-6cross1) ... Setting up libyaml-perl (1.30-2) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up gcc-13-base:ppc64el (13.2.0-6) ... Setting up gcc-13-cross-base (13.2.0-6cross1) ... Setting up autopoint (0.21-13) ... Setting up libncursesw6:amd64 (6.4+20231016-1) ... Setting up autoconf (2.71-3) ... Setting up libitm1-ppc64el-cross (13.2.0-6cross1) ... Setting up libatomic1-ppc64el-cross (13.2.0-6cross1) ... Setting up sensible-utils (0.0.20) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up linux-libc-dev-ppc64el-cross (6.5.8-1cross1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libgcc-s1-ppc64el-cross (13.2.0-6cross1) ... Setting up binutils-powerpc64le-linux-gnu (2.41-6) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-6cross1) ... Setting up libelf1:amd64 (0.190-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3) ... Setting up liblocale-gettext-perl (1.07-6) ... Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-13+b1) ... Setting up libc6-dev-ppc64el-cross (2.37-12cross1) ... Setting up libtool (2.4.7-7) ... Setting up libquadmath0-ppc64el-cross (13.2.0-6cross1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libasan8-ppc64el-cross (13.2.0-6cross1) ... Setting up libgomp1-ppc64el-cross (13.2.0-6cross1) ... Setting up liblsan0-ppc64el-cross (13.2.0-6cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libtsan2-ppc64el-cross (13.2.0-6cross1) ... Setting up dh-autoreconf (20) ... Setting up ucf (3.0043+nmu1) ... Setting up libstdc++6-ppc64el-cross (13.2.0-6cross1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libubsan1-ppc64el-cross (13.2.0-6cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.6-3) ... Setting up man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-13-dev-ppc64el-cross (13.2.0-6cross1) ... Setting up libpython3-stdlib:amd64 (3.11.4-5+b1) ... Setting up python3.11 (3.11.6-3) ... Setting up libstdc++-13-dev-ppc64el-cross (13.2.0-6cross1) ... Setting up debhelper (13.11.8) ... Setting up python3 (3.11.4-5+b1) ... Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-6cross1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-13-powerpc64le-linux-gnu (13.2.0-6cross1) ... Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-1) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up g++-powerpc64le-linux-gnu (4:13.2.0-1) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-ppc64el (12.10) ... Setting up libgcc-s1:ppc64el (13.2.0-6) ... Setting up libc6:ppc64el (2.37-12) ... Setting up libbz2-1.0:ppc64el (1.0.8-5+b1) ... Setting up libstdc++6:ppc64el (13.2.0-6) ... Setting up liblsan0:ppc64el (13.2.0-6) ... Setting up libitm1:ppc64el (13.2.0-6) ... Setting up libtsan0:ppc64el (11.4.0-5) ... Setting up libkeyutils1:ppc64el (1.6.3-2) ... Setting up liblzma5:ppc64el (5.4.4-0.1) ... Setting up libssl3:ppc64el (3.0.12-2) ... Setting up zlib1g:ppc64el (1:1.3.dfsg-2) ... Setting up libcrypt1:ppc64el (1:4.4.36-2) ... Setting up libcom-err2:ppc64el (1.47.0-2+b1) ... Setting up libgomp1:ppc64el (13.2.0-6) ... Setting up libasan6:ppc64el (11.4.0-5) ... Setting up libkrb5support0:ppc64el (1.20.1-5) ... Setting up libquadmath0:ppc64el (13.2.0-6) ... Setting up libatomic1:ppc64el (13.2.0-6) ... Setting up libk5crypto3:ppc64el (1.20.1-5) ... Setting up liblzma-dev:ppc64el (5.4.4-0.1) ... Setting up libubsan1:ppc64el (13.2.0-6) ... Setting up libgcc-11-dev:ppc64el (11.4.0-5) ... Setting up libcrypt-dev:ppc64el (1:4.4.36-2) ... Setting up libkrb5-3:ppc64el (1.20.1-5) ... Setting up libgssapi-krb5-2:ppc64el (1.20.1-5) ... Setting up libtirpc3:ppc64el (1.3.4+ds-1) ... Setting up libtirpc-dev:ppc64el (1.3.4+ds-1) ... Setting up libnsl2:ppc64el (1.3.0-3) ... Setting up libnsl-dev:ppc64el (1.3.0-3) ... Setting up libc6-dev:ppc64el (2.37-12) ... Setting up libbz2-dev:ppc64el (1.0.8-5+b1) ... Setting up libstdc++-11-dev:ppc64el (11.4.0-5) ... Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-2) ... Setting up sbuild-build-depends-main-dummy:ppc64el (0.invalid.0) ... Processing triggers for libc-bin (2.37-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.55-1 (2023-09-29) amd64 (x86_64) Toolchain package versions: binutils_2.41-6 dpkg-dev_1.22.1 g++-11_11.4.0-5 g++-13_13.2.0-6 gcc-11_11.4.0-5 gcc-13_13.2.0-6 libc6-dev_2.37-12 libstdc++-11-dev_11.4.0-5 libstdc++-13-dev_13.2.0-6 libstdc++-13-dev-ppc64el-cross_13.2.0-6cross1 libstdc++6_13.2.0-6 libstdc++6-ppc64el-cross_13.2.0-6cross1 linux-libc-dev_6.5.10-1 Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.2 bash_5.2.15-2+b6 binutils_2.41-6 binutils-common_2.41-6 binutils-powerpc64le-linux-gnu_2.41-6 binutils-x86-64-linux-gnu_2.41-6 bsdextrautils_2.39.2-6 bsdutils_1:2.39.2-6 build-essential_12.10 bzip2_1.0.8-5+b1 coreutils_9.4-2+b1 cpp_4:13.2.0-1 cpp-11_11.4.0-5 cpp-13_13.2.0-6 cpp-13-powerpc64le-linux-gnu_13.2.0-6cross1 cpp-powerpc64le-linux-gnu_4:13.2.0-1 cross-config_2.6.20 crossbuild-essential-ppc64el_12.10 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debian-archive-keyring_2023.4 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.1 dpkg-cross_2.6.20 dpkg-dev_1.22.1 dwz_0.15-1 e2fsprogs_1.47.0-2+b1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1 g++-11_11.4.0-5 g++-13_13.2.0-6 g++-13-powerpc64le-linux-gnu_13.2.0-6cross1 g++-powerpc64le-linux-gnu_4:13.2.0-1 gcc_4:13.2.0-1 gcc-11_11.4.0-5 gcc-11-base_11.4.0-5 gcc-12-base_12.3.0-11 gcc-13_13.2.0-6 gcc-13-base_13.2.0-6 gcc-13-cross-base_13.2.0-6cross1 gcc-13-powerpc64le-linux-gnu_13.2.0-6cross1 gcc-13-powerpc64le-linux-gnu-base_13.2.0-6cross1 gcc-9-base_9.5.0-4 gcc-powerpc64le-linux-gnu_4:13.2.0-1 gettext_0.21-13+b1 gettext-base_0.21-13+b1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan6_11.4.0-5 libasan8_13.2.0-6 libasan8-ppc64el-cross_13.2.0-6cross1 libatomic1_13.2.0-6 libatomic1-ppc64el-cross_13.2.0-6cross1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-6 libblkid1_2.39.2-6 libbz2-1.0_1.0.8-5+b1 libbz2-dev_1.0.8-5+b1 libc-bin_2.37-12 libc-dev-bin_2.37-12 libc6_2.37-12 libc6-dev_2.37-12 libc6-dev-ppc64el-cross_2.37-12cross1 libc6-ppc64el-cross_2.37-12cross1 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-4 libcc1-0_13.2.0-6 libcom-err2_1.47.0-2+b1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6 libctf0_2.41-6 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.8 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.22.1 libelf1_0.190-1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2+b1 libfakeroot_1.32.2-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-11-dev_11.4.0-5 libgcc-13-dev_13.2.0-6 libgcc-13-dev-ppc64el-cross_13.2.0-6cross1 libgcc-s1_13.2.0-6 libgcc-s1-ppc64el-cross_13.2.0-6cross1 libgcrypt20_1.10.2-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4+b1 libgomp1_13.2.0-6 libgomp1-ppc64el-cross_13.2.0-6cross1 libgpg-error0_1.47-3 libgprofng0_2.41-6 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhwasan0_13.2.0-6 libicu72_72.1-4 libidn2-0_2.3.4-1+b1 libio-string-perl_1.08-4 libisl23_0.26-3 libitm1_13.2.0-6 libitm1-ppc64el-cross_13.2.0-6cross1 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 liblocale-gettext-perl_1.07-6 liblsan0_13.2.0-6 liblsan0-ppc64el-cross_13.2.0-6cross1 liblz4-1_1.9.4-1 liblzma-dev_5.4.4-0.1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231016-1 libnettle8_3.9.1-2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.0-5 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.34_5.34.0-5 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpython3-stdlib_3.11.4-5+b1 libpython3.11-minimal_3.11.6-3 libpython3.11-stdlib_3.11.6-3 libquadmath0_13.2.0-6 libquadmath0-ppc64el-cross_13.2.0-6cross1 libreadline8_8.2-1.3 libseccomp2_2.5.4-2 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-6 libsmartcols1_2.39.2-6 libsqlite3-0_3.44.0-1 libss2_1.47.0-2+b1 libssl3_3.0.12-2 libstdc++-11-dev_11.4.0-5 libstdc++-13-dev_13.2.0-6 libstdc++-13-dev-ppc64el-cross_13.2.0-6cross1 libstdc++6_13.2.0-6 libstdc++6-ppc64el-cross_13.2.0-6cross1 libsub-override-perl_0.09-4 libsystemd0_255~rc2-2 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libtsan0_11.4.0-5 libtsan2_13.2.0-6 libtsan2-ppc64el-cross_13.2.0-6cross1 libubsan1_13.2.0-6 libubsan1-ppc64el-cross_13.2.0-6cross1 libuchardet0_0.0.7-1 libudev1_255~rc2-2 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libyaml-perl_1.30-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.10-1 linux-libc-dev-ppc64el-cross_6.5.8-1cross1 login_1:4.13+dfsg1-3 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Source: bedtools Binary: bedtools, bedtools-test Architecture: any all Version: 2.31.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://github.com/arq5x/bedtools2 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bedtools Vcs-Git: https://salsa.debian.org/med-team/bedtools.git Testsuite: autopkgtest Testsuite-Triggers: tabix Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev Package-List: bedtools deb science optional arch=any bedtools-test deb science optional arch=all Checksums-Sha1: c633231ea43281518fc661bb308ff531c0e93f4e 14483704 bedtools_2.31.0+dfsg.orig.tar.xz ffc64ee2b9dc7aad78ab729e21dc245bb2bc330c 14612 bedtools_2.31.0+dfsg-2.debian.tar.xz Checksums-Sha256: c2317d520716a21881ebce5beda510b084d04865f559fcaec53795edfa5e9c15 14483704 bedtools_2.31.0+dfsg.orig.tar.xz a11c7ff99c891175178ce7f79b3a5efd2e71885565d8a931ec09c82f3e924c50 14612 bedtools_2.31.0+dfsg-2.debian.tar.xz Files: a9a31dad279a48f81a0a6db088372e2e 14483704 bedtools_2.31.0+dfsg.orig.tar.xz 9e47e14001ed5d267fd182cf1a56890a 14612 bedtools_2.31.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmVY3/MUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp3+xAAvDEUAMX58mbUN03PReKDYoN/XtWk RCYxXPrajDMAPMqEHZloVjxd2lHci/OVM4hSWv3ZpFVji1cGcDcDHpO57WGS1BVK Y0ZPKrRhRw2IveM5l/qotyhSTIVbnCNiY0Otfdnj6S1RNbqgc8nKZhNhQ10z2A7z 4MNpJsc91MngM+x+gDXIUPVILZeq20yOyO+PY8dqbkdtGUVcTm1DtzPOTs0pKJ1l KHx3uFkS3P6RPMxDFL3pPVBUOQZBQdhsU9NCyRbSmFHpuJcMogs70neBWuButlC+ h+urJShnrTZm8iTxbToS0Pr110hOvsqWmxZgAeBDX+Mu/aghUAPmsqJ+mDjOKL6Z SU++NCEacmwErq0SkNYxYYG2fdogAkX6vzN7q/7YyXoz/U1Hal5IKQbdJUpki6Ua k6tGPRK0V4m3QW/bwxSkkzqDTLRi+2CbYFyYc3ImjnmwubHhoQgnTwPEJCPw+vOj +/sMbXLSkHlIpf+OE7yCj2AHXooJI3SPp9FGhcZmKq+l1xEcRCctnnoKB/Y77KIy xL4kM4ngVlZueJ8OzkKfqlnBvUKCevM/IDzP7wAdK3pmEZQaR1wIt9jwOQVL9/Lq 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Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.ppc64el DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.8InSiQ6qd9/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-961b3836-b004-49d4-972b-9a556004eb2f SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -appc64el -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package bedtools dpkg-buildpackage: info: source version 2.31.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-architecture: warning: specified GNU system type powerpc64le-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el dpkg-source: info: using options from bedtools-2.31.0+dfsg/debian/source/options: --single-debian-patch debian/rules clean dh clean dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' * Cleaning up. make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/bedtools.substvars debian/bedtools-test.substvars debian/files rm -fr -- debian/bedtools/ debian/tmp/ debian/bedtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- VERBOSE=1 make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-gcc VERBOSE=1 make[2]: Entering directory '/<>' Building BEDTools: ========================================================= CXXFLAGS is [-g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security] DETECTED_VERSION = v2.31.0 CURRENT_VERSION = Updating version file. * compiling src/bedtools.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedtools.o -MMD -MP -MF obj/bedtools.Td -c -o obj/bedtools.o src/bedtools.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/driver/BedtoolsDriver.h:1, from src/bedtools.cpp:21: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/htsutil.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/htsutil.o -MMD -MP -MF obj/htsutil.Td -c -o obj/htsutil.o src/htsutil.cpp * compiling src/annotateBed/annotateMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateMain.o -MMD -MP -MF obj/annotateMain.Td -c -o obj/annotateMain.o src/annotateBed/annotateMain.cpp * compiling src/annotateBed/annotateBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateBed.o -MMD -MP -MF obj/annotateBed.Td -c -o obj/annotateBed.o src/annotateBed/annotateBed.cpp * compiling src/bamToBed/bamToBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToBed.o -MMD -MP -MF obj/bamToBed.Td -c -o obj/bamToBed.o src/bamToBed/bamToBed.cpp src/bamToBed/bamToBed.cpp: In function ‘int bamtobed_main(int, char**)’: src/bamToBed/bamToBed.cpp:88:10: warning: variable ‘useAlignmentScore’ set but not used [-Wunused-but-set-variable] 88 | bool useAlignmentScore = false; | ^~~~~~~~~~~~~~~~~ In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToBed/bamToBed.cpp:12: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/bamToFastq/bamToFastqMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastqMain.o -MMD -MP -MF obj/bamToFastqMain.Td -c -o obj/bamToFastqMain.o src/bamToFastq/bamToFastqMain.cpp src/bamToFastq/bamToFastqMain.cpp: In function ‘int bamtofastq_main(int, char**)’: src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable ‘haveFastq2’ set but not used [-Wunused-but-set-variable] 38 | bool haveFastq2 = false; | ^~~~~~~~~~ * compiling src/bamToFastq/bamToFastq.