sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir +==============================================================================+ | bedops 2.4.39+dfsg1-2 (i386) Fri, 03 Sep 2021 16:42:23 +0000 | +==============================================================================+ Package: bedops Version: 2.4.39+dfsg1-2 Source Version: 2.4.39+dfsg1-2 Distribution: unstable Machine Architecture: arm64 Host Architecture: i386 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-44577a7d-90a1-446a-8e33-578aaa51acec' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-LBHRKB/resolver-P0wLh7' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [165 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:4 http://mirror.einval.org/debian sid/main i386 Packages [8695 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9198 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8631 kB] Fetched 26.7 MB in 7s (3826 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'bedops' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bedops.git Please use: git clone https://salsa.debian.org/med-team/bedops.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.5 MB of source archives. Get:1 http://mirror.einval.org/debian sid/main bedops 2.4.39+dfsg1-2 (dsc) [2185 B] Get:2 http://mirror.einval.org/debian sid/main bedops 2.4.39+dfsg1-2 (tar) [13.4 MB] Get:3 http://mirror.einval.org/debian sid/main bedops 2.4.39+dfsg1-2 (diff) [11.1 kB] Fetched 13.5 MB in 0s (45.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedops-LBHRKB/bedops-2.4.39+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-LBHRKB' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 Filtered Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [438 B] Get:5 copy:/<>/apt_archive ./ Packages [527 B] Fetched 1922 B in 0s (47.2 kB/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... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bsdextrautils cpp-10-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-10-i686-linux-gnu g++-i686-linux-gnu gcc-10-base:i386 gcc-10-cross-base gcc-10-i686-linux-gnu gcc-10-i686-linux-gnu-base gcc-11-base:i386 gcc-11-cross-base gcc-i686-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:i386 libasan6-i386-cross libatomic1:i386 libatomic1-i386-cross libbz2-1.0:i386 libbz2-dev:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcom-err2:i386 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:i386 libgcc-10-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgomp1:i386 libgomp1-i386-cross libgssapi-krb5-2:i386 libicu67 libio-string-perl libitm1:i386 libitm1-i386-cross libjansson-dev:i386 libjansson4:i386 libk5crypto3:i386 libkeyutils1:i386 libkrb5-3:i386 libkrb5support0:i386 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libncursesw6 libnsl-dev:i386 libnsl2:i386 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0:i386 libquadmath0-i386-cross libreadline8 libsigsegv2 libsqlite3-0 libssl1.1:i386 libstdc++-10-dev:i386 libstdc++-10-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsub-override-perl libtirpc-dev:i386 libtirpc3:i386 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:i386 linux-libc-dev-i386-cross m4 man-db media-types po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.9 python3.9-minimal readline-common sensible-utils ucf zlib1g:i386 zlib1g-dev:i386 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales cpp-doc dh-make binutils-multiarch g++-10-multilib-i686-linux-gnu gcc-10-doc gcc-10-multilib-i686-linux-gnu manpages-dev flex bison gdb-i686-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:i386 libc-l10n:i386 locales:i386 libnss-nis:i386 libnss-nisplus:i386 manpages-dev:i386 krb5-doc:i386 krb5-user:i386 libstdc++-10-doc:i386 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 python3.9-venv python3.9-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx bzip2-doc:i386 libidn2-0:i386 libarchive-cpio-perl krb5-locales:i386 libgpm2 ca-certificates libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bsdextrautils cpp-10-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-10-i686-linux-gnu g++-i686-linux-gnu gcc-10-base:i386 gcc-10-cross-base gcc-10-i686-linux-gnu gcc-10-i686-linux-gnu-base gcc-11-base:i386 gcc-11-cross-base gcc-i686-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:i386 libasan6-i386-cross libatomic1:i386 libatomic1-i386-cross libbz2-1.0:i386 libbz2-dev:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcom-err2:i386 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:i386 libgcc-10-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgomp1:i386 libgomp1-i386-cross libgssapi-krb5-2:i386 libicu67 libio-string-perl libitm1:i386 libitm1-i386-cross libjansson-dev:i386 libjansson4:i386 libk5crypto3:i386 libkeyutils1:i386 libkrb5-3:i386 libkrb5support0:i386 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libncursesw6 libnsl-dev:i386 libnsl2:i386 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0:i386 libquadmath0-i386-cross libreadline8 libsigsegv2 libsqlite3-0 libssl1.1:i386 libstdc++-10-dev:i386 libstdc++-10-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsub-override-perl libtirpc-dev:i386 libtirpc3:i386 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:i386 linux-libc-dev-i386-cross m4 man-db media-types po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.9 python3.9-minimal readline-common sbuild-build-depends-main-dummy:i386 sensible-utils ucf zlib1g:i386 zlib1g-dev:i386 0 upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 207 MB of archives. After this operation, 929 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [952 B] Get:2 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.37.2-1 [143 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libpython3.9-minimal arm64 3.9.7-2 [800 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 python3.9-minimal arm64 3.9.7-2 [1892 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 media-types all 4.0.0 [30.3 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libmpdec3 arm64 2.5.1-2 [84.4 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libncursesw6 arm64 6.2+20201114-4 [121 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 readline-common all 8.1-2 [73.8 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1-2 [160 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.36.0-2 [768 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libpython3.9-stdlib arm64 3.9.7-2 [1662 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 python3.9 arm64 3.9.7-2 [480 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get:22 http://mirror.einval.org/debian sid/main i386 gcc-10-base i386 10.3.0-9 [205 kB] Get:23 http://mirror.einval.org/debian sid/main i386 gcc-11-base i386 11.2.0-4 [205 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.17 [21.5 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.39-3 [69.1 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-4 [173 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.4-1 [819 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-4 [510 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 gcc-10-i686-linux-gnu-base arm64 10.3.0-8cross1 [205 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 cpp-10-i686-linux-gnu arm64 10.3.0-8cross1 [46.2 MB] Get:38 http://mirror.einval.org/debian sid/main arm64 cpp-i686-linux-gnu arm64 4:10.2.1-1 [16.8 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 binutils-i686-linux-gnu arm64 2.37-5 [2045 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 gcc-10-cross-base all 10.3.0-8cross1 [200 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 gcc-11-cross-base all 11.2.0-2cross1 [200 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libc6-i386-cross all 2.31-17cross3 [1502 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-i386-cross all 11.2.0-2cross1 [50.2 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libgomp1-i386-cross all 11.2.0-2cross1 [109 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libitm1-i386-cross all 11.2.0-2cross1 [27.4 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libatomic1-i386-cross all 11.2.0-2cross1 [7604 B] Get:48 http://mirror.einval.org/debian sid/main arm64 libasan6-i386-cross all 11.2.0-2cross1 [1998 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libstdc++6-i386-cross all 11.2.0-2cross1 [578 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libubsan1-i386-cross all 11.2.0-2cross1 [810 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libquadmath0-i386-cross all 11.2.0-2cross1 [226 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libgcc-10-dev-i386-cross all 10.3.0-8cross1 [2319 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 gcc-10-i686-linux-gnu arm64 10.3.0-8cross1 [52.3 MB] Get:54 http://mirror.einval.org/debian sid/main arm64 gcc-i686-linux-gnu arm64 4:10.2.1-1 [1452 B] Get:55 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-i386-cross all 5.10.46-4cross3 [1468 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libc6-dev-i386-cross all 2.31-17cross3 [2132 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libstdc++-10-dev-i386-cross all 10.3.0-8cross1 [1785 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 g++-10-i686-linux-gnu arm64 10.3.0-8cross1 [49.3 MB] Get:59 http://mirror.einval.org/debian sid/main arm64 g++-i686-linux-gnu arm64 4:10.2.1-1 [1176 B] Get:60 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.12+dfsg-3 [631 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-2 [59.3 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-i386 all 12.9 [6704 B] Get:76 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.5.1 [192 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.6-15 [513 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.185-2 [171 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-4 [1261 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.5.1 [1056 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 help2man arm64 1.48.5 [143 kB] Get:90 http://mirror.einval.org/debian sid/main i386 libgcc-s1 i386 11.2.0-4 [49.8 kB] Get:91 http://mirror.einval.org/debian sid/main i386 libc6 i386 2.31-17 [2756 kB] Get:92 http://mirror.einval.org/debian sid/main i386 libasan6 i386 11.2.0-4 [1933 kB] Get:93 http://mirror.einval.org/debian sid/main i386 libatomic1 i386 11.2.0-4 [7720 B] Get:94 http://mirror.einval.org/debian sid/main i386 libbz2-1.0 i386 1.0.8-4 [46.5 kB] Get:95 http://mirror.einval.org/debian sid/main i386 