sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir +==============================================================================+ | bedops 2.4.40+dfsg-1 (i386) Thu, 14 Apr 2022 02:52:09 +0000 | +==============================================================================+ Package: bedops Version: 2.4.40+dfsg-1 Source Version: 2.4.40+dfsg-1 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-3966b9ef-1c03-4e9b-a6f0-83447e144288' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-403Ukp/resolver-e02mG2' 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 [9045 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9698 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8992 kB] Fetched 27.9 MB in 7s (3798 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 2.4.40+dfsg-1 (dsc) [2178 B] Get:2 http://mirror.einval.org/debian sid/main bedops 2.4.40+dfsg-1 (tar) [13.4 MB] Get:3 http://mirror.einval.org/debian sid/main bedops 2.4.40+dfsg-1 (diff) [10.3 kB] Fetched 13.5 MB in 0s (39.8 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedops-403Ukp/bedops-2.4.40+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-403Ukp' 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 (46.7 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-11-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-11-i686-linux-gnu g++-i686-linux-gnu gcc-11-base:i386 gcc-11-cross-base gcc-11-i686-linux-gnu gcc-11-i686-linux-gnu-base gcc-12-base:i386 gcc-12-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-11-dev:i386 libgcc-11-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 libpython3.10-minimal libpython3.10-stdlib libquadmath0:i386 libquadmath0-i386-cross libreadline8 libsigsegv2 libsqlite3-0 libssl1.1:i386 libstdc++-11-dev:i386 libstdc++-11-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 python3.10 python3.10-minimal readline-common sensible-utils ucf zlib1g:i386 zlib1g-dev:i386 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-11-locales cpp-doc dh-make binutils-multiarch g++-11-multilib-i686-linux-gnu gcc-11-doc gcc-11-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++-11-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 python3.10-venv python3.10-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx bzip2-doc:i386 libidn2-0:i386 libarchive-cpio-perl krb5-locales:i386 libgpm2 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-11-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-11-i686-linux-gnu g++-i686-linux-gnu gcc-11-base:i386 gcc-11-cross-base gcc-11-i686-linux-gnu gcc-11-i686-linux-gnu-base gcc-12-base:i386 gcc-12-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-11-dev:i386 libgcc-11-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 libpython3.10-minimal libpython3.10-stdlib libquadmath0:i386 libquadmath0-i386-cross libreadline8 libsigsegv2 libsqlite3-0 libssl1.1:i386 libstdc++-11-dev:i386 libstdc++-11-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 python3.10 python3.10-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 92.9 MB of archives. After this operation, 354 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 liblocale-gettext-perl arm64 1.07-4+b2 [18.9 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libpython3.10-minimal arm64 3.10.4-3 [819 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.4.8-1 [94.6 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 python3.10-minimal arm64 3.10.4-3 [1950 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 python3-minimal arm64 3.10.4-1 [38.6 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 media-types all 7.1.0 [33.2 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libmpdec3 arm64 2.5.1-2 [84.4 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libncursesw6 arm64 6.3-2 [120 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 readline-common all 8.1.2-1.2 [73.9 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1.2-1.2 [160 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.38.2-1 [779 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libpython3.10-stdlib arm64 3.10.4-3 [1676 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 python3.10 arm64 3.10.4-3 [536 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libpython3-stdlib arm64 3.10.4-1 [21.7 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 