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastq.o -MMD -MP -MF obj/bamToFastq.Td -c -o obj/bamToFastq.o src/bamToFastq/bamToFastq.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToFastq/bamToFastq.h:15, from src/bamToFastq/bamToFastq.cpp:15: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/bedToBam/bedToBam.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedToBam.o -MMD -MP -MF obj/bedToBam.Td -c -o obj/bedToBam.o src/bedToBam/bedToBam.cpp src/bedToBam/bedToBam.cpp: In function ‘int bedtobam_main(int, char**)’: src/bedToBam/bedToBam.cpp:60:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] 60 | bool haveMapQual = false; | ^~~~~~~~~~~ * compiling src/bedpeToBam/bedpeToBam.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedpeToBam.o -MMD -MP -MF obj/bedpeToBam.Td -c -o obj/bedpeToBam.o src/bedpeToBam/bedpeToBam.cpp src/bedpeToBam/bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’: src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] 61 | bool haveMapQual = false; | ^~~~~~~~~~~ * compiling src/bedToIgv/bedToIgv.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedToIgv.o -MMD -MP -MF obj/bedToIgv.Td -c -o obj/bedToIgv.o src/bedToIgv/bedToIgv.cpp * compiling src/bed12ToBed6/bed12ToBed6.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bed12ToBed6.o -MMD -MP -MF obj/bed12ToBed6.Td -c -o obj/bed12ToBed6.o src/bed12ToBed6/bed12ToBed6.cpp * compiling src/closestFile/closestHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestHelp.o -MMD -MP -MF obj/closestHelp.Td -c -o obj/closestHelp.o src/closestFile/closestHelp.cpp * compiling src/closestFile/closestFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestFile.o -MMD -MP -MF obj/closestFile.Td -c -o obj/closestFile.o src/closestFile/closestFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/intersectFile/intersectFile.h:15, from src/closestFile/closestFile.h:11, from src/closestFile/closestFile.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/clusterBed/clusterMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterMain.o -MMD -MP -MF obj/clusterMain.Td -c -o obj/clusterMain.o src/clusterBed/clusterMain.cpp src/clusterBed/clusterMain.cpp: In function ‘int cluster_main(int, char**)’: src/clusterBed/clusterMain.cpp:38:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable] 38 | bool haveMaxDistance = false; | ^~~~~~~~~~~~~~~ * compiling src/clusterBed/clusterBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterBed.o -MMD -MP -MF obj/clusterBed.Td -c -o obj/clusterBed.o src/clusterBed/clusterBed.cpp * compiling src/complementFile/complementHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementHelp.o -MMD -MP -MF obj/complementHelp.Td -c -o obj/complementHelp.o src/complementFile/complementHelp.cpp * compiling src/complementFile/complementFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementFile.o -MMD -MP -MF obj/complementFile.Td -c -o obj/complementFile.o src/complementFile/complementFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/complementFile/complementFile.h:11, from src/complementFile/complementFile.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/coverageFile/coverageHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageHelp.o -MMD -MP -MF obj/coverageHelp.Td -c -o obj/coverageHelp.o src/coverageFile/coverageHelp.cpp * compiling src/coverageFile/coverageFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageFile.o -MMD -MP -MF obj/coverageFile.Td -c -o obj/coverageFile.o src/coverageFile/coverageFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/intersectFile/intersectFile.h:15, from src/coverageFile/coverageFile.h:12, from src/coverageFile/coverageFile.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function ‘virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)’: src/coverageFile/coverageFile.cpp:100:25: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | asprintf(&depthPctString, "%0.7f", depthPct); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)’: src/coverageFile/coverageFile.cpp:181:17: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 181 | asprintf(&meanString, "%0.7f", mean); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)’: src/coverageFile/coverageFile.cpp:210:25: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 210 | asprintf(&coveredFractionString, "%0.7f", coveredFraction); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function ‘void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)’: src/coverageFile/coverageFile.cpp:230:17: warning: ignoring return value of ‘int asprintf(char**, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 230 | asprintf(&coveredFractionString, "%0.7f", coveredFraction); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/expand/expand.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/expand.o -MMD -MP -MF obj/expand.Td -c -o obj/expand.o src/expand/expand.cpp * compiling src/fastaFromBed/fastaFromBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fastaFromBedMain.o -MMD -MP -MF obj/fastaFromBedMain.Td -c -o obj/fastaFromBedMain.o src/fastaFromBed/fastaFromBedMain.cpp * compiling src/fastaFromBed/fastaFromBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fastaFromBed.o -MMD -MP -MF obj/fastaFromBed.Td -c -o obj/fastaFromBed.o src/fastaFromBed/fastaFromBed.cpp * compiling src/flankBed/flankBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/flankBedMain.o -MMD -MP -MF obj/flankBedMain.Td -c -o obj/flankBedMain.o src/flankBed/flankBedMain.cpp * compiling src/flankBed/flankBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/flankBed.o -MMD -MP -MF obj/flankBed.Td -c -o obj/flankBed.o src/flankBed/flankBed.cpp * compiling src/genomeCoverageBed/genomeCoverageMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/genomeCoverageMain.o -MMD -MP -MF obj/genomeCoverageMain.Td -c -o obj/genomeCoverageMain.o src/genomeCoverageBed/genomeCoverageMain.cpp * compiling src/genomeCoverageBed/genomeCoverageBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/genomeCoverageBed.o -MMD -MP -MF obj/genomeCoverageBed.Td -c -o obj/genomeCoverageBed.o src/genomeCoverageBed/genomeCoverageBed.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/GenomeFile/NewGenomeFile.h:20, from src/genomeCoverageBed/genomeCoverageBed.h:13, from src/genomeCoverageBed/genomeCoverageBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/13/ios:44, from /usr/powerpc64le-linux-gnu/include/c++/13/istream:40, from /usr/powerpc64le-linux-gnu/include/c++/13/sstream:40, from src/utils/lineFileUtilities/lineFileUtilities.h:8, from src/genomeCoverageBed/genomeCoverageBed.cpp:12: In member function ‘std::streamsize std::ios_base::precision(std::streamsize)’, inlined from ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:541:23: /usr/powerpc64le-linux-gnu/include/c++/13/bits/ios_base.h:744:20: warning: ‘prec’ may be used uninitialized [-Wmaybe-uninitialized] 744 | _M_precision = __prec; | ~~~~~~~~~~~~~^~~~~~~~ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)’: src/genomeCoverageBed/genomeCoverageBed.cpp:491:16: note: ‘prec’ was declared here 491 | streamsize prec; | ^~~~ In function ‘constexpr std::_Ios_Fmtflags std::operator|(_Ios_Fmtflags, _Ios_Fmtflags)’, inlined from ‘const std::_Ios_Fmtflags& std::operator|=(_Ios_Fmtflags&, _Ios_Fmtflags)’ at /usr/powerpc64le-linux-gnu/include/c++/13/bits/ios_base.h:100:22, inlined from ‘std::ios_base::fmtflags std::ios_base::setf(fmtflags)’ at /usr/powerpc64le-linux-gnu/include/c++/13/bits/ios_base.h:692:19, inlined from ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:542:18: /usr/powerpc64le-linux-gnu/include/c++/13/bits/ios_base.h:88:71: warning: ‘fflags’ may be used uninitialized [-Wmaybe-uninitialized] 88 | { return _Ios_Fmtflags(static_cast(__a) | static_cast(__b)); } | ^ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)’: src/genomeCoverageBed/genomeCoverageBed.cpp:492:29: note: ‘fflags’ was declared here 492 | std::ios_base::fmtflags fflags; | ^~~~~~ In member function ‘std::streamsize std::ios_base::precision(std::streamsize)’, inlined from ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:401:27: /usr/powerpc64le-linux-gnu/include/c++/13/bits/ios_base.h:744:20: warning: ‘prec’ may be used uninitialized [-Wmaybe-uninitialized] 744 | _M_precision = __prec; | ~~~~~~~~~~~~~^~~~~~~~ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)’: src/genomeCoverageBed/genomeCoverageBed.cpp:381:20: note: ‘prec’ was declared here 381 | streamsize prec; | ^~~~ In function ‘constexpr std::_Ios_Fmtflags std::operator|(_Ios_Fmtflags, _Ios_Fmtflags)’, inlined from ‘const std::_Ios_Fmtflags& std::operator|=(_Ios_Fmtflags&, _Ios_Fmtflags)’ at /usr/powerpc64le-linux-gnu/include/c++/13/bits/ios_base.h:100:22, inlined from ‘std::ios_base::fmtflags std::ios_base::setf(fmtflags)’ at /usr/powerpc64le-linux-gnu/include/c++/13/bits/ios_base.h:692:19, inlined from ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)’ at src/genomeCoverageBed/genomeCoverageBed.cpp:402:22: /usr/powerpc64le-linux-gnu/include/c++/13/bits/ios_base.h:88:71: warning: ‘fflags’ may be used uninitialized [-Wmaybe-uninitialized] 88 | { return _Ios_Fmtflags(static_cast(__a) | static_cast(__b)); } | ^ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)’: src/genomeCoverageBed/genomeCoverageBed.cpp:382:33: note: ‘fflags’ was declared here 382 | std::ios_base::fmtflags fflags; | ^~~~~~ * compiling src/getOverlap/getOverlap.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/getOverlap.o -MMD -MP -MF obj/getOverlap.Td -c -o obj/getOverlap.o src/getOverlap/getOverlap.cpp src/getOverlap/getOverlap.cpp: In function ‘int getoverlap_main(int, char**)’: src/getOverlap/getOverlap.cpp:44:10: warning: variable ‘haveColumns’ set but not used [-Wunused-but-set-variable] 44 | bool haveColumns = false; | ^~~~~~~~~~~ * compiling src/groupBy/groupByHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupByHelp.o -MMD -MP -MF obj/groupByHelp.Td -c -o obj/groupByHelp.o src/groupBy/groupByHelp.cpp * compiling src/groupBy/groupBy.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupBy.o -MMD -MP -MF obj/groupBy.Td -c -o obj/groupBy.o src/groupBy/groupBy.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/groupBy/groupBy.h:10, from src/groupBy/groupBy.cpp:7: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/intersectFile/intersectHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectHelp.o -MMD -MP -MF obj/intersectHelp.Td -c -o obj/intersectHelp.o src/intersectFile/intersectHelp.cpp * compiling src/intersectFile/intersectFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectFile.o -MMD -MP -MF obj/intersectFile.Td -c -o obj/intersectFile.o src/intersectFile/intersectFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/intersectFile/intersectFile.h:15, from src/intersectFile/intersectFile.cpp:13: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/fisher/fisherHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fisherHelp.o -MMD -MP -MF obj/fisherHelp.Td -c -o obj/fisherHelp.o src/fisher/fisherHelp.cpp * compiling src/fisher/fisher.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fisher.o -MMD -MP -MF obj/fisher.Td -c -o obj/fisher.o src/fisher/fisher.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextJaccard.h:11, from src/jaccard/jaccard.h:11, from src/fisher/fisher.h:11, from src/fisher/fisher.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/fisher/kfunc.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/kfunc.o -MMD -MP -MF obj/kfunc.Td -c -o obj/kfunc.o src/fisher/kfunc.cpp * compiling src/jaccard/jaccardHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/jaccardHelp.o -MMD -MP -MF obj/jaccardHelp.Td -c -o obj/jaccardHelp.o src/jaccard/jaccardHelp.cpp * compiling src/jaccard/jaccard.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/jaccard.o -MMD -MP -MF obj/jaccard.Td -c -o obj/jaccard.o src/jaccard/jaccard.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextJaccard.h:11, from src/jaccard/jaccard.h:11, from src/jaccard/jaccard.