linux-libc-dev i386 5.10.46-4 [1362 kB] Get:96 http://mirror.einval.org/debian sid/main i386 libcrypt1 i386 1:4.4.25-1 [98.5 kB] Get:97 http://mirror.einval.org/debian sid/main i386 libcrypt-dev i386 1:4.4.25-1 [115 kB] Get:98 http://mirror.einval.org/debian sid/main i386 libcom-err2 i386 1.46.4-1 [75.6 kB] Get:99 http://mirror.einval.org/debian sid/main i386 libkrb5support0 i386 1.18.3-7 [68.6 kB] Get:100 http://mirror.einval.org/debian sid/main i386 libk5crypto3 i386 1.18.3-7 [117 kB] Get:101 http://mirror.einval.org/debian sid/main i386 libkeyutils1 i386 1.6.1-2 [15.9 kB] Get:102 http://mirror.einval.org/debian sid/main i386 libssl1.1 i386 1.1.1l-1 [1552 kB] Get:103 http://mirror.einval.org/debian sid/main i386 libkrb5-3 i386 1.18.3-7 [390 kB] Get:104 http://mirror.einval.org/debian sid/main i386 libgssapi-krb5-2 i386 1.18.3-7 [176 kB] Get:105 http://mirror.einval.org/debian sid/main i386 libtirpc3 i386 1.3.2-2 [91.3 kB] Get:106 http://mirror.einval.org/debian sid/main i386 libnsl2 i386 1.3.0-2 [42.2 kB] Get:107 http://mirror.einval.org/debian sid/main i386 libtirpc-dev i386 1.3.2-2 [201 kB] Get:108 http://mirror.einval.org/debian sid/main i386 libnsl-dev i386 1.3.0-2 [70.6 kB] Get:109 http://mirror.einval.org/debian sid/main i386 libc6-dev i386 2.31-17 [2315 kB] Get:110 http://mirror.einval.org/debian sid/main i386 libbz2-dev i386 1.0.8-4 [31.3 kB] Get:111 http://mirror.einval.org/debian sid/main i386 libgomp1 i386 11.2.0-4 [110 kB] Get:112 http://mirror.einval.org/debian sid/main i386 libitm1 i386 11.2.0-4 [27.7 kB] Get:113 http://mirror.einval.org/debian sid/main i386 libstdc++6 i386 11.2.0-4 [616 kB] Get:114 http://mirror.einval.org/debian sid/main i386 libubsan1 i386 11.2.0-4 [813 kB] Get:115 http://mirror.einval.org/debian sid/main i386 libquadmath0 i386 11.2.0-4 [226 kB] Get:116 http://mirror.einval.org/debian sid/main i386 libgcc-10-dev i386 10.3.0-9 [2317 kB] Get:117 http://mirror.einval.org/debian sid/main i386 libjansson4 i386 2.13.1-1.1 [41.7 kB] Get:118 http://mirror.einval.org/debian sid/main i386 libjansson-dev i386 2.13.1-1.1 [46.1 kB] Get:119 http://mirror.einval.org/debian sid/main i386 libstdc++-10-dev i386 10.3.0-9 [1795 kB] Get:120 http://mirror.einval.org/debian sid/main arm64 python3-lib2to3 all 3.9.7-1 [79.4 kB] Get:121 http://mirror.einval.org/debian sid/main arm64 python3-distutils all 3.9.7-1 [146 kB] Get:122 http://mirror.einval.org/debian sid/main i386 zlib1g i386 1:1.2.11.dfsg-2 [93.1 kB] Get:123 http://mirror.einval.org/debian sid/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 207 MB in 2s (84.6 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12270 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.37.2-1_arm64.deb ... Unpacking bsdextrautils (2.37.2-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up binutils-i686-linux-gnu (2.37-5) ... Setting up libdebhelper-perl (13.5.1) ... Setting up libsqlite3-0:arm64 (3.36.0-2) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up linux-libc-dev:i386 (5.10.46-4) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libyaml-perl (1.30-1) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up gcc-10-base:i386 (10.3.0-9) ... Setting up linux-libc-dev-i386-cross (5.10.46-4cross3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libncursesw6:arm64 (6.2+20201114-4) ... Setting up gcc-10-cross-base (10.3.0-8cross1) ... Setting up gcc-11-cross-base (11.2.0-2cross1) ... Setting up sensible-utils (0.0.17) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-2) ... Setting up libc6-i386-cross (2.31-17cross3) ... Setting up libsub-override-perl (0.09-2) ... Setting up gcc-10-i686-linux-gnu-base:arm64 (10.3.0-8cross1) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up libquadmath0-i386-cross (11.2.0-2cross1) ... Setting up libelf1:arm64 (0.185-2) ... Setting up readline-common (8.1-2) ... Setting up libxml2:arm64 (2.9.12+dfsg-3) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libatomic1-i386-cross (11.2.0-2cross1) ... Setting up libreadline8:arm64 (8.1-2) ... Setting up m4 (1.4.18-5) ... Setting up libgomp1-i386-cross (11.2.0-2cross1) ... Setting up libc6-dev-i386-cross (2.31-17cross3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.5) ... Setting up libgcc-s1-i386-cross (11.2.0-2cross1) ... Setting up libasan6-i386-cross (11.2.0-2cross1) ... Setting up cpp-10-i686-linux-gnu (10.3.0-8cross1) ... Setting up libitm1-i386-cross (11.2.0-2cross1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-6) ... Setting up cpp-i686-linux-gnu (4:10.2.1-1) ... Setting up libpython3.9-stdlib:arm64 (3.9.7-2) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up automake (1:1.16.4-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-2) ... 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 libstdc++6-i386-cross (11.2.0-2cross1) ... Setting up dh-autoreconf (20) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+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 python3.9 (3.9.7-2) ... Setting up debhelper (13.5.1) ... Setting up python3 (3.9.2-3) ... Setting up libubsan1-i386-cross (11.2.0-2cross1) ... Setting up libgcc-10-dev-i386-cross (10.3.0-8cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up python3-lib2to3 (3.9.7-1) ... Setting up python3-distutils (3.9.7-1) ... Setting up libstdc++-10-dev-i386-cross (10.3.0-8cross1) ... Setting up gcc-10-i686-linux-gnu (10.3.0-8cross1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up gcc-i686-linux-gnu (4:10.2.1-1) ... Setting up g++-10-i686-linux-gnu (10.3.0-8cross1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up g++-i686-linux-gnu (4:10.2.1-1) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-i386 (12.9) ... Setting up libgcc-s1:i386 (11.2.0-4) ... Setting up libc6:i386 (2.31-17) ... Setting up libbz2-1.0:i386 (1.0.8-4) ... Setting up libstdc++6:i386 (11.2.0-4) ... Setting up libitm1:i386 (11.2.0-4) ... Setting up libkeyutils1:i386 (1.6.1-2) ... Setting up libssl1.1:i386 (1.1.1l-1) ... Setting up zlib1g:i386 (1:1.2.11.dfsg-2) ... Setting up libcrypt1:i386 (1:4.4.25-1) ... Setting up libcom-err2:i386 (1.46.4-1) ... Setting up libgomp1:i386 (11.2.0-4) ... Setting up libasan6:i386 (11.2.0-4) ... Setting up libjansson4:i386 (2.13.1-1.1) ... Setting up libkrb5support0:i386 (1.18.3-7) ... Setting up libquadmath0:i386 (11.2.0-4) ... Setting up libatomic1:i386 (11.2.0-4) ... Setting up libk5crypto3:i386 (1.18.3-7) ... Setting up libubsan1:i386 (11.2.0-4) ... Setting up libcrypt-dev:i386 (1:4.4.25-1) ... Setting up libkrb5-3:i386 (1.18.3-7) ... Setting up libjansson-dev:i386 (2.13.1-1.1) ... Setting up libgcc-10-dev:i386 (10.3.0-9) ... Setting up libgssapi-krb5-2:i386 (1.18.3-7) ... Setting up libtirpc3:i386 (1.3.2-2) ... Setting up libtirpc-dev:i386 (1.3.2-2) ... Setting up libnsl2:i386 (1.3.0-2) ... Setting up libnsl-dev:i386 (1.3.0-2) ... Setting up libc6-dev:i386 (2.31-17) ... Setting up libbz2-dev:i386 (1.0.8-4) ... Setting up libstdc++-10-dev:i386 (10.3.0-9) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.31-17) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (i386 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64) Toolchain package versions: binutils_2.37-5 dpkg-dev_1.20.9 g++-10_10.3.0-9 gcc-10_10.3.0-9 libc6-dev_2.31-17 libstdc++-10-dev_10.3.0-9 libstdc++-10-dev-i386-cross_10.3.0-8cross1 libstdc++6_11.2.0-4 libstdc++6-i386-cross_11.2.0-2cross1 linux-libc-dev_5.10.46-4 Package versions: adduser_3.118 apt_2.3.8 autoconf_2.71-2 automake_1:1.16.4-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.51 bash_5.1-3+b1 binutils_2.37-5 binutils-aarch64-linux-gnu_2.37-5 binutils-common_2.37-5 binutils-i686-linux-gnu_2.37-5 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1 cpp-10_10.3.0-9 cpp-10-i686-linux-gnu_10.3.0-8cross1 cpp-i686-linux-gnu_4:10.2.1-1 cross-config_2.6.18+nmu2 crossbuild-essential-i386_12.9 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.1 debian-archive-keyring_2021.1.1 debianutils_5.4-3 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dpkg_1.20.9 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.20.9 dwz_0.14-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1 g++-10_10.3.0-9 g++-10-i686-linux-gnu_10.3.0-8cross1 g++-i686-linux-gnu_4:10.2.1-1 gcc_4:10.2.1-1 gcc-10_10.3.0-9 gcc-10-base_10.3.0-9 gcc-10-cross-base_10.3.0-8cross1 gcc-10-i686-linux-gnu_10.3.0-8cross1 gcc-10-i686-linux-gnu-base_10.3.0-8cross1 gcc-11-base_11.2.0-4 gcc-11-cross-base_11.2.0-2cross1 gcc-i686-linux-gnu_4:10.2.1-1 gettext_0.21-4 gettext-base_0.21-4 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-6 gzip_1.10-4 help2man_1.48.5 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.8 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4 libasan6-i386-cross_11.2.0-2cross1 libatomic1_11.2.0-4 libatomic1-i386-cross_11.2.0-2cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5 libblkid1_2.37.2-1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-17 libc-dev-bin_2.31-17 libc6_2.31-17 libc6-dev_2.31-17 libc6-dev-i386-cross_2.31-17cross3 libc6-i386-cross_2.31-17cross3 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4 libcom-err2_1.46.4-1 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.25-1 libcrypt1_1:4.4.25-1 libctf-nobfd0_2.37-5 libctf0_2.37-5 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.1 libdebian-dpkgcross-perl_2.6.18+nmu2 libdpkg-perl_1.20.9 libelf1_0.185-2 libexpat1_2.2.10-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.12.0-1 libfile-which-perl_1.23-1 libgcc-10-dev_10.3.0-9 libgcc-10-dev-i386-cross_10.3.0-8cross1 libgcc-s1_11.2.0-4 libgcc-s1-i386-cross_11.2.0-2cross1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.20-1 libgdbm6_1.20-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.2-2 libgomp1_11.2.0-4 libgomp1-i386-cross_11.2.0-2cross1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl23_0.23-1 libitm1_11.2.0-4 libitm1-i386-cross_11.2.0-2cross1 libjansson-dev_2.13.1-1.1 libjansson4_2.13.1-1.1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 liblocale-gettext-perl_1.07-4+b1 liblsan0_11.2.0-4 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-2 libpython3.9-stdlib_3.9.7-2 libquadmath0_11.2.0-4 libquadmath0-i386-cross_11.2.0-2cross1 libreadline8_8.1-2 libseccomp2_2.5.1-1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9 libstdc++-10-dev-i386-cross_10.3.0-8cross1 libstdc++6_11.2.0-4 libstdc++6-i386-cross_11.2.0-2cross1 libsub-override-perl_0.09-2 libsystemd0_247.9-1 libtasn1-6_4.17.0-2 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtsan0_11.2.0-4 libubsan1_11.2.0-4 libubsan1-i386-cross_11.2.0-2cross1 libuchardet0_0.0.7-1 libudev1_247.9-1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml-libxml-perl_2.0134+dfsg-2+b1 libxml-namespacesupport-perl_1.12-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-2 libxml-simple-perl_2.25-1 libxml2_2.9.12+dfsg-3 libxxhash0_0.8.0-2 libyaml-perl_1.30-1 libzstd1_1.4.8+dfsg-2.1 linux-libc-dev_5.10.46-4 linux-libc-dev-i386-cross_5.10.46-4cross3 login_1:4.8.1-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-distutils_3.9.7-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3.9_3.9.7-2 python3.9-minimal_3.9.7-2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 ucf_3.0043 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bedops Binary: bedops, bedops-doc Architecture: any all Version: 2.4.39+dfsg1-2 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Homepage: https://github.com/bedops/bedops Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/bedops Vcs-Git: https://salsa.debian.org/med-team/bedops.