python3 arm64 3.10.4-1 [38.1 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.17 [21.5 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.41-3 [295 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.41-3 [124 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.41-3 [66.9 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-6 [173 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-8 [882 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.38-2 [144 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.5-1 [35.8 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.10.2-1 [1392 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libsigsegv2 arm64 2.14-1 [37.0 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-6 [510 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 gcc-11-i686-linux-gnu-base arm64 11.2.0-18cross1 [208 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 cpp-11-i686-linux-gnu arm64 11.2.0-18cross1 [7859 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 cpp-i686-linux-gnu arm64 4:11.2.0-2 [17.0 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 binutils-i686-linux-gnu arm64 2.38-3 [2321 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 gcc-11-cross-base all 11.2.0-18cross1 [203 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 gcc-12-cross-base all 12-20220222-1cross1 [202 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libc6-i386-cross all 2.33-1cross1 [1526 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-i386-cross all 12-20220222-1cross1 [60.3 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libgomp1-i386-cross all 12-20220222-1cross1 [118 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libitm1-i386-cross all 12-20220222-1cross1 [27.2 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libatomic1-i386-cross all 12-20220222-1cross1 [7492 B] Get:46 http://mirror.einval.org/debian sid/main arm64 libasan6-i386-cross all 11.2.0-18cross1 [1927 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libstdc++6-i386-cross all 12-20220222-1cross1 [622 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libubsan1-i386-cross all 12-20220222-1cross1 [867 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libquadmath0-i386-cross all 12-20220222-1cross1 [225 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libgcc-11-dev-i386-cross all 11.2.0-18cross1 [2331 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 gcc-11-i686-linux-gnu arm64 11.2.0-18cross1 [15.6 MB] Get:52 http://mirror.einval.org/debian sid/main arm64 gcc-i686-linux-gnu arm64 4:11.2.0-2 [1452 B] Get:53 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-i386-cross all 5.15.5-1cross1 [1576 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 libc6-dev-i386-cross all 2.33-1cross1 [2170 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libstdc++-11-dev-i386-cross all 11.2.0-18cross1 [2012 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 g++-11-i686-linux-gnu arm64 11.2.0-18cross1 [8676 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 g++-i686-linux-gnu arm64 4:11.2.0-2 [1168 B] Get:58 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.13+dfsg-1 [641 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1 [326 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.27-1 [17.3 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-i386 all 12.9 [6704 B] Get:74 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.6 [193 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.7-3 [526 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.186-1 [177 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-6 [1260 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.6 [1054 kB] Get:87 http://mirror.einval.org/debian sid/main i386 gcc-11-base i386 11.2.0-19 [208 kB] Get:88 http://mirror.einval.org/debian sid/main i386 gcc-12-base i386 12-20220319-1 [206 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 help2man arm64 1.49.2 [202 kB] Get:90 http://mirror.einval.org/debian sid/main i386 libgcc-s1 i386 12-20220319-1 [60.0 kB] Get:91 http://mirror.einval.org/debian sid/main i386 libc6 i386 2.33-7 [2790 kB] Get:92 http://mirror.einval.org/debian sid/main i386 libasan6 i386 11.2.0-19 [1934 kB] Get:93 http://mirror.einval.org/debian sid/main i386 libatomic1 i386 12-20220319-1 [7704 B] Get:94 