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/linksBed/linksMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/linksMain.o -MMD -MP -MF obj/linksMain.Td -c -o obj/linksMain.o src/linksBed/linksMain.cpp * compiling src/linksBed/linksBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/linksBed.o -MMD -MP -MF obj/linksBed.Td -c -o obj/linksBed.o src/linksBed/linksBed.cpp * compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/maskFastaFromBedMain.o -MMD -MP -MF obj/maskFastaFromBedMain.Td -c -o obj/maskFastaFromBedMain.o src/maskFastaFromBed/maskFastaFromBedMain.cpp * compiling src/maskFastaFromBed/maskFastaFromBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/maskFastaFromBed.o -MMD -MP -MF obj/maskFastaFromBed.Td -c -o obj/maskFastaFromBed.o src/maskFastaFromBed/maskFastaFromBed.cpp * compiling src/mapFile/mapHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mapHelp.o -MMD -MP -MF obj/mapHelp.Td -c -o obj/mapHelp.o src/mapFile/mapHelp.cpp * compiling src/mapFile/mapFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mapFile.o -MMD -MP -MF obj/mapFile.Td -c -o obj/mapFile.o src/mapFile/mapFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/intersectFile/intersectFile.h:15, from src/mapFile/mapFile.h:11, from src/mapFile/mapFile.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/mergeFile/mergeHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mergeHelp.o -MMD -MP -MF obj/mergeHelp.Td -c -o obj/mergeHelp.o src/mergeFile/mergeHelp.cpp * compiling src/mergeFile/mergeFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mergeFile.o -MMD -MP -MF obj/mergeFile.Td -c -o obj/mergeFile.o src/mergeFile/mergeFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/mergeFile/mergeFile.h:11, from src/mergeFile/mergeFile.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/multiBamCov/multiBamCovMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiBamCovMain.o -MMD -MP -MF obj/multiBamCovMain.Td -c -o obj/multiBamCovMain.o src/multiBamCov/multiBamCovMain.cpp src/multiBamCov/multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’: src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable] 38 | bool haveBed = false; | ^~~~~~~ src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable] 39 | bool haveBams = false; | ^~~~~~~~ src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 47 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/multiBamCov/multiBamCov.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiBamCov.o -MMD -MP -MF obj/multiBamCov.Td -c -o obj/multiBamCov.o src/multiBamCov/multiBamCov.cpp In file included from src/utils/BamTools/include/BamReader.hpp:4, from src/utils/BamTools/include/api/BamMultiReader.h:4, from src/multiBamCov/multiBamCov.h:16, from src/multiBamCov/multiBamCov.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/multiIntersectBed/multiIntersectBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiIntersectBedMain.o -MMD -MP -MF obj/multiIntersectBedMain.Td -c -o obj/multiIntersectBedMain.o src/multiIntersectBed/multiIntersectBedMain.cpp src/multiIntersectBed/multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’: src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] 45 | bool haveFiles = false; | ^~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] 47 | bool haveGenome = false; | ^~~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] 48 | bool haveFiller = true; | ^~~~~~~~~~ * compiling src/multiIntersectBed/multiIntersectBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiIntersectBed.o -MMD -MP -MF obj/multiIntersectBed.Td -c -o obj/multiIntersectBed.o src/multiIntersectBed/multiIntersectBed.cpp * compiling src/nucBed/nucBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/nucBedMain.o -MMD -MP -MF obj/nucBedMain.Td -c -o obj/nucBedMain.o src/nucBed/nucBedMain.cpp * compiling src/nucBed/nucBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/nucBed.o -MMD -MP -MF obj/nucBed.Td -c -o obj/nucBed.o src/nucBed/nucBed.cpp * compiling src/pairToBed/pairToBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToBedMain.o -MMD -MP -MF obj/pairToBedMain.Td -c -o obj/pairToBedMain.o src/pairToBed/pairToBedMain.cpp src/pairToBed/pairToBedMain.cpp: In function ‘int pairtobed_main(int, char**)’: src/pairToBed/pairToBedMain.cpp:43:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 43 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/pairToBed/pairToBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToBed.o -MMD -MP -MF obj/pairToBed.Td -c -o obj/pairToBed.o src/pairToBed/pairToBed.cpp src/pairToBed/pairToBed.cpp: In member function ‘void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const std::string&)’: src/pairToBed/pairToBed.cpp:257:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable] 257 | CHRPOS spanLength = 0; | ^~~~~~~~~~ src/pairToBed/pairToBed.cpp: In member function ‘bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const std::string&)’: src/pairToBed/pairToBed.cpp:310:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable] 310 | CHRPOS spanLength = 0; | ^~~~~~~~~~ In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/pairToBed/pairToBed.h:15, from src/pairToBed/pairToBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/pairToPair/pairToPairMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToPairMain.o -MMD -MP -MF obj/pairToPairMain.Td -c -o obj/pairToPairMain.o src/pairToPair/pairToPairMain.cpp src/pairToPair/pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’: src/pairToPair/pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] 44 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/pairToPair/pairToPair.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToPair.o -MMD -MP -MF obj/pairToPair.Td -c -o obj/pairToPair.o src/pairToPair/pairToPair.cpp src/pairToPair/pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’: src/pairToPair/pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable] 112 | bool found1 = false; | ^~~~~~ src/pairToPair/pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable] 113 | bool found2 = false; | ^~~~~~ * compiling src/randomBed/randomBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBedMain.o -MMD -MP -MF obj/randomBedMain.Td -c -o obj/randomBedMain.o src/randomBed/randomBedMain.cpp * compiling src/randomBed/randomBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBed.o -MMD -MP -MF obj/randomBed.Td -c -o obj/randomBed.o src/randomBed/randomBed.cpp * compiling src/regressTest/regressTestMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/regressTestMain.o -MMD -MP -MF obj/regressTestMain.Td -c -o obj/regressTestMain.o src/regressTest/regressTestMain.cpp * compiling src/regressTest/RegressTest.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RegressTest.o -MMD -MP -MF obj/RegressTest.Td -c -o obj/RegressTest.o src/regressTest/RegressTest.cpp src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’: src/regressTest/RegressTest.cpp:431:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 431 | system(diffCmd.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’: src/regressTest/RegressTest.cpp:573:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 573 | fgets(sLine, 4192, fp); | ~~~~~^~~~~~~~~~~~~~~~~ src/regressTest/RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’: src/regressTest/RegressTest.cpp:622:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 622 | fgets(sLine, 4192, fp); | ~~~~~^~~~~~~~~~~~~~~~~ * compiling src/reldist/reldistMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/reldistMain.o -MMD -MP -MF obj/reldistMain.Td -c -o obj/reldistMain.o src/reldist/reldistMain.cpp * compiling src/reldist/reldist.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/reldist.o -MMD -MP -MF obj/reldist.Td -c -o obj/reldist.o src/reldist/reldist.cpp src/reldist/reldist.cpp: In member function ‘void RelativeDistance::CalculateRelativeDistance()’: src/reldist/reldist.cpp:129:25: warning: comparison of integer expressions of different signedness: ‘CHRPOS’ {aka ‘long int’} and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 129 | if (low_idx != chrom_mids->size() - 1) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/sampleFile/sampleHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sampleHelp.o -MMD -MP -MF obj/sampleHelp.Td -c -o obj/sampleHelp.o src/sampleFile/sampleHelp.cpp * compiling src/sampleFile/sampleFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sampleFile.o -MMD -MP -MF obj/sampleFile.Td -c -o obj/sampleFile.o src/sampleFile/sampleFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/sampleFile/sampleFile.h:11, from src/sampleFile/sampleFile.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/shiftBed/shiftBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shiftBedMain.o -MMD -MP -MF obj/shiftBedMain.Td -c -o obj/shiftBedMain.o src/shiftBed/shiftBedMain.cpp * compiling src/shiftBed/shiftBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shiftBed.o -MMD -MP -MF obj/shiftBed.Td -c -o obj/shiftBed.o src/shiftBed/shiftBed.cpp * compiling src/shuffleBed/shuffleBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shuffleBedMain.o -MMD -MP -MF obj/shuffleBedMain.Td -c -o obj/shuffleBedMain.o src/shuffleBed/shuffleBedMain.cpp * compiling src/shuffleBed/shuffleBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shuffleBed.o -MMD -MP -MF obj/shuffleBed.Td -c -o obj/shuffleBed.o src/shuffleBed/shuffleBed.cpp * compiling src/slopBed/slopBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBedMain.o -MMD -MP -MF obj/slopBedMain.Td -c -o obj/slopBedMain.o src/slopBed/slopBedMain.cpp * compiling src/slopBed/slopBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBed.o -MMD -MP -MF obj/slopBed.Td -c -o obj/slopBed.o src/slopBed/slopBed.cpp * compiling src/sortBed/sortMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortMain.o -MMD -MP -MF obj/sortMain.Td -c -o obj/sortMain.o src/sortBed/sortMain.cpp * compiling src/sortBed/sortBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortBed.o -MMD -MP -MF obj/sortBed.Td -c -o obj/sortBed.o src/sortBed/sortBed.cpp * compiling src/spacingFile/spacingHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/spacingHelp.o -MMD -MP -MF obj/spacingHelp.Td -c -o obj/spacingHelp.o src/spacingFile/spacingHelp.cpp * compiling src/spacingFile/spacingFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/spacingFile.o -MMD -MP -MF obj/spacingFile.Td -c -o obj/spacingFile.o src/spacingFile/spacingFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/spacingFile/spacingFile.h:12, from src/spacingFile/spacingFile.cpp:7: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/split/splitBedMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/splitBedMain.o -MMD -MP -MF obj/splitBedMain.Td -c -o obj/splitBedMain.o src/split/splitBedMain.cpp * compiling src/split/splitBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/splitBed.o -MMD -MP -MF obj/splitBed.Td -c -o obj/splitBed.o src/split/splitBed.cpp * compiling src/subtractFile/subtractHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/subtractHelp.o -MMD -MP -MF obj/subtractHelp.Td -c -o obj/subtractHelp.o src/subtractFile/subtractHelp.cpp * compiling src/subtractFile/subtractFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/subtractFile.o -MMD -MP -MF obj/subtractFile.Td -c -o obj/subtractFile.o src/subtractFile/subtractFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/intersectFile/intersectFile.h:15, from src/subtractFile/subtractFile.h:12, from src/subtractFile/subtractFile.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/summaryFile/summaryHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/summaryHelp.o -MMD -MP -MF obj/summaryHelp.Td -c -o obj/summaryHelp.o src/summaryFile/summaryHelp.cpp * compiling src/summaryFile/summaryFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/summaryFile.o -MMD -MP -MF obj/summaryFile.Td -c -o obj/summaryFile.o src/summaryFile/summaryFile.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/summaryFile/summaryFile.h:12, from src/summaryFile/summaryFile.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/tagBam/tagBamMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tagBamMain.o -MMD -MP -MF obj/tagBamMain.Td -c -o obj/tagBamMain.o src/tagBam/tagBamMain.cpp * compiling src/tagBam/tagBam.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tagBam.o -MMD -MP -MF obj/tagBam.Td -c -o obj/tagBam.o src/tagBam/tagBam.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/tagBam/tagBam.h:17, from src/tagBam/tagBam.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/unionBedGraphs/unionBedGraphsMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/unionBedGraphsMain.o -MMD -MP -MF obj/unionBedGraphsMain.Td -c -o obj/unionBedGraphsMain.o src/unionBedGraphs/unionBedGraphsMain.cpp src/unionBedGraphs/unionBedGraphsMain.cpp: In function ‘int unionbedgraphs_main(int, char**)’: src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] 46 | bool haveFiles = false; | ^~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] 48 | bool haveGenome = false; | ^~~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] 49 | bool haveFiller = true; | ^~~~~~~~~~ * compiling src/unionBedGraphs/unionBedGraphs.