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev Build-Depends-Indep: sphinx-common, libjs-mathjax, python3-sphinx Package-List: bedops deb science optional arch=any bedops-doc deb doc optional arch=all Checksums-Sha1: 4d9474ee3486ac33679866b87651884b45d0ab91 13440720 bedops_2.4.39+dfsg1.orig.tar.xz 37fa86e7d27c344eee083190d132240709a5cd63 11072 bedops_2.4.39+dfsg1-2.debian.tar.xz Checksums-Sha256: 550fe1473e93f406b577b9cdf097fb919e32349741e03a2741563ef45946e788 13440720 bedops_2.4.39+dfsg1.orig.tar.xz 1501befb37a66ff2295884995200251bf88d9207df806147313bada8fa792872 11072 bedops_2.4.39+dfsg1-2.debian.tar.xz Files: a3df3c35bd857999eb0e5b68c4f8f078 13440720 bedops_2.4.39+dfsg1.orig.tar.xz 0136d1fbffd563982a994c0228d28641 11072 bedops_2.4.39+dfsg1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmAvvlMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFxBQ/+OkgTNAJavFJjPT/S3qb8osr+gNHT7M95 HMdtTsBy+mpZcLKNX0EE6ONfsr8b0ffJC5WBch0m+ubuZdD8UuLSxOxDXTQSQGYA tN2gafDCjq65+oU7sUu8+TmrES0N80EziMagvlUUdHS+7zdBX4SwSffrgnEIRugj dazcjGanpTj3xxBvii+YnigO34sqoYK8IcXaRCHlCArqivUO0Gjhkx9naVXGkDeM RHaBJ9JBrdSvQuagDrD9vMjZKXditghYwbyl9+zt5UyMo+DQRBStG+O+LaL9zDxf s0xTKcEuxF6tk4eC4d5swK+n+uAyenYBOcjZtIeN5VBTpHt4dgOVBn/TSSZM++3J ennSzMENfgr/4HvVTOiU0wAakBaCWDKy2zPTuAHAe/5hxlMn8SAYx2q/aq0NFQWo qW4zx9xnSl9+HTUQCnZ0TvMHswRnL0gaHi38bEf6so9qmNai4wdUSm/BgjNx3o28 ry2HU4Xca12GfmLJ073P9tiGmH0ndBVqdnRYk2kWvvyqGrLBSSUUridXBUxP/Uhm nXeJ4d6FEvIoZQnc2x/fQewOlRTMLESX4QbT2k2tQ64z7OZu4GldSg3Zaz2kgX+E PhI7yClVe2LuWR2FfhtI9IBJFYwRySHW9yvahTYU8hVNRuZDo1Xl5UcTfk+4JNRz Z6ys4aIDDKY= =FHKk -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.flKmsyPA/trustedkeys.kbx': General error gpgv: Signature made Fri Feb 19 13:34:11 2021 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedops_2.4.39+dfsg1-2.dsc dpkg-source: info: extracting bedops in /<> dpkg-source: info: unpacking bedops_2.4.39+dfsg1.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.39+dfsg1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests_use_installed_binaries.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying use_debian_libs dpkg-source: info: applying hardening.patch dpkg-source: info: applying parallel.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ ulimit -c --------- 0 I: Finished running 'ulimit -c'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.i386 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmutg PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=crossqa-sid SCHROOT_CHROOT_NAME=crossqa-sid SCHROOT_COMMAND=env SCHROOT_GID=1002 SCHROOT_GROUP=helmutg SCHROOT_SESSION_ID=crossqa-sid-44577a7d-90a1-446a-8e33-578aaa51acec SCHROOT_UID=1002 SCHROOT_USER=helmutg SHELL=/bin/sh USER=helmutg dpkg-buildpackage ----------------- Command: dpkg-buildpackage -ai386 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.39+dfsg1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Juhani Numminen dpkg-architecture: warning: specified GNU system type i686-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j1 clean make[2]: Entering directory '/<>' make clean -f system.mk/Makefile.linux make[3]: Entering directory '/<>' rm -rf bin rm -rf bin rm -rf bin rm -rf modules make -C applications/bed/bedmap/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedmap/src' rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedmap/src' make -C applications/bed/sort-bed/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/sort-bed/src' rm -rf objects-typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/sort-bed/src' make -C applications/bed/bedops/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedops/src' rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedops/src' make -C applications/bed/closestfeats/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/closestfeats/src' rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/closestfeats/src' make -C applications/bed/bedextract/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedextract/src' rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedextract/src' make -C applications/bed/starch/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/starch/src' rm -rf ../lib rm -f ../lib/libstarch_debug.a rm -f ../lib/libstarch_gprof.a rm -rf objects rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/starch/src' make -C applications/bed/conversion/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/conversion/src' rm -rf ../bin rm -rf objects rm -rf *.so *~ make[4]: Leaving directory '/<>/applications/bed/conversion/src' rm -rf third-party/bzip2-1.0.6 rm -f third-party/bzip2 rm -rf third-party/jansson-2.6 rm -f third-party/jansson rm -rf third-party/zlib-1.2.7 rm -f third-party/zlib rm -rf bin make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' rm -rf docs/_build/ make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc make[1]: Entering directory '/<>' make -f system.mk/Makefile.linux make[2]: Entering directory '/<>' #bzcat | tar -x -C third-party #cd third-party/jansson-2.6 && ./configure --prefix=/<>/third-party/jansson-2.6 && make && make install && cd /<> && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #bzcat | tar -x -C third-party #cd third-party/bzip2-1.0.6 && make libbz2.a && cd /<> && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2 #bzcat | tar -x -C third-party #cd third-party/zlib-1.2.7 && ./configure --static && make && cd /<> && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib make build -f /<>/system.mk/Makefile.linux make[3]: Entering directory '/<>' make -C applications/bed/bedmap/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedmap/src' mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && i686-linux-gnu-g++ -o ../bin/bedmap-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedmap.cpp In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘const char* starch::Starch::getCurrentChromosome()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘void starch::Starch::iterateArchiveMdIter()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedmap/src' make -C applications/bed/sort-bed/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/sort-bed/src' mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘void starch::UNSTARCH_printMetadataSignature(const unsigned char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2278 | static_cast( mdSha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from SortDetails.cpp:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘ChromBedData* initializeChromBedData(char*, double*)’ at SortDetails.cpp:250:12: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘ChromBedData* initializeChromBedData(char*, double*)’: SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from SortDetails.cpp:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void lexSortBedData(BedData*)’ at SortDetails.cpp:1343:20: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘void lexSortBedData(BedData*)’: SortDetails.cpp:1342:33: note: length computed here 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::listJSONMetadata(FILE*, FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1226:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1226 | static_cast( getArchiveType() ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1230 | static_cast( getArchiveHeaderFlag() ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1231:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1231 | static_cast( getArchiveShowNewlineFlag() )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractAllData(const string&, FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:2003:51: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2003 | static_cast( getArchiveHeaderFlag() )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:2014:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2014 | static_cast( getArchiveHeaderFlag() )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of ‘Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’: CheckSort.cpp:51:28: required from here ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:268:12: warning: implicitly-declared ‘Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)’ is deprecated [-Wdeprecated-copy] 268 | auto __tmp = *this; | ^~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because ‘Bed::bed_check_iterator*, 16>’ has user-provided ‘bool Bed::bed_check_iterator::operator=(const Bed::bed_check_iterator&) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’ 308 | bool operator=(const bed_check_iterator& b); | ^~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:295:14: warning: implicitly-declared ‘Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)’ is deprecated [-Wdeprecated-copy] 295 | return __tmp; | ^~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because ‘Bed::bed_check_iterator*, 16>’ has user-provided ‘bool Bed::bed_check_iterator::operator=(const Bed::bed_check_iterator&) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’ 308 | bool operator=(const bed_check_iterator& b); | ^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, from CheckSort.cpp:28: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, inlined from ‘int checkSort(const char**, unsigned int)’ at CheckSort.cpp:51:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘int checkSort(const char**, unsigned int)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ mkdir -p ../bin && i686-linux-gnu-g++ -o ../bin/sort-bed-typical -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical rm -rf objects-typical make[4]: Leaving directory '/<>/applications/bed/sort-bed/src' make -C applications/bed/bedops/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedops/src' mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && i686-linux-gnu-g++ -o ../bin/bedops-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘const char* starch::Starch::getCurrentChromosome()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’ at BedPadReader.hpp:140:11: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from Bedops.