http://mirror.einval.org/debian sid/main i386 libbz2-1.0 i386 1.0.8-5 [46.1 kB] Get:95 http://mirror.einval.org/debian sid/main i386 linux-libc-dev i386 5.16.18-1 [1517 kB] Get:96 http://mirror.einval.org/debian sid/main i386 libcrypt1 i386 1:4.4.27-1.1 [99.5 kB] Get:97 http://mirror.einval.org/debian sid/main i386 libcrypt-dev i386 1:4.4.27-1.1 [129 kB] Get:98 http://mirror.einval.org/debian sid/main i386 libcom-err2 i386 1.46.5-2 [76.1 kB] Get:99 http://mirror.einval.org/debian sid/main i386 libkrb5support0 i386 1.19.2-2+b1 [69.0 kB] Get:100 http://mirror.einval.org/debian sid/main i386 libk5crypto3 i386 1.19.2-2+b1 [117 kB] Get:101 http://mirror.einval.org/debian sid/main i386 libkeyutils1 i386 1.6.1-3 [16.0 kB] Get:102 http://mirror.einval.org/debian sid/main i386 libssl1.1 i386 1.1.1n-1 [1552 kB] Get:103 http://mirror.einval.org/debian sid/main i386 libkrb5-3 i386 1.19.2-2+b1 [391 kB] Get:104 http://mirror.einval.org/debian sid/main i386 libgssapi-krb5-2 i386 1.19.2-2+b1 [177 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 2.33-7 [2172 kB] Get:110 http://mirror.einval.org/debian sid/main i386 libbz2-dev i386 1.0.8-5 [30.6 kB] Get:111 http://mirror.einval.org/debian sid/main i386 libgomp1 i386 12-20220319-1 [121 kB] Get:112 http://mirror.einval.org/debian sid/main i386 libitm1 i386 12-20220319-1 [27.7 kB] Get:113 http://mirror.einval.org/debian sid/main i386 libstdc++6 i386 12-20220319-1 [664 kB] Get:114 http://mirror.einval.org/debian sid/main i386 libubsan1 i386 12-20220319-1 [870 kB] Get:115 http://mirror.einval.org/debian sid/main i386 libquadmath0 i386 12-20220319-1 [227 kB] Get:116 http://mirror.einval.org/debian sid/main i386 libgcc-11-dev i386 11.2.0-19 [2331 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++-11-dev i386 11.2.0-19 [2007 kB] Get:120 http://mirror.einval.org/debian sid/main arm64 python3-lib2to3 all 3.9.12-1 [79.9 kB] Get:121 http://mirror.einval.org/debian sid/main arm64 python3-distutils all 3.9.12-1 [146 kB] Get:122 http://mirror.einval.org/debian sid/main i386 zlib1g i386 1:1.2.11.dfsg-4 [93.0 kB] Get:123 http://mirror.einval.org/debian sid/main i386 zlib1g-dev i386 1:1.2.11.dfsg-4 [194 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 92.9 MB in 1s (78.4 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12415 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4+b2_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b2) ... Selecting previously unselected package libpython3.10-minimal:arm64. Preparing to unpack .../libpython3.10-minimal_3.10.4-3_arm64.deb ... Unpacking libpython3.10-minimal:arm64 (3.10.4-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.4.8-1_arm64.deb ... Unpacking libexpat1:arm64 (2.4.8-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.4-3_arm64.deb ... Unpacking python3.10-minimal (3.10.4-3) ... Setting up libpython3.10-minimal:arm64 (3.10.4-3) ... Setting up libexpat1:arm64 (2.4.8-1) ... Setting up python3.10-minimal (3.10.4-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 12733 files and directories currently installed.) 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Setting up media-types (7.1.0) ... Setting up gcc-11-i686-linux-gnu-base:arm64 (11.2.0-18cross1) ... Setting up libpipeline1:arm64 (1.5.5-1) ... Setting up gcc-11-base:i386 (11.2.0-19) ... Setting up libfile-which-perl (1.27-1) ... Setting up gcc-12-cross-base (12-20220222-1cross1) ... Setting up bsdextrautils (2.38-2) ... Setting up libicu67:arm64 (67.1-7) ... Setting up libmagic-mgc (1:5.41-3) ... Setting up cpp-11-i686-linux-gnu (11.2.0-18cross1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up binutils-i686-linux-gnu (2.38-3) ... Setting up libdebhelper-perl (13.6) ... Setting up libsqlite3-0:arm64 (3.38.2-1) ... Setting up libmagic1:arm64 (1:5.41-3) ... Setting up linux-libc-dev:i386 (5.16.18-1) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up gettext-base (0.21-6) ... Setting up file (1:5.41-3) ... Setting up libyaml-perl (1.30-1) ... Setting up gcc-12-base:i386 (12-20220319-1) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up linux-libc-dev-i386-cross (5.15.5-1cross1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libsigsegv2:arm64 (2.14-1) ... Setting up autopoint (0.21-6) ... Setting up libncursesw6:arm64 (6.3-2) ... Setting up gcc-11-cross-base (11.2.0-18cross1) ... 