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/unionBedGraphs.o -MMD -MP -MF obj/unionBedGraphs.Td -c -o obj/unionBedGraphs.o src/unionBedGraphs/unionBedGraphs.cpp * compiling src/windowBed/windowMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMain.o -MMD -MP -MF obj/windowMain.Td -c -o obj/windowMain.o src/windowBed/windowMain.cpp * compiling src/windowBed/windowBed.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowBed.o -MMD -MP -MF obj/windowBed.Td -c -o obj/windowBed.o src/windowBed/windowBed.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/windowBed/windowBed.h:15, from src/windowBed/windowBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/windowMaker/windowMakerMain.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMakerMain.o -MMD -MP -MF obj/windowMakerMain.Td -c -o obj/windowMakerMain.o src/windowMaker/windowMakerMain.cpp * compiling src/windowMaker/windowMaker.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMaker.o -MMD -MP -MF obj/windowMaker.Td -c -o obj/windowMaker.o src/windowMaker/windowMaker.cpp * compiling src/utils/FileRecordTools/FileRecordMgr.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordMgr.o -MMD -MP -MF obj/FileRecordMgr.Td -c -o obj/FileRecordMgr.o src/utils/FileRecordTools/FileRecordMgr.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMgr.cpp:2: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordMergeMgr.o -MMD -MP -MF obj/FileRecordMergeMgr.Td -c -o obj/FileRecordMergeMgr.o src/utils/FileRecordTools/FileRecordMergeMgr.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/FileRecordTools/FileRecordMergeMgr.cpp:9: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileReader.o -MMD -MP -MF obj/FileReader.Td -c -o obj/FileReader.o src/utils/FileRecordTools/FileReaders/FileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/SingleLineDelimTextFileReader.o -MMD -MP -MF obj/SingleLineDelimTextFileReader.Td -c -o obj/SingleLineDelimTextFileReader.o src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamFileReader.o -MMD -MP -MF obj/BamFileReader.Td -c -o obj/BamFileReader.o src/utils/FileRecordTools/FileReaders/BamFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BufferedStreamMgr.o -MMD -MP -MF obj/BufferedStreamMgr.Td -c -o obj/BufferedStreamMgr.o src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function ‘bool BufferedStreamMgr::readFileChunk()’: src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 148 | if (_mainBufCurrLen < _useBufSize) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/InputStreamMgr.o -MMD -MP -MF obj/InputStreamMgr.Td -c -o obj/InputStreamMgr.o src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:14, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:8: src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’: src/utils/BamTools/include/SamHeader.hpp:32:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/utils/FileRecordTools/Records/Record.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Record.o -MMD -MP -MF obj/Record.Td -c -o obj/Record.o src/utils/FileRecordTools/Records/Record.cpp * compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/EmptyRecord.o -MMD -MP -MF obj/EmptyRecord.Td -c -o obj/EmptyRecord.o src/utils/FileRecordTools/Records/EmptyRecord.cpp In file included from src/utils/FileRecordTools/Records/EmptyRecord.h:11, from src/utils/FileRecordTools/Records/EmptyRecord.cpp:9: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed3Interval.o -MMD -MP -MF obj/Bed3Interval.Td -c -o obj/Bed3Interval.o src/utils/FileRecordTools/Records/Bed3Interval.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/Bed3Interval.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed4Interval.o -MMD -MP -MF obj/Bed4Interval.Td -c -o obj/Bed4Interval.o src/utils/FileRecordTools/Records/Bed4Interval.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/Bed4Interval.h:13, from src/utils/FileRecordTools/Records/Bed4Interval.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedGraphInterval.o -MMD -MP -MF obj/BedGraphInterval.Td -c -o obj/BedGraphInterval.o src/utils/FileRecordTools/Records/BedGraphInterval.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/BedGraphInterval.h:12, from src/utils/FileRecordTools/Records/BedGraphInterval.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed5Interval.o -MMD -MP -MF obj/Bed5Interval.Td -c -o obj/Bed5Interval.o src/utils/FileRecordTools/Records/Bed5Interval.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/Bed5Interval.h:12, from src/utils/FileRecordTools/Records/Bed5Interval.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed6Interval.o -MMD -MP -MF obj/Bed6Interval.Td -c -o obj/Bed6Interval.o src/utils/FileRecordTools/Records/Bed6Interval.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/Bed6Interval.h:12, from src/utils/FileRecordTools/Records/Bed6Interval.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/PlusFields.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/PlusFields.o -MMD -MP -MF obj/PlusFields.Td -c -o obj/PlusFields.o src/utils/FileRecordTools/Records/PlusFields.cpp * compiling src/utils/FileRecordTools/Records/GffRecord.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffRecord.o -MMD -MP -MF obj/GffRecord.Td -c -o obj/GffRecord.o src/utils/FileRecordTools/Records/GffRecord.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/Bed6Interval.h:12, from src/utils/FileRecordTools/Records/GffRecord.h:11, from src/utils/FileRecordTools/Records/GffRecord.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffPlusRecord.o -MMD -MP -MF obj/GffPlusRecord.Td -c -o obj/GffPlusRecord.o src/utils/FileRecordTools/Records/GffPlusRecord.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/Bed6Interval.h:12, from src/utils/FileRecordTools/Records/GffRecord.h:11, from src/utils/FileRecordTools/Records/GffPlusRecord.h:11, from src/utils/FileRecordTools/Records/GffPlusRecord.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NoPosPlusRecord.o -MMD -MP -MF obj/NoPosPlusRecord.Td -c -o obj/NoPosPlusRecord.o src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp In file included from src/utils/FileRecordTools/Records/NoPosPlusRecord.h:11, from src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedPlusInterval.o -MMD -MP -MF obj/BedPlusInterval.Td -c -o obj/BedPlusInterval.o src/utils/FileRecordTools/Records/BedPlusInterval.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/BedPlusInterval.h:11, from src/utils/FileRecordTools/Records/BedPlusInterval.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/Bed12Interval.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed12Interval.o -MMD -MP -MF obj/Bed12Interval.Td -c -o obj/Bed12Interval.o src/utils/FileRecordTools/Records/Bed12Interval.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/Bed6Interval.h:12, from src/utils/FileRecordTools/Records/Bed12Interval.h:11, from src/utils/FileRecordTools/Records/Bed12Interval.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ * compiling src/utils/FileRecordTools/Records/BamRecord.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamRecord.o -MMD -MP -MF obj/BamRecord.Td -c -o obj/BamRecord.o src/utils/FileRecordTools/Records/BamRecord.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/Bed6Interval.h:12, from src/utils/FileRecordTools/Records/BamRecord.h:11, from src/utils/FileRecordTools/Records/BamRecord.cpp:9: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ * compiling src/utils/FileRecordTools/Records/VcfRecord.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VcfRecord.o -MMD -MP -MF obj/VcfRecord.Td -c -o obj/VcfRecord.o src/utils/FileRecordTools/Records/VcfRecord.cpp In file included from src/utils/FileRecordTools/Records/Bed3Interval.h:11, from src/utils/FileRecordTools/Records/BedPlusInterval.h:11, from src/utils/FileRecordTools/Records/VcfRecord.h:11, from src/utils/FileRecordTools/Records/VcfRecord.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ * compiling src/utils/FileRecordTools/Records/BlockMgr.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BlockMgr.o -MMD -MP -MF obj/BlockMgr.Td -c -o obj/BlockMgr.o src/utils/FileRecordTools/Records/BlockMgr.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/FileRecordTools/Records/BlockMgr.h:17, from src/utils/FileRecordTools/Records/BlockMgr.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/Records/BlockMgr.cpp:9: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function ‘int BlockMgr::getNonRedundantOverlap()’: src/utils/FileRecordTools/Records/BlockMgr.cpp:194:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 194 | for (int i = 1; i < _overlapStarts.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/StrandQueue.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/StrandQueue.o -MMD -MP -MF obj/StrandQueue.Td -c -o obj/StrandQueue.o src/utils/FileRecordTools/Records/StrandQueue.cpp * compiling src/utils/FileRecordTools/Records/RecordMgr.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordMgr.o -MMD -MP -MF obj/RecordMgr.Td -c -o obj/RecordMgr.o src/utils/FileRecordTools/Records/RecordMgr.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/Records/RecordMgr.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/RecordList.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordList.o -MMD -MP -MF obj/RecordList.Td -c -o obj/RecordList.o src/utils/FileRecordTools/Records/RecordList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyList.o -MMD -MP -MF obj/RecordKeyList.Td -c -o obj/RecordKeyList.o src/utils/FileRecordTools/Records/RecordKeyList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyVector.o -MMD -MP -MF obj/RecordKeyVector.Td -c -o obj/RecordKeyVector.o src/utils/FileRecordTools/Records/RecordKeyVector.cpp * compiling src/utils/bedFile/bedFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedFile.o -MMD -MP -MF obj/bedFile.Td -c -o obj/bedFile.o src/utils/bedFile/bedFile.cpp * compiling src/utils/BinTree/BinTree.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BinTree.o -MMD -MP -MF obj/BinTree.Td -c -o obj/BinTree.o src/utils/BinTree/BinTree.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyList.h:11, from src/utils/BinTree/BinTree.h:19, from src/utils/BinTree/BinTree.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/BinTree/BinTree.h:20: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/version/version.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/version.o -MMD -MP -MF obj/version.Td -c -o obj/version.o src/utils/version/version.cpp * compiling src/utils/bedGraphFile/bedGraphFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedGraphFile.o -MMD -MP -MF obj/bedGraphFile.Td -c -o obj/bedGraphFile.o src/utils/bedGraphFile/bedGraphFile.cpp * compiling src/utils/chromsweep/chromsweep.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/chromsweep.o -MMD -MP -MF obj/chromsweep.Td -c -o obj/chromsweep.o src/utils/chromsweep/chromsweep.cpp * compiling src/utils/Contexts/ContextBase.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextBase.o -MMD -MP -MF obj/ContextBase.Td -c -o obj/ContextBase.o src/utils/Contexts/ContextBase.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextBase.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextIntersect.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextIntersect.o -MMD -MP -MF obj/ContextIntersect.Td -c -o obj/ContextIntersect.o src/utils/Contexts/ContextIntersect.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextIntersect.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextFisher.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextFisher.o -MMD -MP -MF obj/ContextFisher.Td -c -o obj/ContextFisher.o src/utils/Contexts/ContextFisher.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextJaccard.h:11, from src/utils/Contexts/ContextFisher.h:11, from src/utils/Contexts/ContextFisher.cpp:6: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextMap.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextMap.o -MMD -MP -MF obj/ContextMap.Td -c -o obj/ContextMap.o src/utils/Contexts/ContextMap.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextMap.h:11, from src/utils/Contexts/ContextMap.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextSample.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSample.o -MMD -MP -MF obj/ContextSample.Td -c -o obj/ContextSample.o src/utils/Contexts/ContextSample.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextSample.h:11, from src/utils/Contexts/ContextSample.cpp:7: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextSpacing.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSpacing.o -MMD -MP -MF obj/ContextSpacing.Td -c -o obj/ContextSpacing.o src/utils/Contexts/ContextSpacing.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextSpacing.h:11, from src/utils/Contexts/ContextSpacing.cpp:7: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextMerge.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextMerge.o -MMD -MP -MF obj/ContextMerge.Td -c -o obj/ContextMerge.o src/utils/Contexts/ContextMerge.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextMerge.h:11, from src/utils/Contexts/ContextMerge.cpp:9: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextJaccard.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextJaccard.o -MMD -MP -MF obj/ContextJaccard.Td -c -o obj/ContextJaccard.o src/utils/Contexts/ContextJaccard.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextJaccard.h:11, from src/utils/Contexts/ContextJaccard.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextClosest.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextClosest.o -MMD -MP -MF obj/ContextClosest.Td -c -o obj/ContextClosest.o src/utils/Contexts/ContextClosest.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextClosest.h:12, from src/utils/Contexts/ContextClosest.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextSubtract.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSubtract.o -MMD -MP -MF obj/ContextSubtract.Td -c -o obj/ContextSubtract.o src/utils/Contexts/ContextSubtract.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextSubtract.h:12, from src/utils/Contexts/ContextSubtract.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextCoverage.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextCoverage.o -MMD -MP -MF obj/ContextCoverage.Td -c -o obj/ContextCoverage.o src/utils/Contexts/ContextCoverage.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextCoverage.h:12, from src/utils/Contexts/ContextCoverage.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextComplement.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextComplement.o -MMD -MP -MF obj/ContextComplement.Td -c -o obj/ContextComplement.o src/utils/Contexts/ContextComplement.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextComplement.h:12, from src/utils/Contexts/ContextComplement.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextGroupBy.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextGroupBy.o -MMD -MP -MF obj/ContextGroupBy.Td -c -o obj/ContextGroupBy.o src/utils/Contexts/ContextGroupBy.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextGroupBy.h:11, from src/utils/Contexts/ContextGroupBy.cpp:9: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/Contexts/ContextSummary.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSummary.o -MMD -MP -MF obj/ContextSummary.Td -c -o obj/ContextSummary.o src/utils/Contexts/ContextSummary.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextSummary.h:11, from src/utils/Contexts/ContextSummary.cpp:7: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/general/ParseTools.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ParseTools.o -MMD -MP -MF obj/ParseTools.Td -c -o obj/ParseTools.o src/utils/general/ParseTools.cpp * compiling src/utils/general/PushBackStreamBuf.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/PushBackStreamBuf.o -MMD -MP -MF obj/PushBackStreamBuf.Td -c -o obj/PushBackStreamBuf.o src/utils/general/PushBackStreamBuf.cpp * compiling src/utils/general/CompressionTools.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CompressionTools.o -MMD -MP -MF obj/CompressionTools.Td -c -o obj/CompressionTools.o src/utils/general/CompressionTools.cpp * compiling src/utils/general/Tokenizer.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Tokenizer.o -MMD -MP -MF obj/Tokenizer.Td -c -o obj/Tokenizer.o src/utils/general/Tokenizer.cpp * compiling src/utils/general/CommonHelp.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CommonHelp.o -MMD -MP -MF obj/CommonHelp.Td -c -o obj/CommonHelp.o src/utils/general/CommonHelp.cpp * compiling src/utils/general/ErrorMsg.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ErrorMsg.o -MMD -MP -MF obj/ErrorMsg.Td -c -o obj/ErrorMsg.o src/utils/general/ErrorMsg.cpp * compiling src/utils/general/Random.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Random.o -MMD -MP -MF obj/Random.Td -c -o obj/Random.o src/utils/general/Random.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Isrc/utils/gzstream -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/gzstream.o src/utils/gzstream/gzstream.C * compiling src/utils/fileType/fileType.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fileType.o -MMD -MP -MF obj/fileType.Td -c -o obj/fileType.o src/utils/fileType/fileType.cpp * compiling src/utils/fileType/FileRecordTypeChecker.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordTypeChecker.o -MMD -MP -MF obj/FileRecordTypeChecker.Td -c -o obj/FileRecordTypeChecker.o src/utils/fileType/FileRecordTypeChecker.cpp src/utils/fileType/FileRecordTypeChecker.cpp: In member function ‘bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)’: src/utils/fileType/FileRecordTypeChecker.cpp:366:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 366 | for (int j=0; j < len; j++) { | ~~^~~~~ * compiling src/utils/bedFilePE/bedFilePE.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedFilePE.o -MMD -MP -MF obj/bedFilePE.Td -c -o obj/bedFilePE.o src/utils/bedFilePE/bedFilePE.cpp * compiling src/utils/KeyListOps/KeyListOps.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/KeyListOps.o -MMD -MP -MF obj/KeyListOps.Td -c -o obj/KeyListOps.o src/utils/KeyListOps/KeyListOps.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/KeyListOps/KeyListOpsMethods.h:15, from src/utils/KeyListOps/KeyListOps.h:11, from src/utils/KeyListOps/KeyListOps.cpp:7: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/KeyListOps/KeyListOps.cpp:8: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/KeyListOps/KeyListOpsMethods.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/KeyListOpsMethods.o -MMD -MP -MF obj/KeyListOpsMethods.Td -c -o obj/KeyListOpsMethods.o src/utils/KeyListOps/KeyListOpsMethods.cpp * compiling src/utils/NewChromsweep/NewChromsweep.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NewChromsweep.o -MMD -MP -MF obj/NewChromsweep.Td -c -o obj/NewChromsweep.o src/utils/NewChromsweep/NewChromsweep.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyList.h:11, from src/utils/NewChromsweep/NewChromsweep.h:17, from src/utils/NewChromsweep/NewChromsweep.cpp:13: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/NewChromsweep/NewChromsweep.cpp:14: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ src/utils/NewChromsweep/NewChromsweep.h: In constructor ‘NewChromSweep::NewChromSweep(ContextIntersect*)’: src/utils/NewChromsweep/NewChromsweep.h:124:10: warning: ‘NewChromSweep::_testLastQueryRec’ will be initialized after [-Wreorder] 124 | bool _testLastQueryRec; | ^~~~~~~~~~~~~~~~~ src/utils/NewChromsweep/NewChromsweep.h:93:14: warning: ‘bool NewChromSweep::_runToDbEnd’ [-Wreorder] 93 | bool _runToDbEnd; | ^~~~~~~~~~~ src/utils/NewChromsweep/NewChromsweep.cpp:17:1: warning: when initialized here [-Wreorder] 17 | NewChromSweep::NewChromSweep(ContextIntersect *context) | ^~~~~~~~~~~~~ * compiling src/utils/NewChromsweep/CloseSweep.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CloseSweep.o -MMD -MP -MF obj/CloseSweep.Td -c -o obj/CloseSweep.o src/utils/NewChromsweep/CloseSweep.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyList.h:11, from src/utils/NewChromsweep/NewChromsweep.h:17, from src/utils/NewChromsweep/CloseSweep.h:11, from src/utils/NewChromsweep/CloseSweep.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/Contexts/ContextIntersect.h:11, from src/utils/Contexts/ContextClosest.h:12, from src/utils/NewChromsweep/CloseSweep.h:15: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/sequenceUtilities/sequenceUtils.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sequenceUtils.o -MMD -MP -MF obj/sequenceUtils.Td -c -o obj/sequenceUtils.o src/utils/sequenceUtilities/sequenceUtils.cpp * compiling src/utils/tabFile/tabFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tabFile.o -MMD -MP -MF obj/tabFile.Td -c -o obj/tabFile.o src/utils/tabFile/tabFile.cpp * compiling src/utils/BamTools-Ancillary/BamAncillary.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamAncillary.o -MMD -MP -MF obj/BamAncillary.Td -c -o obj/BamAncillary.o src/utils/BamTools-Ancillary/BamAncillary.cpp * compiling src/utils/BlockedIntervals/BlockedIntervals.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BlockedIntervals.o -MMD -MP -MF obj/BlockedIntervals.Td -c -o obj/BlockedIntervals.o src/utils/BlockedIntervals/BlockedIntervals.cpp * compiling src/utils/Fasta/Fasta.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Fasta.o -MMD -MP -MF obj/Fasta.Td -c -o obj/Fasta.o src/utils/Fasta/Fasta.cpp * compiling src/utils/Fasta/split.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/split.o -MMD -MP -MF obj/split.Td -c -o obj/split.o src/utils/Fasta/split.cpp * compiling src/utils/VectorOps/VectorOps.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VectorOps.o -MMD -MP -MF obj/VectorOps.Td -c -o obj/VectorOps.o src/utils/VectorOps/VectorOps.cpp * compiling src/utils/GenomeFile/NewGenomeFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NewGenomeFile.o -MMD -MP -MF obj/NewGenomeFile.Td -c -o obj/NewGenomeFile.o src/utils/GenomeFile/NewGenomeFile.cpp * compiling src/utils/GenomeFile/GenomeFile.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GenomeFile.o -MMD -MP -MF obj/GenomeFile.Td -c -o obj/GenomeFile.o src/utils/GenomeFile/GenomeFile.cpp src/utils/GenomeFile/GenomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 60 | long c2; | ^~ * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordOutputMgr.o -MMD -MP -MF obj/RecordOutputMgr.Td -c -o obj/RecordOutputMgr.o src/utils/RecordOutputMgr/RecordOutputMgr.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/RecordOutputMgr/RecordOutputMgr.cpp:8: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector*)’: src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 170 | if (context->getNumClosestHitsWanted() > keyList.size()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)’: src/utils/RecordOutputMgr/RecordOutputMgr.cpp:456:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 456 | for (size_t i = 0; i < _context->getNumInputFiles(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/ToolBase/ToolBase.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ToolBase.o -MMD -MP -MF obj/ToolBase.Td -c -o obj/ToolBase.o src/utils/ToolBase/ToolBase.cpp In file included from src/utils/FileRecordTools/Records/RecordKeyVector.h:12, from src/utils/ToolBase/ToolBase.h:11, from src/utils/ToolBase/ToolBase.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/RecordOutputMgr/RecordOutputMgr.h:11, from src/utils/ToolBase/ToolBase.h:12: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ * compiling src/utils/driver/BedtoolsDriver.cpp powerpc64le-linux-gnu-g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedtoolsDriver.o -MMD -MP -MF obj/BedtoolsDriver.Td -c -o obj/BedtoolsDriver.o src/utils/driver/BedtoolsDriver.cpp In file included from src/utils/FileRecordTools/Records/RecordMgr.h:12, from src/utils/FileRecordTools/FileRecordMgr.h:23, from src/utils/FileRecordTools/FileRecordMergeMgr.h:11, from src/utils/Contexts/ContextBase.h:23, from src/utils/driver/BedtoolsDriver.h:1, from src/utils/driver/BedtoolsDriver.cpp:1: src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:13: src/utils/FileRecordTools/Records/EmptyRecord.h:15:7: note: by ‘EmptyRecord& EmptyRecord::operator=(const EmptyRecord&)’ 15 | class EmptyRecord : public Record { | ^~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:14: src/utils/FileRecordTools/Records/Bed3Interval.h:19:7: note: by ‘Bed3Interval& Bed3Interval::operator=(const Bed3Interval&)’ 19 | class Bed3Interval : public Record { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:15: src/utils/FileRecordTools/Records/Bed4Interval.h:17:7: note: by ‘Bed4Interval& Bed4Interval::operator=(const Bed4Interval&)’ 17 | class Bed4Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:16: src/utils/FileRecordTools/Records/Bed5Interval.h:16:7: note: by ‘Bed5Interval& Bed5Interval::operator=(const Bed5Interval&)’ 16 | class Bed5Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:17: src/utils/FileRecordTools/Records/BedGraphInterval.h:16:7: note: by ‘BedGraphInterval& BedGraphInterval::operator=(const BedGraphInterval&)’ 16 | class BedGraphInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:18: src/utils/FileRecordTools/Records/Bed6Interval.h:16:7: note: by ‘Bed6Interval& Bed6Interval::operator=(const Bed6Interval&)’ 16 | class Bed6Interval : public Bed3Interval { | ^~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:19: src/utils/FileRecordTools/Records/BedPlusInterval.h:16:7: note: by ‘BedPlusInterval& BedPlusInterval::operator=(const BedPlusInterval&)’ 16 | class BedPlusInterval : public Bed3Interval { | ^~~~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:20: src/utils/FileRecordTools/Records/Bed12Interval.h:30:30: note: by ‘const Bed12Interval& Bed12Interval::operator=(const Bed12Interval&)’ 30 | const Bed12Interval &operator=(const Bed12Interval &other); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:21: src/utils/FileRecordTools/Records/BamRecord.h:25:34: note: by ‘virtual const BamRecord& BamRecord::operator=(const BamRecord&)’ 25 | virtual const BamRecord &operator=(const BamRecord &); | ^~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:22: src/utils/FileRecordTools/Records/VcfRecord.h:15:7: note: by ‘VcfRecord::operator=’ 15 | class VcfRecord : public BedPlusInterval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:23: src/utils/FileRecordTools/Records/GffRecord.h:15:7: note: by ‘GffRecord& GffRecord::operator=(const GffRecord&)’ 15 | class GffRecord : public Bed6Interval { | ^~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:24: src/utils/FileRecordTools/Records/GffPlusRecord.h:16:7: note: by ‘GffPlusRecord& GffPlusRecord::operator=(const GffPlusRecord&)’ 16 | class GffPlusRecord : public GffRecord { | ^~~~~~~~~~~~~ src/utils/FileRecordTools/Records/Record.h:76:32: warning: ‘virtual const Record& Record::operator=(const Record&)’ was hidden [-Woverloaded-virtual=] 76 | virtual const Record & operator=(const Record &); | ^~~~~~~~ In file included from src/utils/FileRecordTools/Records/RecordMgr.h:25: src/utils/FileRecordTools/Records/NoPosPlusRecord.h:16:7: note: by ‘NoPosPlusRecord& NoPosPlusRecord::operator=(const NoPosPlusRecord&)’ 16 | class NoPosPlusRecord : public Record { | ^~~~~~~~~~~~~~~ cd src/utils/htslib && make config.h make[3]: Entering directory '/<>/src/utils/htslib' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h make[3]: Leaving directory '/<>/src/utils/htslib' cd src/utils/htslib && make lib-static make[3]: Entering directory '/<>/src/utils/htslib' powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c hts.c: In function ‘hts_idx_init’: hts.c:1397:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1397 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c powerpc64le-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a make[3]: Leaving directory '/<>/src/utils/htslib' - Building main bedtools binary. powerpc64le-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o bin/bedtools obj/bedtools.o obj/htsutil.o obj/annotateMain.o obj/annotateBed.o obj/bamToBed.o obj/bamToFastqMain.o obj/bamToFastq.o obj/bedToBam.o obj/bedpeToBam.o obj/bedToIgv.o obj/bed12ToBed6.o obj/closestHelp.o obj/closestFile.o obj/clusterMain.o obj/clusterBed.o obj/complementHelp.o obj/complementFile.o obj/coverageHelp.o obj/coverageFile.o obj/expand.o obj/fastaFromBedMain.o obj/fastaFromBed.o obj/flankBedMain.o obj/flankBed.o obj/genomeCoverageMain.o obj/genomeCoverageBed.o obj/getOverlap.o obj/groupByHelp.o obj/groupBy.o obj/intersectHelp.o obj/intersectFile.o obj/fisherHelp.o obj/fisher.o obj/kfunc.o obj/jaccardHelp.o obj/jaccard.o obj/linksMain.o obj/linksBed.o obj/maskFastaFromBedMain.o obj/maskFastaFromBed.o obj/mapHelp.o obj/mapFile.o obj/mergeHelp.o obj/mergeFile.o obj/multiBamCovMain.o obj/multiBamCov.o obj/multiIntersectBedMain.o obj/multiIntersectBed.o obj/nucBedMain.o obj/nucBed.o obj/pairToBedMain.o obj/pairToBed.o obj/pairToPairMain.o obj/pairToPair.o obj/randomBedMain.o obj/randomBed.o obj/regressTestMain.o obj/RegressTest.o obj/reldistMain.o obj/reldist.o obj/sampleHelp.o obj/sampleFile.o obj/shiftBedMain.o obj/shiftBed.o obj/shuffleBedMain.o obj/shuffleBed.o obj/slopBedMain.o obj/slopBed.o obj/sortMain.o obj/sortBed.o obj/spacingHelp.o obj/spacingFile.o obj/splitBedMain.o obj/splitBed.o obj/subtractHelp.o obj/subtractFile.o obj/summaryHelp.o obj/summaryFile.o obj/tagBamMain.o obj/tagBam.o obj/unionBedGraphsMain.o obj/unionBedGraphs.o obj/windowMain.o obj/windowBed.o obj/windowMakerMain.o obj/windowMaker.o obj/FileRecordMgr.o obj/FileRecordMergeMgr.o obj/FileReader.o obj/SingleLineDelimTextFileReader.o obj/BamFileReader.o obj/BufferedStreamMgr.o obj/InputStreamMgr.o obj/Record.o obj/EmptyRecord.o obj/Bed3Interval.o obj/Bed4Interval.o obj/BedGraphInterval.o obj/Bed5Interval.o obj/Bed6Interval.o obj/PlusFields.o obj/GffRecord.o obj/GffPlusRecord.o obj/NoPosPlusRecord.o obj/BedPlusInterval.o obj/Bed12Interval.o obj/BamRecord.o obj/VcfRecord.o obj/BlockMgr.o obj/StrandQueue.o obj/RecordMgr.o obj/RecordList.o obj/RecordKeyList.o obj/RecordKeyVector.o obj/bedFile.o obj/BinTree.o obj/version.o obj/bedGraphFile.o obj/chromsweep.o obj/ContextBase.o obj/ContextIntersect.o obj/ContextFisher.o obj/ContextMap.o obj/ContextSample.o obj/ContextSpacing.o obj/ContextMerge.o obj/ContextJaccard.o obj/ContextClosest.o obj/ContextSubtract.o obj/ContextCoverage.o obj/ContextComplement.o obj/ContextGroupBy.o obj/ContextSummary.o obj/ParseTools.o obj/PushBackStreamBuf.o obj/CompressionTools.o obj/Tokenizer.o obj/CommonHelp.o obj/ErrorMsg.o obj/Random.o obj/gzstream.o obj/fileType.o obj/FileRecordTypeChecker.o obj/bedFilePE.o obj/KeyListOps.o obj/KeyListOpsMethods.o obj/NewChromsweep.o obj/CloseSweep.o obj/sequenceUtils.o obj/tabFile.o obj/BamAncillary.o obj/BlockedIntervals.o obj/Fasta.o obj/split.o obj/VectorOps.o obj/NewGenomeFile.o obj/GenomeFile.o obj/RecordOutputMgr.o obj/ToolBase.o obj/BedtoolsDriver.o src/utils/htslib/libhts.a -lz -lm -lbz2 -llzma -lpthread done. - Creating executables for old CLI. done. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a rm -f -- debian/bedtools.substvars rm -fr -- debian/.debhelper/generated/bedtools/ debian/bedtools/ debian/tmp/ rm -f debian/bedtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- VERBOSE=1 install -m0755 -d /<>/bedtools-2.31.0\+dfsg/debian/tmp make -j1 install DESTDIR=/<>/bedtools-2.31.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/<>' mkdir -p /<>/debian/tmp/usr/local/bin for file in bin/* ; do \ cp -f $file /<>/debian/tmp/usr/local/bin; \ done make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/bedtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install install -m0755 -d debian/bedtools/usr/bin cp --reflink=auto -a debian/tmp/usr/local/bin/annotateBed debian/tmp/usr/local/bin/bamToBed debian/tmp/usr/local/bin/bamToFastq debian/tmp/usr/local/bin/bed12ToBed6 debian/tmp/usr/local/bin/bedToBam debian/tmp/usr/local/bin/bedToIgv debian/tmp/usr/local/bin/bedpeToBam debian/tmp/usr/local/bin/bedtools debian/tmp/usr/local/bin/closestBed debian/tmp/usr/local/bin/clusterBed debian/tmp/usr/local/bin/complementBed debian/tmp/usr/local/bin/coverageBed debian/tmp/usr/local/bin/expandCols debian/tmp/usr/local/bin/fastaFromBed debian/tmp/usr/local/bin/flankBed debian/tmp/usr/local/bin/genomeCoverageBed debian/tmp/usr/local/bin/getOverlap debian/tmp/usr/local/bin/groupBy debian/tmp/usr/local/bin/intersectBed debian/tmp/usr/local/bin/linksBed debian/tmp/usr/local/bin/mapBed debian/tmp/usr/local/bin/maskFastaFromBed debian/tmp/usr/local/bin/mergeBed debian/tmp/usr/local/bin/multiBamCov debian/tmp/usr/local/bin/multiIntersectBed debian/tmp/usr/local/bin/nucBed debian/tmp/usr/local/bin/pairToBed debian/tmp/usr/local/bin/pairToPair debian/tmp/usr/local/bin/randomBed debian/tmp/usr/local/bin/shiftBed debian/tmp/usr/local/bin/shuffleBed debian/tmp/usr/local/bin/slopBed debian/tmp/usr/local/bin/sortBed debian/tmp/usr/local/bin/subtractBed debian/tmp/usr/local/bin/tagBam debian/tmp/usr/local/bin/unionBedGraphs debian/tmp/usr/local/bin/windowBed debian/tmp/usr/local/bin/windowMaker debian/bedtools/usr/bin/ install -m0755 -d debian/bedtools/usr/share/bash-completion/completions cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools/usr/share/bash-completion/completions/ install -m0755 -d debian/bedtools/usr/share/bedtools cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/ # make sure all *.sh files are featuring a '#!/bin/bash' as first line # since there are at least two files (test/intersect/{new_test-intersect.sh,performanceTest.sh} # requiring bash this is taken for all scripts instead of checking first via /bin/sh -n for sh in `find /<>/debian -name "*.sh"` ; do \ if ! head -n1 ${sh} | grep -q '^#! */bin/[ba]*sh' ; then \ sed -i '1 i #!/bin/bash' ${sh} ; \ fi ; \ done make[1]: Leaving directory '/<>' dh_installdocs -a install -m0755 -d debian/bedtools/usr/share/doc/bedtools install -m0755 -d debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./README.md debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/README.test debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/tests/run-unit-test debian/bedtools/usr/share/doc/bedtools chmod -R u\+rw,go=rX debian/bedtools/usr/share/doc install -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright dh_installchangelogs -a install -m0755 -d debian/bedtools/usr/share/doc/bedtools install -p -m0644 debian/.debhelper/generated/bedtools/dh_installchangelogs.dch.trimmed debian/bedtools/usr/share/doc/bedtools/changelog.Debian dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/bedtools chmod a-x usr/share/doc/bedtools/changelog.Debian gzip -9nf usr/share/doc/bedtools/changelog.Debian cd '/<>' rm -f debian/bedtools.debhelper.log debian/rules override_dh_fixperms-arch make[1]: Entering directory '/<>' dh_fixperms find debian/bedtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/bedtools/usr/share/doc -type f -a -true -a ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/bedtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x chmod -x /<>/debian/bedtools/usr/share/bedtools/genomes/*.genome find /<>/debian -name "*.bed" -executable -exec chmod -x \{\} \; find /<>/debian -name "*.sam" -executable -exec chmod -x \{\} \; find /<>/debian -name "*.sh" -not -executable -exec chmod +x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a dwz -- debian/bedtools/usr/bin/bedtools dh_strip -a install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/63 powerpc64le-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/63/838803c4bf336a78f7f4bfa29a41ad98229119.debug chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/63/838803c4bf336a78f7f4bfa29a41ad98229119.debug powerpc64le-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools powerpc64le-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/63/838803c4bf336a78f7f4bfa29a41ad98229119.debug debian/bedtools/usr/bin/bedtools install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym install -m0755 -d debian/.debhelper/bedtools dh_makeshlibs -a rm -f debian/bedtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/bedtools/DEBIAN dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools dh_installdeb -a install -m0755 -d debian/bedtools/DEBIAN dh_gencontrol -a install -m0755 -d debian/bedtools/DEBIAN echo misc:Depends= >> debian/bedtools.substvars echo misc:Pre-Depends= >> debian/bedtools.substvars install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=63838803c4bf336a78f7f4bfa29a41ad98229119 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools chmod 0644 -- debian/bedtools/DEBIAN/control dh_md5sums -a install -m0755 -d debian/bedtools/DEBIAN cd debian/bedtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/bedtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN cd debian/.debhelper/bedtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/bedtools .. dpkg-deb: building package 'bedtools' in '../bedtools_2.31.0+dfsg-2_ppc64el.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/bedtools/dbgsym-root .. dpkg-deb: building package 'bedtools-dbgsym' in '../bedtools-dbgsym_2.31.0+dfsg-2_ppc64el.deb'. dpkg-genbuildinfo --build=any -O../bedtools_2.31.0+dfsg-2_ppc64el.buildinfo dpkg-genchanges --build=any -O../bedtools_2.31.0+dfsg-2_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from bedtools-2.31.0+dfsg/debian/source/options: --single-debian-patch dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-11-19T18:50:14Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedtools_2.31.0+dfsg-2_ppc64el.changes: --------------------------------------- Format: 1.8 Date: Sat, 18 Nov 2023 16:34:59 +0100 Source: bedtools Binary: bedtools bedtools-dbgsym Built-For-Profiles: cross nocheck Architecture: ppc64el Version: 2.31.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bedtools - suite of utilities for comparing genomic features Closes: 1055414 Changes: bedtools (2.31.0+dfsg-2) unstable; urgency=medium . * gcc-13.patch: fixed upstream by different change. The Applied-Upstream field is set accordingly to point to PR 1067. * d/rules: use sse for floating point calculations. This fixes bedtools "intersect" test failures during build time. This change is brought for consistency with htslib's own settings. While this is an architecture baseline violation, the alternative is no htslib support at all for the i386 distribution, since it fails its own test suite with anything else than sse for floating point calculations. (Closes: #1055414) * d/control: depend on python3:any per M-A hint. 