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’ at BedPadReader.hpp:140:11: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedops/src' make -C applications/bed/closestfeats/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/closestfeats/src' mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && i686-linux-gnu-g++ -o ../bin/closest-features-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ClosestFeature.cpp In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, inlined from ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedReader.hpp:78:13: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed::allocate_iterator_starch_bed(Ext::FPWrap&, Ext::PooledMemory&, const string&) [with ErrorType = Ext::Exception, 0>; BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:117:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::allocate_iterator_starch_bed::allocate_iterator_starch_bed(Ext::FPWrap&, Ext::PooledMemory&, const string&) [with ErrorType = Ext::Exception, 0>; BedType = Bed::BasicCoords; unsigned int SZ = 512]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ClosestFeature.cpp:26: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::allocate_iterator_starch_bed Bed::allocate_iterator_starch_bed::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:207:36, inlined from ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’ at BedReader.hpp:78:19: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/closestfeats/src' make -C applications/bed/bedextract/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedextract/src' mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && i686-linux-gnu-g++ -o ../bin/bedextract-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ExtractRows.cpp In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, inlined from ‘std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]’ at ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:102:58: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedextract/src' make -C applications/bed/starch/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/starch/src' mkdir -p objects i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘void starch::UNSTARCH_printMetadataSignature(const unsigned char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2278 | static_cast( mdSha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here 383 | strncpy(*chr, s, strlen(s) + 1); | ~~~~~~^~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncat(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here 2228 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); | ~~~~~~^~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p ../lib ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o mkdir -p ../bin i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../.. starch.c: In function ‘int main(int, char**)’: starch.c:106:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 106 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:121:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 121 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:123:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 123 | static_cast( kStarchFinalizeTransformTrue ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:146:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 146 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:161:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 161 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:163:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 163 | static_cast( kStarchFinalizeTransformTrue ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:191:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 191 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:194:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 194 | static_cast( bedGeneratePerChrSignatureFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:195:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 195 | static_cast( bedHeaderFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:196:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 196 | static_cast( bedReportProgressFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:197:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 197 | static_cast( bedReportProgressN )) != STARCH_EXIT_SUCCESS) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. unstarch.c: In function ‘int main(int, char**)’: unstarch.c:401:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 401 | static_cast( metadataOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:402:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 402 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:422:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 422 | static_cast( metadataOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:423:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 423 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:452:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 452 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:453:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 453 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:473:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 473 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:474:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 474 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:567:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 567 | UNSTARCH_printCompressionType(static_cast( type )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:798:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 798 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:809:82: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 809 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c: In function ‘void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)’: unstarch.c:1334:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1334 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:1336:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1336 | static_cast( sha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. In file included from /usr/i686-linux-gnu/include/c++/10/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int main(int, char**)’: starchcat.c:136:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 136 | assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:137:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 137 | assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:138:87: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:138:133: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:139:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 139 | assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:140:145: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 140 | assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, &numChromosomes, reinterpret_cast( mdRecords ), static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:141:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 141 | assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:142:124: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:142:213: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:143:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 143 | assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:144:127: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 144 | assert( STARCHCAT_buildChromosomeSummaries ( &summaries, reinterpret_cast( summary ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:164:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 164 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:178:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 178 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:223:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 223 | assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:233:68: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 233 | assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: starchcat.c:1338:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1338 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:1806:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1806 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2131:78: warning: left shift count >= width of type [-Wshift-count-overflow] 2131 | bzOutBytesWritten = static_cast( bzOutBytesWrittenHi32 ) << 32 | bzOutBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ starchcat.c: In function ‘int starch::STARCHCAT_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*)’: starchcat.c:2450:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2450 | static_cast( inRec->mdOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2451:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2451 | static_cast( inRec->hFlag )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2471:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2471 | static_cast( inRec->mdOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2472:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2472 | static_cast( inRec->hFlag )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2509:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2509 | static_cast( outType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2511:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2511 | static_cast( kStarchFinalizeTransformFalse ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’: starchcat.c:3152:54: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast( inRecIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3316:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3316 | static_cast( summary->numRecords ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3455:77: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3455 | static_cast( flushZStreamFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_mergeInputRecordsToOutput(starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*)’: starchcat.c:4265:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4265 | static_cast( outType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4267:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4267 | static_cast( kStarchFinalizeTransformFalse ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/c++/10/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*)’: starchcat.c:4402:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4402 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4420:63: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4420 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4447:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4447 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4479:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4479 | static_cast( hFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_freeChromosomeSummaries(starch::ChromosomeSummaries**)’: starchcat.c:4541:62: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4541 | STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), static_cast( (*chrSums)->numChromosomes )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/c++/10/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: starchcat.c:5902:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5902 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5929:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5929 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5952:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5952 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5990:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5990 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6025:38: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6025 | static_cast( hFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6053:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6053 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6055:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6055 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(starch::Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, starch::TransformState*)’: starchcat.c:6719:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6719 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_fillExtractionBufferFromGzipStream(starch::Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, starch::TransformState*)’: starchcat.c:7060:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 7060 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from starchcat.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)’ at starchcat.c:5368:20: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)’: starchcat.c:5368:53: note: length computed here 5368 | strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/i686-linux-gnu/include/string.h:495, from /usr/i686-linux-gnu/include/c++/10/cstring:42, from starchcat.c:31: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’ at starchcat.c:3123:16: /usr/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’: starchcat.c:3123:78: note: length computed here 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~^~~~~~~ i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical mkdir -p ../bin cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical mkdir -p ../bin cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical mkdir -p ../bin cp starch-diff.py ../bin/starch-diff-typical mkdir -p ../bin i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. starchstrip.c: In function ‘void starch::STARCHSTRIP_write_updated_metadata(FILE*)’: starchstrip.c:124:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 124 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchstrip.c:126:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 126 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now rm -rf objects make[4]: Leaving directory '/<>/applications/bed/starch/src' make -C applications/bed/conversion/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/conversion/src' mkdir -p ../bin && i686-linux-gnu-gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote"/<>/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" -Wl,-z,relro -Wl,-z,now convert2bed.c -o ../bin/convert2bed-typical -lpthread convert2bed.c: In function ‘c2b_process_intermediate_bytes_by_lines’: convert2bed.c:6315:103: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int long unsigned int | %lu convert2bed.c:6315:109: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘long unsigned int’ [-Wformat=] 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int long unsigned int | %lu convert2bed.c:6315:115: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘long unsigned int’ [-Wformat=] 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int long unsigned int | %lu rm -rf objects make[4]: Leaving directory '/<>/applications/bed/conversion/src' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/bedops-2.4.39\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' mkdir -p bin cp applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/wig2starch bin cp applications/bed/starch/bin/starchcluster_sge-typical bin/starchcluster_sge cp applications/bed/starch/bin/starchcluster_gnuParallel-typical bin/starchcluster_gnuParallel cp applications/bed/starch/bin/starchcluster_slurm-typical bin/starchcluster_slurm cp applications/bed/starch/bin/starch-diff-typical bin/starch-diff cp applications/bed/sort-bed/bin/sort-bed-typical bin/sort-bed cp applications/bed/sort-bed/bin/update-sort-bed-slurm-typical bin/update-sort-bed-slurm cp applications/bed/sort-bed/bin/update-sort-bed-starch-slurm-typical bin/update-sort-bed-starch-slurm cp applications/bed/sort-bed/bin/update-sort-bed-migrate-candidates-typical bin/update-sort-bed-migrate-candidates cp applications/bed/bedops/bin/bedops-typical bin/bedops cp applications/bed/closestfeats/bin/closest-features-typical bin/closest-features cp applications/bed/bedmap/bin/bedmap-typical bin/bedmap cp applications/bed/bedextract/bin/bedextract-typical bin/bedextract cp applications/bed/starch/bin/starch-typical bin/starch cp applications/bed/starch/bin/unstarch-typical bin/unstarch cp applications/bed/starch/bin/starchcat-typical bin/starchcat cp applications/bed/starch/bin/starchstrip-typical bin/starchstrip cp applications/bed/conversion/bin/convert2bed-typical bin/convert2bed make[1]: Leaving directory '/<>' debian/rules override_dh_install-arch make[1]: Entering directory '/<>' dh_install -a mv bin/starch bin/bedops-starch mkdir -p debian/bedops/usr/bin/ cp bin/* debian/bedops/usr/bin/ make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman-arch make[1]: Entering directory '/<>' cd bin && for f in * ; do help2man --no-discard-stderr --version-string="2.4.39+dfsg1" -o $f.1 ./$f; done help2man: can't get `--help' info from ./bam2bed_gnuParallel help2man: can't get `--help' info from ./bam2bed_sge help2man: can't get `--help' info from ./bam2bed_slurm help2man: can't get `--help' info from ./bam2starch_gnuParallel help2man: can't get `--help' info from ./bam2starch_sge help2man: can't get `--help' info from ./bam2starch_slurm help2man: can't get `--help' info from ./starchcluster_gnuParallel help2man: can't get `--help' info from ./starchcluster_sge help2man: can't get `--help' info from ./starchcluster_slurm dh_installman -a make[1]: Leaving directory '/<>' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a debian/rules override_dh_dwz make[1]: Entering directory '/<>' # Work around: dwz: Too few files for multifile optimization echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/<>' dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'bedops' in '../bedops_2.4.39+dfsg1-2_i386.deb'. dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.39+dfsg1-2_i386.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bedops_2.4.39+dfsg1-2_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-09-03T17:12:15Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedops_2.4.39+dfsg1-2_i386.changes: ----------------------------------- Format: 1.8 Date: Fri, 19 Feb 2021 11:50:32 +0200 Source: bedops Binary: bedops bedops-dbgsym Built-For-Profiles: cross nocheck Architecture: i386 Version: 2.4.39+dfsg1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Juhani Numminen Description: bedops - high-performance genomic feature operations Changes: bedops (2.4.39+dfsg1-2) unstable; urgency=medium . * Team upload. * Add parallel.patch: toplevel Makefile should use our -jN argument. * Update hardening.patch: our optimization flags now override upstream -O3. Checksums-Sha1: 5e8d929540ec7c62f9eb176ed216b40082e7c295 95464 bedops-dbgsym_2.4.39+dfsg1-2_i386.deb c75a59e73645bee5c5a493e2e68c36df60ced7fa 5517 bedops_2.4.39+dfsg1-2_i386.buildinfo 1578a09d9e3fbbaeeb163c7b399df40175254698 1323524 bedops_2.4.39+dfsg1-2_i386.deb Checksums-Sha256: dc7bff66841058aac459bf3460141ed50d2223cd2794881c8465f4c673cf1368 95464 bedops-dbgsym_2.4.39+dfsg1-2_i386.deb 0bfaf56b0e80751a991571349e94ded2ca8d653255272916103cc6176b5d703c 5517 bedops_2.4.39+dfsg1-2_i386.buildinfo 96ab82fb5ac2fbcc0162a9f486cd12841c5c9b5e71354dadb4d58bb5b4fea31e 1323524 bedops_2.4.39+dfsg1-2_i386.deb Files: 65689efb9ee32443f1006fe42485d6c2 95464 debug optional bedops-dbgsym_2.4.39+dfsg1-2_i386.deb 696290b97350652f882d7964e0304ae8 5517 science optional bedops_2.4.39+dfsg1-2_i386.buildinfo 8bdb28aebe09d65d06c7628a5f7d360f 1323524 science optional bedops_2.4.39+dfsg1-2_i386.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bedops Binary: bedops bedops-dbgsym Architecture: i386 Version: 2.4.39+dfsg1-2 Checksums-Md5: 65689efb9ee32443f1006fe42485d6c2 95464 bedops-dbgsym_2.4.39+dfsg1-2_i386.deb 8bdb28aebe09d65d06c7628a5f7d360f 1323524 bedops_2.4.39+dfsg1-2_i386.deb Checksums-Sha1: 5e8d929540ec7c62f9eb176ed216b40082e7c295 95464 bedops-dbgsym_2.4.39+dfsg1-2_i386.deb 1578a09d9e3fbbaeeb163c7b399df40175254698 1323524 bedops_2.4.39+dfsg1-2_i386.deb Checksums-Sha256: dc7bff66841058aac459bf3460141ed50d2223cd2794881c8465f4c673cf1368 95464 bedops-dbgsym_2.4.39+dfsg1-2_i386.deb 96ab82fb5ac2fbcc0162a9f486cd12841c5c9b5e71354dadb4d58bb5b4fea31e 1323524 bedops_2.4.39+dfsg1-2_i386.