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+------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bedtools Binary: bedtools bedtools-dbgsym Architecture: ppc64el Version: 2.31.0+dfsg-2 Checksums-Md5: b6d47220e8e94511737c1ac02ff23068 11115496 bedtools-dbgsym_2.31.0+dfsg-2_ppc64el.deb bab03cd3c4fc92405face8f9dad32a80 680428 bedtools_2.31.0+dfsg-2_ppc64el.deb Checksums-Sha1: 36dc802ac426c0ca12c5ccc4db4ca9eb5d0f1e92 11115496 bedtools-dbgsym_2.31.0+dfsg-2_ppc64el.deb 6c4b981e9c397430674a8c1bfa6c8a5ceb0579c2 680428 bedtools_2.31.0+dfsg-2_ppc64el.deb Checksums-Sha256: 99fb8a644b08b52ed29e3ff1860c7233b4f7165f5de8982817a3ba7147cb3025 11115496 bedtools-dbgsym_2.31.0+dfsg-2_ppc64el.deb 6a9057ab9fa83238fcbd4d864da4711e077ddcb3062a0c90201bde59c897a0ae 680428 bedtools_2.31.0+dfsg-2_ppc64el.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 19 Nov 2023 18:50:13 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-13), autotools-dev (= 20220109.1), base-files (= 13), base-passwd (= 3.6.2), bash (= 5.2.15-2+b6), binutils (= 2.41-6), binutils-common (= 2.41-6), binutils-x86-64-linux-gnu (= 2.41-6), bsdextrautils (= 2.39.2-6), bsdutils (= 1:2.39.2-6), build-essential (= 12.10), bzip2 (= 1.0.8-5+b1), coreutils (= 9.4-2+b1), cpp (= 4:13.2.0-1), cpp-11 (= 11.4.0-5), cpp-13 (= 13.2.0-6), dash (= 0.5.12-6), debconf (= 1.5.82), debhelper (= 13.11.8), debianutils (= 5.14), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.1), dpkg-dev (= 1.22.1), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-1), g++-13 (= 13.2.0-6), gcc (= 4:13.2.0-1), gcc-11 (= 11.4.0-5), gcc-11-base (= 11.4.0-5), gcc-13 (= 13.2.0-6), gcc-13-base (= 13.2.0-6), gettext (= 0.21-13+b1), gettext-base (= 0.21-13+b1), grep (= 3.11-3), groff-base (= 1.23.0-3), gzip (= 1.12-1), hostname (= 3.23+nmu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.4.0-5), libasan8 (= 13.2.0-6), libatomic1 (= 13.2.0-6), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1), libaudit1 (= 1:3.1.1-1), libbinutils (= 2.41-6), libblkid1 (= 2.39.2-6), libbz2-1.0 (= 1.0.8-5+b1), libbz2-dev (= 1.0.8-5+b1), libc-bin (= 2.37-12), libc-dev-bin (= 2.37-12), libc6 (= 2.37-12), libc6-dev (= 2.37-12), libcap-ng0 (= 0.8.3-1+b3), libcap2 (= 1:2.66-4), libcc1-0 (= 13.2.0-6), libcom-err2 (= 1.47.0-2+b1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41-6), libctf0 (= 2.41-6), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271), libdebhelper-perl (= 13.11.8), libdpkg-perl (= 1.22.1), libelf1 (= 0.190-1), libexpat1 (= 2.5.0-2), libffi8 (= 3.4.4-1), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-11-dev (= 11.4.0-5), libgcc-13-dev (= 13.2.0-6), libgcc-s1 (= 13.2.0-6), libgcrypt20 (= 1.10.2-3), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.3.0+dfsg-2), libgomp1 (= 13.2.0-6), libgpg-error0 (= 1.47-3), libgprofng0 (= 2.41-6), libgssapi-krb5-2 (= 1.20.1-5), libhwasan0 (= 13.2.0-6), libicu72 (= 72.1-4), libisl23 (= 0.26-3), libitm1 (= 13.2.0-6), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5), libkrb5support0 (= 1.20.1-5), liblsan0 (= 13.2.0-6), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.4-0.1), liblzma5 (= 5.4.4-0.1), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-1), libmount1 (= 2.39.2-6), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20231016-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libnumber-compare-perl (= 0.03-3), libpam-modules (= 1.5.2-9.1), libpam-modules-bin (= 1.5.2-9.1), libpam-runtime (= 1.5.2-9.1), libpam0g (= 1.5.2-9.1), libpcre2-8-0 (= 10.42-4), libperl5.36 (= 5.36.0-9), libpipeline1 (= 1.5.7-1), libpython3-stdlib (= 3.11.4-5+b1), libpython3.11-minimal (= 3.11.6-3), libpython3.11-stdlib (= 3.11.6-3), libquadmath0 (= 13.2.0-6), libreadline8 (= 8.2-1.3), libseccomp2 (= 2.5.4-2), libselinux1 (= 3.5-1), libsframe1 (= 2.41-6), libsmartcols1 (= 2.39.2-6), libsqlite3-0 (= 3.44.0-1), libssl3 (= 3.0.12-2), libstdc++-13-dev (= 13.2.0-6), libstdc++6 (= 13.2.0-6), libsub-override-perl (= 0.09-4), libsystemd0 (= 255~rc2-2), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.4+20231016-1), libtirpc-common (= 1.3.4+ds-1), libtirpc-dev (= 1.3.4+ds-1), libtirpc3 (= 1.3.4+ds-1), libtool (= 2.4.7-7), libtsan0 (= 11.4.0-5), libtsan2 (= 13.2.0-6), libubsan1 (= 13.2.0-6), libuchardet0 (= 0.0.7-1), libudev1 (= 255~rc2-2), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6), libxml2 (= 2.9.14+dfsg-1.3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.5.10-1), login (= 1:4.13+dfsg1-3), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.0-1), mawk (= 1.3.4.20231102-1), media-types (= 10.1.0), ncurses-base (= 6.4+20231016-1), ncurses-bin (= 6.4+20231016-1), patch (= 2.7.6-7), perl (= 5.36.0-9), perl-base (= 5.36.0-9), perl-modules-5.36 (= 5.36.0-9), po-debconf (= 1.0.21+nmu1), python3 (= 3.11.4-5+b1), python3-minimal (= 3.11.4-5+b1), python3.11 (= 3.11.6-3), python3.11-minimal (= 3.11.6-3), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-3), tar (= 1.34+dfsg-1.2), tzdata (= 2023c-10), usrmerge (= 38), util-linux (= 2.39.2-6), xz-utils (= 5.4.4-0.1), zlib1g (= 1:1.3.dfsg-2), zlib1g-dev (= 1:1.3.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1700321699" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedtools-dbgsym_2.31.0+dfsg-2_ppc64el.deb ----------------------------------------- new Debian package, version 2.0. size 11115496 bytes: control archive=540 bytes. 390 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: bedtools-dbgsym Source: bedtools Version: 2.31.0+dfsg-2 Auto-Built-Package: debug-symbols Architecture: ppc64el Maintainer: Debian Med Packaging Team Installed-Size: 11119 Depends: bedtools (= 2.31.0+dfsg-2) Section: debug Priority: optional Description: debug symbols for bedtools Build-Ids: 63838803c4bf336a78f7f4bfa29a41ad98229119 drwxr-xr-x root/root 0 2023-11-18 15:34 ./ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/lib/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/lib/debug/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/lib/debug/.build-id/63/ -rw-r--r-- root/root 11375280 2023-11-18 15:34 ./usr/lib/debug/.build-id/63/838803c4bf336a78f7f4bfa29a41ad98229119.debug drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/doc/ lrwxrwxrwx root/root 0 2023-11-18 15:34 ./usr/share/doc/bedtools-dbgsym -> bedtools bedtools_2.31.0+dfsg-2_ppc64el.deb ---------------------------------- new Debian package, version 2.0. size 680428 bytes: control archive=2188 bytes. 919 bytes, 20 lines control 2915 bytes, 50 lines md5sums Package: bedtools Version: 2.31.0+dfsg-2 Architecture: ppc64el Maintainer: Debian Med Packaging Team Installed-Size: 2518 Depends: libbz2-1.0, libc6 (>= 2.34), libgcc-s1 (>= 4.2), liblzma5 (>= 5.1.1alpha+20120614), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4) Conflicts: filo Replaces: filo Provides: filo Section: science Priority: optional Homepage: https://github.com/arq5x/bedtools2 Description: suite of utilities for comparing genomic features The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together. . The groupBy utility is distributed in the filo package. drwxr-xr-x root/root 0 2023-11-18 15:34 ./ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/bin/ -rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/annotateBed -rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/bamToBed -rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/bamToFastq -rwxr-xr-x root/root 44 2023-11-18 15:34 ./usr/bin/bed12ToBed6 -rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/bedToBam -rwxr-xr-x root/root 36 2023-11-18 15:34 ./usr/bin/bedToIgv -rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/bedpeToBam -rwxr-xr-x root/root 2492880 2023-11-18 15:34 ./usr/bin/bedtools -rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/closestBed -rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/clusterBed -rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/complementBed -rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/coverageBed -rwxr-xr-x root/root 39 2023-11-18 15:34 ./usr/bin/expandCols -rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/fastaFromBed -rwxr-xr-x root/root 38 2023-11-18 15:34 ./usr/bin/flankBed -rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/genomeCoverageBed -rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/getOverlap -rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/groupBy -rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/intersectBed -rwxr-xr-x root/root 38 2023-11-18 15:34 ./usr/bin/linksBed -rwxr-xr-x root/root 36 2023-11-18 15:34 ./usr/bin/mapBed -rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/maskFastaFromBed -rwxr-xr-x root/root 38 2023-11-18 15:34 ./usr/bin/mergeBed -rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/multiBamCov -rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/multiIntersectBed -rwxr-xr-x root/root 36 2023-11-18 15:34 ./usr/bin/nucBed -rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/pairToBed -rwxr-xr-x root/root 43 2023-11-18 15:34 ./usr/bin/pairToPair -rwxr-xr-x root/root 39 2023-11-18 15:34 ./usr/bin/randomBed -rwxr-xr-x root/root 38 2023-11-18 15:34 ./usr/bin/shiftBed -rwxr-xr-x root/root 40 2023-11-18 15:34 ./usr/bin/shuffleBed -rwxr-xr-x root/root 37 2023-11-18 15:34 ./usr/bin/slopBed -rwxr-xr-x root/root 37 2023-11-18 15:34 ./usr/bin/sortBed -rwxr-xr-x root/root 41 2023-11-18 15:34 ./usr/bin/subtractBed -rwxr-xr-x root/root 36 2023-11-18 15:34 ./usr/bin/tagBam -rwxr-xr-x root/root 42 2023-11-18 15:34 ./usr/bin/unionBedGraphs -rwxr-xr-x root/root 39 2023-11-18 15:34 ./usr/bin/windowBed -rwxr-xr-x root/root 44 2023-11-18 15:34 ./usr/bin/windowMaker drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/bash-completion/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/bash-completion/completions/ -rw-r--r-- root/root 638 2023-06-23 19:59 ./usr/share/bash-completion/completions/bedtools drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/bedtools/ drwxr-xr-x root/root 0 2023-04-28 12:08 ./usr/share/bedtools/genomes/ -rw-r--r-- root/root 868 2023-04-28 12:08 ./usr/share/bedtools/genomes/human.hg18.genome -rw-r--r-- root/root 1984 2023-04-28 12:08 ./usr/share/bedtools/genomes/human.hg19.genome -rw-r--r-- root/root 11684 2023-04-28 12:08 ./usr/share/bedtools/genomes/human.hg38.genome -rw-r--r-- root/root 1417 2023-04-28 12:08 ./usr/share/bedtools/genomes/mouse.mm10.genome -rw-r--r-- root/root 577 2023-04-28 12:08 ./usr/share/bedtools/genomes/mouse.mm8.genome -rw-r--r-- root/root 596 2023-04-28 12:08 ./usr/share/bedtools/genomes/mouse.mm9.genome drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-11-18 15:34 ./usr/share/doc/bedtools/ -rw-r--r-- root/root 3355 2023-04-28 12:08 ./usr/share/doc/bedtools/README.md -rw-r--r-- root/root 278 2023-06-23 19:59 ./usr/share/doc/bedtools/README.test -rw-r--r-- root/root 2525 2023-11-18 15:34 ./usr/share/doc/bedtools/changelog.Debian.gz -rw-r--r-- root/root 5451 2023-06-23 20:13 ./usr/share/doc/bedtools/copyright -rw-r--r-- root/root 628 2023-06-23 19:59 ./usr/share/doc/bedtools/run-unit-test lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1352 B] Get:5 copy:/<>/apt_archive ./ Packages [1435 B] Fetched 3402 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl libio-compress-brotli-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:ppc64el t1utils unzip 0 upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 12.7 MB of archives. After this operation, 49.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.12-2 [1419 kB] Get:4 http://localhost:3142/debian sid/main amd64 ca-certificates all 20230311 [153 kB] Get:5 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.65-1 [33.3 kB] Get:6 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.6-1 [49.9 kB] Get:7 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get:8 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get:9 http://localhost:3142/debian sid/main amd64 iso-codes all 4.15.0-1 [2906 kB] Get:10 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:11 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB] Get:12 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:13 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:14 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:15 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:16 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:17 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:19 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:20 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.63-1+b1 [44.0 kB] Get:21 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:22 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b1 [123 kB] Get:23 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:24 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:25 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.21-1 [95.6 kB] Get:26 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get:27 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.60-1 [219 kB] Get:28 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:29 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:30 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get:31 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:32 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:33 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:34 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:35 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:36 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:37 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:38 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.37-1 [131 kB] Get:39 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:40 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:41 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:42 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:43 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.59-1 [43.6 kB] Get:44 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB] Get:45 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:46 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:47 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:48 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:49 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB] Get:50 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:51 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:52 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB] Get:53 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB] Get:54 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:55 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:56 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:57 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:58 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:59 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:60 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:61 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:62 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:63 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:64 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:65 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:66 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:69 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:70 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:71 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.084-1 [216 kB] Get:72 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:73 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.11-1 [10.5 kB] Get:74 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:75 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.72-1 [187 kB] Get:76 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:77 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:78 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:79 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:80 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get:81 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:82 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:83 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:84 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-6 [37.8 kB] Get:85 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:86 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:87 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:88 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:89 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:90 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:91 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:92 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:93 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB] Get:94 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:95 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB] Get:96 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.27-1 [12.5 kB] Get:97 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:98 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:99 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB] Get:100 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:101 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.636-1 [43.0 kB] Get:102 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:103 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.004+ds-1 [99.5 kB] Get:104 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.004+ds-1 [102 kB] Get:105 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:106 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.38-1 [60.0 kB] Get:107 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.29-1 [28.8 kB] Get:108 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB] Get:109 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B] Get:110 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1 [13.0 kB] Get:111 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB] Get:112 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:113 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB] Get:114 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2 [20.2 kB] Get:115 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.17-1 [116 kB] Get:116 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:117 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.86+ds-1 [34.4 kB] Get:118 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-6 [63.1 kB] Get:119 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:120 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:121 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:122 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:123 http://localhost:3142/debian sid/main amd64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.7 MB in 0s (74.4 MB/s) Selecting previously unselected package netbase. (Reading database ... 21606 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.0.12-2_amd64.deb ... Unpacking openssl (3.0.12-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../002-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../003-diffstat_1.65-1_amd64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../004-libassuan0_2.5.6-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.6-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../005-gpgconf_2.2.40-1.1_amd64.deb ... Unpacking gpgconf (2.2.40-1.1) ... Selecting previously unselected package gpg. Preparing to unpack .../006-gpg_2.2.40-1.1_amd64.deb ... Unpacking gpg (2.2.40-1.1) ... Selecting previously unselected package iso-codes. Preparing to unpack .../007-iso-codes_4.15.0-1_all.deb ... Unpacking iso-codes (4.15.0-1) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../008-libaliased-perl_0.34-3_all.deb ... Unpacking libaliased-perl (0.34-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../009-libapt-pkg-perl_0.1.40+b2_amd64.deb ... Unpacking libapt-pkg-perl (0.1.40+b2) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../010-libb-hooks-op-check-perl_0.22-2+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../011-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../012-libdevel-callchecker-perl_0.008-2_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.008-2) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../013-libparams-classify-perl_0.015-2+b1_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../014-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../015-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../016-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../017-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../018-libvariable-magic-perl_0.63-1+b1_amd64.deb ... Unpacking libvariable-magic-perl (0.63-1+b1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../019-libb-hooks-endofscope-perl_0.26-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.26-1) ... Selecting previously unselected package libberkeleydb-perl:amd64. Preparing to unpack .../020-libberkeleydb-perl_0.64-2+b1_amd64.deb ... Unpacking libberkeleydb-perl:amd64 (0.64-2+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../021-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../022-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../023-liburi-perl_5.21-1_all.deb ... Unpacking liburi-perl (5.21-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. Preparing to unpack .../024-libhtml-parser-perl_3.81-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.81-1) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../025-libcgi-pm-perl_4.60-1_all.deb ... Unpacking libcgi-pm-perl (4.60-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../026-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../027-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../028-libclass-xsaccessor-perl_1.19-4+b1_amd64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b1) ... Selecting previously unselected package libclone-perl:amd64. Preparing to unpack .../029-libclone-perl_0.46-1_amd64.deb ... Unpacking libclone-perl:amd64 (0.46-1) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../030-libconfig-tiny-perl_2.30-1_all.deb ... Unpacking libconfig-tiny-perl (2.30-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../031-libparams-util-perl_1.102-2+b1_amd64.deb ... Unpacking libparams-util-perl (1.102-2+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../032-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../033-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../034-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../035-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libcpanel-json-xs-perl:amd64. Preparing to unpack .../036-libcpanel-json-xs-perl_4.37-1_amd64.deb ... Unpacking libcpanel-json-xs-perl:amd64 (4.37-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../037-libdevel-stacktrace-perl_2.0400-2_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-2) ... 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Preparing to unpack .../120-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package lintian. Preparing to unpack .../121-lintian_2.116.3_all.deb ... Unpacking lintian (2.116.3) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:ppc64el. Preparing to unpack .../122-sbuild-build-depends-lintian-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-lintian-dummy:ppc64el (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b2) ... Setting up liblz1:amd64 (1.13-6) ... Setting up libberkeleydb-perl:amd64 (0.64-2+b1) ... Setting up plzip (1.10-6) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-2) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:amd64 (4.37-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-28) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.86+ds-1) ... Setting up libio-interactive-perl (1.025-1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:amd64 (2.5.6-1) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004005-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.38-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.65-1) ... Setting up libvariable-magic-perl (0.63-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:amd64 (0.27-1) ... Setting up libsyntax-keyword-try-perl (0.29-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.636-1) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up lzop (1.04-2) ... Setting up gpgconf (2.2.40-1.1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-3) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.12-2) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.21-1) ... Setting up iso-codes (4.15.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up gpg (2.2.40-1.1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libtext-markdown-discount-perl (0.16-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libio-socket-ssl-perl (2.084-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.60-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.59-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.72-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.17-1) ... Setting up liblwp-protocol-https-perl (6.11-1) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:ppc64el (0.invalid.0) ... Processing triggers for libc-bin (2.37-12) ... Processing triggers for man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 281452 Build-Time: 226 Distribution: unstable Foreign Architectures: ppc64el Host Architecture: ppc64el Install-Time: 14 Job: bedtools_2.31.0+dfsg-2 Lintian: pass Machine Architecture: amd64 Package: bedtools Package-Time: 252 Source-Version: 2.31.0+dfsg-2 Space: 281452 Status: successful Version: 2.31.0+dfsg-2 -------------------------------------------------------------------------------- Finished at 2023-11-19T18:50:14Z Build needed 00:04:12, 281452k disk space