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Fri, 03 Sep 2021 17:12:14 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.4-1), autopoint (= 0.21-4), autotools-dev (= 20180224.1+nmu1), base-files (= 12), base-passwd (= 3.5.51), bash (= 5.1-3+b1), binutils (= 2.37-5), binutils-aarch64-linux-gnu (= 2.37-5), binutils-common (= 2.37-5), bsdextrautils (= 2.37.2-1), bsdutils (= 1:2.37.2-1), build-essential (= 12.9), bzip2 (= 1.0.8-4), coreutils (= 8.32-4), cpp (= 4:10.2.1-1), cpp-10 (= 10.3.0-9), dash (= 0.5.11+git20210120+802ebd4-1), debconf (= 1.5.77), debhelper (= 13.5.1), debianutils (= 5.4-3), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.12.0-1), diffutils (= 1:3.7-5), dpkg (= 1.20.9), dpkg-dev (= 1.20.9), dwz (= 0.14-1), file (= 1:5.39-3), findutils (= 4.8.0-1), g++ (= 4:10.2.1-1), g++-10 (= 10.3.0-9), gcc (= 4:10.2.1-1), gcc-10 (= 10.3.0-9), gcc-10-base (= 10.3.0-9), gcc-11-base (= 11.2.0-4), gettext (= 0.21-4), gettext-base (= 0.21-4), grep (= 3.7-1), groff-base (= 1.22.4-6), gzip (= 1.10-4), help2man (= 1.48.5), hostname (= 3.23), init-system-helpers (= 1.60), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-4), libatomic1 (= 11.2.0-4), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.5-1), libaudit1 (= 1:3.0.5-1), libbinutils (= 2.37-5), libblkid1 (= 2.37.2-1), libbz2-1.0 (= 1.0.8-4), libbz2-dev (= 1.0.8-4), libc-bin (= 2.31-17), libc-dev-bin (= 2.31-17), libc6 (= 2.31-17), libc6-dev (= 2.31-17), libcap-ng0 (= 0.7.9-2.2+b1), libcc1-0 (= 11.2.0-4), libcom-err2 (= 1.46.4-1), libcrypt-dev (= 1:4.4.25-1), libcrypt1 (= 1:4.4.25-1), libctf-nobfd0 (= 2.37-5), libctf0 (= 2.37-5), libdb5.3 (= 5.3.28+dfsg1-0.8), libdebconfclient0 (= 0.260), libdebhelper-perl (= 13.5.1), libdpkg-perl (= 1.20.9), libelf1 (= 0.185-2), libexpat1 (= 2.2.10-2), libffi7 (= 3.3-6), libfile-stripnondeterminism-perl (= 1.12.0-1), libgcc-10-dev (= 10.3.0-9), libgcc-s1 (= 11.2.0-4), libgcrypt20 (= 1.8.7-6), libgdbm-compat4 (= 1.20-1), libgdbm6 (= 1.20-1), libgmp10 (= 2:6.2.1+dfsg-1), libgomp1 (= 11.2.0-4), libgpg-error0 (= 1.42-3), libgssapi-krb5-2 (= 1.18.3-7), libicu67 (= 67.1-7), libisl23 (= 0.23-1), libitm1 (= 11.2.0-4), libjansson-dev (= 2.13.1-1.1), libjansson4 (= 2.13.1-1.1), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), liblocale-gettext-perl (= 1.07-4+b1), liblsan0 (= 11.2.0-4), liblz4-1 (= 1.9.3-2), liblzma5 (= 5.2.5-2), libmagic-mgc (= 1:5.39-3), libmagic1 (= 1:5.39-3), libmount1 (= 2.37.2-1), libmpc3 (= 1.2.0-1), libmpdec3 (= 2.5.1-2), libmpfr6 (= 4.1.0-3), libncursesw6 (= 6.2+20201114-4), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libpam-modules (= 1.4.0-10), libpam-modules-bin (= 1.4.0-10), libpam-runtime (= 1.4.0-10), libpam0g (= 1.4.0-10), libpcre2-8-0 (= 10.36-2), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.1-5), libpipeline1 (= 1.5.3-1), libpython3-stdlib (= 3.9.2-3), libpython3.9-minimal (= 3.9.7-2), libpython3.9-stdlib (= 3.9.7-2), libreadline8 (= 8.1-2), libseccomp2 (= 2.5.1-1), libselinux1 (= 3.1-3), libsigsegv2 (= 2.13-1), libsmartcols1 (= 2.37.2-1), libsqlite3-0 (= 3.36.0-2), libssl1.1 (= 1.1.1l-1), libstdc++-10-dev (= 10.3.0-9), libstdc++6 (= 11.2.0-4), libsub-override-perl (= 0.09-2), libsystemd0 (= 247.9-1), libtinfo6 (= 6.2+20201114-4), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15), libtsan0 (= 11.2.0-4), libubsan1 (= 11.2.0-4), libuchardet0 (= 0.0.7-1), libudev1 (= 247.9-1), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-1), libxml2 (= 2.9.12+dfsg-3), libzstd1 (= 1.4.8+dfsg-2.1), linux-libc-dev (= 5.10.46-4), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-5), make (= 4.3-4.1), man-db (= 2.9.4-2), mawk (= 1.3.4.20200120-2), media-types (= 4.0.0), ncurses-base (= 6.2+20201114-4), ncurses-bin (= 6.2+20201114-4), patch (= 2.7.6-7), perl (= 5.32.1-5), perl-base (= 5.32.1-5), perl-modules-5.32 (= 5.32.1-5), po-debconf (= 1.0.21+nmu1), python3 (= 3.9.2-3), python3-distutils (= 3.9.7-1), python3-lib2to3 (= 3.9.7-1), python3-minimal (= 3.9.2-3), python3.9 (= 3.9.7-2), python3.9-minimal (= 3.9.7-2), readline-common (= 8.1-2), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 2.96-7), tar (= 1.34+dfsg-1), tzdata (= 2021a-1), util-linux (= 2.37.2-1), xz-utils (= 5.2.5-2), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1613728232" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedops-dbgsym_2.4.39+dfsg1-2_i386.deb ------------------------------------- new Debian package, version 2.0. size 95464 bytes: control archive=540 bytes. 379 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: bedops-dbgsym Source: bedops Version: 2.4.39+dfsg1-2 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 109 Depends: bedops (= 2.4.39+dfsg1-2) Section: debug Priority: optional Description: debug symbols for bedops Build-Ids: 0caa28b43aee8f7317bbb7aa95d0ec0b966269d7 drwxr-xr-x root/root 0 2021-02-19 09:50 ./ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/lib/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/lib/debug/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/lib/debug/.build-id/0c/ -rw-r--r-- root/root 101072 2021-02-19 09:50 ./usr/lib/debug/.build-id/0c/aa28b43aee8f7317bbb7aa95d0ec0b966269d7.debug drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/ lrwxrwxrwx root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops-dbgsym -> bedops bedops_2.4.39+dfsg1-2_i386.deb ------------------------------ new Debian package, version 2.0. size 1323524 bytes: control archive=5380 bytes. 730 bytes, 15 lines control 17229 bytes, 204 lines md5sums Package: bedops Version: 2.4.39+dfsg1-2 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 10099 Depends: libbz2-1.0, libc6 (>= 2.28), libgcc-s1 (>= 4.2), libjansson4 (>= 2.3), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), python3, tcsh Section: science Priority: optional Homepage: https://github.com/bedops/bedops Description: high-performance genomic feature operations BEDOPS is a suite of tools to address common questions raised in genomic studies, mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data. drwxr-xr-x root/root 0 2021-02-19 09:50 ./ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/bin/ -rwxr-xr-x root/root 4711 2021-02-19 09:50 ./usr/bin/bam2bed -rwxr-xr-x root/root 4501 2021-02-19 09:50 ./usr/bin/bam2bed_gnuParallel -rwxr-xr-x root/root 5022 2021-02-19 09:50 ./usr/bin/bam2bed_sge -rwxr-xr-x root/root 5021 2021-02-19 09:50 ./usr/bin/bam2bed_slurm -rwxr-xr-x root/root 5842 2021-02-19 09:50 ./usr/bin/bam2starch -rwxr-xr-x root/root 4507 2021-02-19 09:50 ./usr/bin/bam2starch_gnuParallel -rwxr-xr-x root/root 5076 2021-02-19 09:50 ./usr/bin/bam2starch_sge -rwxr-xr-x root/root 5014 2021-02-19 09:50 ./usr/bin/bam2starch_slurm -rwxr-xr-x root/root 234948 2021-02-19 09:50 ./usr/bin/bedextract -rwxr-xr-x root/root 7935456 2021-02-19 09:50 ./usr/bin/bedmap -rwxr-xr-x root/root 509392 2021-02-19 09:50 ./usr/bin/bedops -rwxr-xr-x root/root 107956 2021-02-19 09:50 ./usr/bin/bedops-starch -rwxr-xr-x root/root 288200 2021-02-19 09:50 ./usr/bin/closest-features -rwxr-xr-x root/root 129000 2021-02-19 09:50 ./usr/bin/convert2bed -rwxr-xr-x root/root 3773 2021-02-19 09:50 ./usr/bin/gff2bed -rwxr-xr-x root/root 4904 2021-02-19 09:50 ./usr/bin/gff2starch -rwxr-xr-x root/root 3532 2021-02-19 09:50 ./usr/bin/gtf2bed -rwxr-xr-x root/root 4663 2021-02-19 09:50 ./usr/bin/gtf2starch -rwxr-xr-x root/root 3773 2021-02-19 09:50 ./usr/bin/gvf2bed -rwxr-xr-x root/root 4904 2021-02-19 09:50 ./usr/bin/gvf2starch -rwxr-xr-x root/root 3976 2021-02-19 09:50 ./usr/bin/psl2bed -rwxr-xr-x root/root 5107 2021-02-19 09:50 ./usr/bin/psl2starch -rwxr-xr-x root/root 3776 2021-02-19 09:50 ./usr/bin/rmsk2bed -rwxr-xr-x root/root 4907 2021-02-19 09:50 ./usr/bin/rmsk2starch -rwxr-xr-x root/root 4711 2021-02-19 09:50 ./usr/bin/sam2bed -rwxr-xr-x root/root 5842 2021-02-19 09:50 ./usr/bin/sam2starch -rwxr-xr-x root/root 243124 2021-02-19 09:50 ./usr/bin/sort-bed -rwxr-xr-x root/root 10163 2021-02-19 09:50 ./usr/bin/starch-diff -rwxr-xr-x root/root 202148 2021-02-19 09:50 ./usr/bin/starchcat -rwxr-xr-x root/root 4299 2021-02-19 09:50 ./usr/bin/starchcluster_gnuParallel -rwxr-xr-x root/root 4810 2021-02-19 09:50 ./usr/bin/starchcluster_sge -rwxr-xr-x root/root 4716 2021-02-19 09:50 ./usr/bin/starchcluster_slurm -rwxr-xr-x root/root 111988 2021-02-19 09:50 ./usr/bin/starchstrip -rwxr-xr-x root/root 148748 2021-02-19 09:50 ./usr/bin/unstarch -rwxr-xr-x root/root 32686 2021-02-19 09:50 ./usr/bin/update-sort-bed-migrate-candidates -rwxr-xr-x root/root 20701 2021-02-19 09:50 ./usr/bin/update-sort-bed-slurm -rwxr-xr-x root/root 22682 2021-02-19 09:50 ./usr/bin/update-sort-bed-starch-slurm -rwxr-xr-x root/root 4675 2021-02-19 09:50 ./usr/bin/vcf2bed -rwxr-xr-x root/root 5806 2021-02-19 09:50 ./usr/bin/vcf2starch -rwxr-xr-x root/root 4598 2021-02-19 09:50 ./usr/bin/wig2bed -rwxr-xr-x root/root 5729 2021-02-19 09:50 ./usr/bin/wig2starch drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops/ -rw-r--r-- root/root 267 2021-02-19 09:50 ./usr/share/doc/bedops/README.Debian -rw-r--r-- root/root 1506 2021-02-19 09:50 ./usr/share/doc/bedops/changelog.Debian.gz -rw-r--r-- root/root 1156 2021-02-19 09:50 ./usr/share/doc/bedops/copyright drwxr-xr-x root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/ -rw-r--r-- root/root 718 2020-04-06 20:55 ./usr/share/doc/bedops/tests/Makefile drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops/tests/bedops/ -rw-r--r-- root/root 2166 2021-02-19 09:50 ./usr/share/doc/bedops/tests/bedops/Makefile.gz drwxr-xr-x root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/ -rw-r--r-- root/root 197 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001.expected -rw-r--r-- root/root 44 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001a.test -rw-r--r-- root/root 53 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001b.test -rw-r--r-- root/root 24 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.chrom.001.expected -rw-r--r-- root/root 26 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.complement.001.expected -rw-r--r-- root/root 31 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.difference.001.expected -rw-r--r-- root/root 23 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.ec.001a.test -rw-r--r-- root/root 69 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.element-of.001.expected -rw-r--r-- root/root 91 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001.expected -rw-r--r-- root/root 52 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001a.test -rw-r--r-- root/root 104 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001b.test -rw-r--r-- root/root 37 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.expected -rw-r--r-- root/root 111 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.test -rw-r--r-- root/root 368 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.named-pipe.001.expected -rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.not-element-of.001.expected -rw-r--r-- root/root 148 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001.expected -rw-r--r-- root/root 39 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001a.test -rw-r--r-- root/root 56 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001b.test -rw-r--r-- root/root 40 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001c.test -rw-r--r-- root/root 257 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.stdin.001.expected -rw-r--r-- root/root 130 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.symdiff.001.expected -rw-r--r-- root/root 134 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.expected -rw-r--r-- root/root 126 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.test -rw-r--r-- root/root 171 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.chop.002.expected -rw-r--r-- root/root 20 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.chrom.002.expected -rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.complement.002.expected -rw-r--r-- root/root 2172 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002.expected -rw-r--r-- root/root 3033 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002a.test -rw-r--r-- root/root 2941 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002b.test -rw-r--r-- root/root 18 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.element-of.002.expected -rw-r--r-- root/root 13 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.expected -rw-r--r-- root/root 26 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.test -rw-r--r-- root/root 11 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.merge.002.expected -rw-r--r-- root/root 11 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.not-element-of.002.expected -rw-r--r-- root/root 376 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002.expected -rw-r--r-- root/root 48 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002a.test -rw-r--r-- root/root 49 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002b.test -rw-r--r-- root/root 101 2020-04-06 20:55 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./usr/share/doc/bedops/tests/bedops/data/003.element-of.003.expected -rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.intersection.003.expected -rw-r--r-- root/root 35 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.expected -rw-r--r-- root/root 46 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.test -rw-r--r-- root/root 21 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003.expected -rw-r--r-- root/root 63 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003a.test -rw-r--r-- root/root 42 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003b.test -rw-r--r-- root/root 153 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.expected -rw-r--r-- root/root 398 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.test -rw-r--r-- root/root 22 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003.expected -rw-r--r-- root/root 18 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003a.test -rw-r--r-- root/root 29 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003b.test -rw-r--r-- root/root 9 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003c.test -rw-r--r-- root/root 11 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003d.test -rw-r--r-- root/root 355 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.expected -rw-r--r-- root/root 360 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.test -rw-r--r-- root/root 257 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.chop.004.expected -rw-r--r-- root/root 24 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.chrom.004.expected -rw-r--r-- root/root 111 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004.expected -rw-r--r-- root/root 46 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004a.test -rw-r--r-- root/root 132 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004b.test -rw-r--r-- root/root 94 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004c.test -rw-r--r-- root/root 30 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004.expected -rw-r--r-- root/root 30 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004a.test -rw-r--r-- root/root 31 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004b.test -rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004.expected -rw-r--r-- root/root 92 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004a.test -rw-r--r-- root/root 23 2020-04-06 20:55 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./usr/share/doc/bedops/tests/bedops/data/004.union.004.expected -rw-r--r-- root/root 32 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.test -rw-r--r-- root/root 385 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.expected -rw-r--r-- root/root 87 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.test -rw-r--r-- root/root 20 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.expected -rw-r--r-- root/root 40 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.test -rw-r--r-- root/root 31 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.difference.005.expected -rw-r--r-- root/root 93 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.expected -rw-r--r-- root/root 43 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.test -rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.symdiff.005.expected -rw-r--r-- root/root 11 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.union.005.expected -rw-r--r-- root/root 35 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.complement.006.expected -rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.difference.006.expected -rw-r--r-- root/root 41 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006.expected -rw-r--r-- root/root 37 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006a.test -rw-r--r-- root/root 35 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006b.test -rw-r--r-- root/root 31 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006c.test -rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.union.006.expected -rw-r--r-- root/root 9 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.complement.007.expected -rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.difference.007.expected -rw-r--r-- root/root 55 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007.expected -rw-r--r-- root/root 56 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007a.test -rw-r--r-- root/root 69 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007b.test -rw-r--r-- root/root 33 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.union.007.expected -rw-r--r-- root/root 79 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/008.complement.008.expected -rw-r--r-- root/root 197 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/008.merge.008.expected -rw-r--r-- root/root 33 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/008.union.008.expected -rw-r--r-- root/root 175 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/009.complement.009.expected -rw-r--r-- root/root 52 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/009.merge.009.expected -rw-r--r-- root/root 33 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.expected -rw-r--r-- root/root 43 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.test drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops/tests/starch/ -rw-r--r-- root/root 1078 2021-02-19 09:50 ./usr/share/doc/bedops/tests/starch/Makefile.gz drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops/tests/starch/data/ -rw-r--r-- root/root 1935 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.expected -rw-r--r-- root/root 2813 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.test.gz -rw-r--r-- root/root 772 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1.001.test -rw-r--r-- root/root 1166 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1andChr2.001.expected -rw-r--r-- root/root 772 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr2.001.test -rw-r--r-- root/root 764 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.expected -rw-r--r-- root/root 2851 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.test.gz -rw-r--r-- root/root 218 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.expected -rw-r--r-- root/root 2254 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.test.gz -rw-r--r-- root/root 109 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/README -rw-r--r-- root/root 426 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/hg38.bed -rw-r--r-- root/root 1516 2021-02-19 09:50 ./usr/share/doc/bedops/tests/starch/generate_random_intervals.sh drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/man/ drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/man/man1/ -rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/bam2bed.1.gz -rw-r--r-- root/root 357 2021-02-19 09:50 ./usr/share/man/man1/bam2starch.1.gz -rw-r--r-- root/root 357 2021-02-19 09:50 ./usr/share/man/man1/bedextract.1.gz -rw-r--r-- root/root 514 2021-02-19 09:50 ./usr/share/man/man1/bedmap.1.gz -rw-r--r-- root/root 374 2021-02-19 09:50 ./usr/share/man/man1/bedops-starch.1.gz -rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/bedops.1.gz -rw-r--r-- root/root 366 2021-02-19 09:50 ./usr/share/man/man1/closest-features.1.gz -rw-r--r-- root/root 359 2021-02-19 09:50 ./usr/share/man/man1/convert2bed.1.gz -rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/gff2bed.1.gz -rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/gff2starch.1.gz -rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/gtf2bed.1.gz -rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/gtf2starch.1.gz -rw-r--r-- root/root 350 2021-02-19 09:50 ./usr/share/man/man1/gvf2bed.1.gz -rw-r--r-- root/root 357 2021-02-19 09:50 ./usr/share/man/man1/gvf2starch.1.gz -rw-r--r-- root/root 348 2021-02-19 09:50 ./usr/share/man/man1/psl2bed.1.gz -rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/psl2starch.1.gz -rw-r--r-- root/root 351 2021-02-19 09:50 ./usr/share/man/man1/rmsk2bed.1.gz -rw-r--r-- root/root 359 2021-02-19 09:50 ./usr/share/man/man1/rmsk2starch.1.gz -rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/sam2bed.1.gz -rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/sam2starch.1.gz -rw-r--r-- root/root 355 2021-02-19 09:50 ./usr/share/man/man1/sort-bed.1.gz -rw-r--r-- root/root 722 2021-02-19 09:50 ./usr/share/man/man1/starch-diff.1.gz -rw-r--r-- root/root 354 2021-02-19 09:50 ./usr/share/man/man1/starchcat.1.gz -rw-r--r-- root/root 360 2021-02-19 09:50 ./usr/share/man/man1/starchstrip.1.gz -rw-r--r-- root/root 352 2021-02-19 09:50 ./usr/share/man/man1/unstarch.1.gz -rw-r--r-- root/root 1766 2021-02-19 09:50 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz -rw-r--r-- root/root 1332 2021-02-19 09:50 ./usr/share/man/man1/update-sort-bed-slurm.1.gz -rw-r--r-- root/root 1384 2021-02-19 09:50 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz -rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/vcf2bed.1.gz -rw-r--r-- root/root 357 2021-02-19 09:50 ./usr/share/man/man1/vcf2starch.1.gz -rw-r--r-- root/root 350 2021-02-19 09:50 ./usr/share/man/man1/wig2bed.1.gz -rw-r--r-- root/root 357 2021-02-19 09:50 ./usr/share/man/man1/wig2starch.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 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 [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [571 B] Get:5 copy:/<>/apt_archive ./ Packages [655 B] Fetched 2189 B in 0s (52.4 kB/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... The following additional packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libproc-processtable-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils t1utils unzip Suggested packages: libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libwww-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libpackage-stash-xs-perl libref-util-perl libtype-tiny-xs-perl The following NEW packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libproc-processtable-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils sbuild-build-depends-lintian-dummy:i386 t1utils unzip 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 6467 kB of archives. After this operation, 19.2 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [856 B] Get:2 http://mirror.einval.org/debian sid/main arm64 diffstat arm64 1.64-1 [34.6 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libassuan0 arm64 2.5.5-1 [49.3 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 gpgconf arm64 2.2.27-2 [540 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.27-2 [883 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 libaliased-perl all 0.34-1.1 [14.1 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40 [69.4 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-1+b3 [11.2 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.008-1+b2 [15.8 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-1+b3 [25.5 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:16 http://mirror.einval.org/debian sid/main arm64 libvariable-magic-perl arm64 0.62-1+b3 [44.2 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libb-hooks-endofscope-perl all 0.24-1.1 [18.9 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:20 http://mirror.einval.org/debian sid/main arm64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-3+b7 [36.9 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 libclone-perl arm64 0.45-1+b1 [15.3 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 libconfig-tiny-perl all 2.26-1 [16.5 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.26-1 [126 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libexception-class-perl all 1.44-1 [32.3 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libiterator-perl all 0.03+ds1-1.1 [18.4 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-2 [36.8 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-1+b1 [25.3 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.110-1.1 [10.8 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.987-1 [47.2 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.01-2 [34.3 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libdevel-size-perl arm64 0.83-1+b2 [25.8 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.04-1+b3 [26.7 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:45 http://mirror.einval.org/debian sid/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:46 http://mirror.einval.org/debian sid/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libmarkdown2 arm64 2.2.6-1 [34.3 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.005004-2 [60.4 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b1 [170 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-1+b3 [11.9 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-1+b1 [13.5 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.118-1 [53.5 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.19-1+b7 [17.0 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.611-1 [45.7 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 4.018+ds-1+b1 [95.3 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 4.018+ds-1+b1 [98.3 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-4+b8 [8680 B] Get:72 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.13-1 [13.1 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.8-1+b1 [195 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-1+b3 [75.1 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libtype-tiny-perl all 1.012004-1 [351 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b2 [19.8 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.08-1 [90.6 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.82+repack-1+b1 [34.5 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 lzip arm64 1.22-3 [84.7 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-26 [165 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 lintian all 2.104.0 [1265 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6467 kB in 0s (37.1 MB/s) Selecting previously unselected package diffstat. (Reading database ... 19565 files and directories currently installed.) Preparing to unpack .../00-diffstat_1.64-1_arm64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../01-libassuan0_2.5.5-1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.5-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../02-gpgconf_2.2.27-2_arm64.deb ... Unpacking gpgconf (2.2.27-2) ... Selecting previously unselected package gpg. Preparing to unpack .../03-gpg_2.2.27-2_arm64.deb ... Unpacking gpg (2.2.27-2) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../04-libaliased-perl_0.34-1.1_all.deb ... Unpacking libaliased-perl (0.34-1.1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../05-libapt-pkg-perl_0.1.40_arm64.deb ... Unpacking libapt-pkg-perl (0.1.40) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../06-libb-hooks-op-check-perl_0.22-1+b3_arm64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b3) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../07-libdynaloader-functions-perl_0.003-1.1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1.1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../08-libdevel-callchecker-perl_0.008-1+b2_arm64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b2) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../09-libparams-classify-perl_0.015-1+b3_arm64.deb ... Unpacking libparams-classify-perl (0.015-1+b3) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../10-libmodule-runtime-perl_0.016-1_all.deb ... Unpacking libmodule-runtime-perl (0.016-1) ... Selecting previously unselected package libtry-tiny-perl. 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Unpacking libconfig-tiny-perl (2.26-1) ... Selecting previously unselected package libcpanel-json-xs-perl. Preparing to unpack .../22-libcpanel-json-xs-perl_4.26-1_arm64.deb ... Unpacking libcpanel-json-xs-perl (4.26-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../23-libdevel-stacktrace-perl_2.0400-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../24-libexception-class-perl_1.44-1_all.deb ... Unpacking libexception-class-perl (1.44-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../25-libiterator-perl_0.03+ds1-1.1_all.deb ... Unpacking libiterator-perl (0.03+ds1-1.1) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../26-libiterator-util-perl_0.02+ds1-1.1_all.deb ... Unpacking libiterator-util-perl (0.02+ds1-1.1) ... 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Setting up lzop (1.04-2) ... Setting up gpgconf (2.2.27-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-2) ... Setting up libaliased-perl (0.34-1.1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b7) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libfont-ttf-perl (1.06-1.1) ... Setting up libtext-levenshteinxs-perl (0.03-4+b8) ... Setting up libperlio-gzip-perl (0.19-1+b7) ... Setting up libhtml-html5-entities-perl (0.004-1.1) ... Setting up libsereal-decoder-perl (4.018+ds-1+b1) ... Setting up libmarkdown2:arm64 (2.2.6-1) ... Setting up liburi-perl (5.08-1) ... Setting up gpg (2.2.27-2) ... Setting up libemail-address-xs-perl (1.04-1+b3) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libtype-tiny-perl (1.012004-1) ... Setting up libtext-markdown-discount-perl:arm64 (0.13-1) ... Setting up libexception-class-perl (1.44-1) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up libdata-optlist-perl (0.110-1.1) ... Setting up libsub-exporter-perl (0.987-1) ... Setting up libiterator-perl (0.03+ds1-1.1) ... Setting up libiterator-util-perl (0.02+ds1-1.1) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libpackage-stash-perl (0.39-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.005004-2) ... Setting up libmoox-aliases-perl (0.001006-1.1) ... Setting up libb-hooks-endofscope-perl (0.24-1.1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.104.0) ... Setting up sbuild-build-depends-lintian-dummy:i386 (0.invalid.0) ... Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.31-17) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 54692 Build-Time: 1696 Distribution: unstable Foreign Architectures: i386 Host Architecture: i386 Install-Time: 66 Job: bedops_2.4.39+dfsg1-2 Lintian: pass Machine Architecture: arm64 Package: bedops Package-Time: 1792 Source-Version: 2.4.39+dfsg1-2 Space: 54692 Status: successful Version: 2.4.39+dfsg1-2 -------------------------------------------------------------------------------- Finished at 2021-09-03T17:12:15Z Build needed 00:29:52, 54692k disk space