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 (2.33-1cross1) ... Setting up libsub-override-perl (0.09-2) ... Setting up cpp-i686-linux-gnu (4:11.2.0-2) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up libquadmath0-i386-cross (12-20220222-1cross1) ... Setting up libelf1:arm64 (0.186-1) ... Setting up readline-common (8.1.2-1.2) ... Setting up libxml2:arm64 (2.9.13+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-4+b2) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up gettext (0.21-6) ... Setting up libtool (2.4.7-3) ... Setting up libatomic1-i386-cross (12-20220222-1cross1) ... Setting up libreadline8:arm64 (8.1.2-1.2) ... Setting up m4 (1.4.18-5) ... Setting up libgomp1-i386-cross (12-20220222-1cross1) ... Setting up libc6-dev-i386-cross (2.33-1cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.49.2) ... Setting up libpython3.10-stdlib:arm64 (3.10.4-3) ... Setting up libgcc-s1-i386-cross (12-20220222-1cross1) ... Setting up libasan6-i386-cross (11.2.0-18cross1) ... Setting up libitm1-i386-cross (12-20220222-1cross1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-8) ... Setting up libpython3-stdlib:arm64 (3.10.4-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.10 (3.10.4-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.10.4-1) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++6-i386-cross (12-20220222-1cross1) ... Setting up dh-autoreconf (20) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1) ... 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-lib2to3 (3.9.12-1) ... Setting up python3-distutils (3.9.12-1) ... Setting up debhelper (13.6) ... Setting up libubsan1-i386-cross (12-20220222-1cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libgcc-11-dev-i386-cross (11.2.0-18cross1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up gcc-11-i686-linux-gnu (11.2.0-18cross1) ... Setting up gcc-i686-linux-gnu (4:11.2.0-2) ... Setting up libstdc++-11-dev-i386-cross (11.2.0-18cross1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up g++-11-i686-linux-gnu (11.2.0-18cross1) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up g++-i686-linux-gnu (4:11.2.0-2) ... Setting up crossbuild-essential-i386 (12.9) ... Setting up libgcc-s1:i386 (12-20220319-1) ... Setting up libc6:i386 (2.33-7) ... Setting up libbz2-1.0:i386 (1.0.8-5) ... Setting up libstdc++6:i386 (12-20220319-1) ... Setting up libitm1:i386 (12-20220319-1) ... Setting up libkeyutils1:i386 (1.6.1-3) ... Setting up libssl1.1:i386 (1.1.1n-1) ... Setting up zlib1g:i386 (1:1.2.11.dfsg-4) ... Setting up libcrypt1:i386 (1:4.4.27-1.1) ... Setting up libcom-err2:i386 (1.46.5-2) ... Setting up libgomp1:i386 (12-20220319-1) ... Setting up libasan6:i386 (11.2.0-19) ... Setting up libjansson4:i386 (2.13.1-1.1) ... Setting up libkrb5support0:i386 (1.19.2-2+b1) ... Setting up libquadmath0:i386 (12-20220319-1) ... Setting up libatomic1:i386 (12-20220319-1) ... Setting up libk5crypto3:i386 (1.19.2-2+b1) ... Setting up libubsan1:i386 (12-20220319-1) ... Setting up libgcc-11-dev:i386 (11.2.0-19) ... Setting up libcrypt-dev:i386 (1:4.4.27-1.1) ... Setting up libkrb5-3:i386 (1.19.2-2+b1) ... Setting up libjansson-dev:i386 (2.13.1-1.1) ... Setting up libgssapi-krb5-2:i386 (1.19.2-2+b1) ... 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 (2.33-7) ... Setting up libbz2-dev:i386 (1.0.8-5) ... Setting up libstdc++-11-dev:i386 (11.2.0-19) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-4) ... Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.33-7) ... +------------------------------------------------------------------------------+ | 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_2.38-3 dpkg-dev_1.21.7 g++-11_11.2.0-19 gcc-11_11.2.0-19 libc6-dev_2.33-7 libstdc++-11-dev_11.2.0-19 libstdc++-11-dev-i386-cross_11.2.0-18cross1 libstdc++6_12-20220319-1 libstdc++6-i386-cross_12-20220222-1cross1 linux-libc-dev_5.16.18-1 Package versions: adduser_3.121 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3 binutils-aarch64-linux-gnu_2.38-3 binutils-common_2.38-3 binutils-i686-linux-gnu_2.38-3 bsdextrautils_2.38-2 bsdutils_1:2.38-2 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2 cpp-11_11.2.0-19 cpp-11-i686-linux-gnu_11.2.0-18cross1 cpp-i686-linux-gnu_4:11.2.0-2 cross-config_2.6.18+nmu2 crossbuild-essential-i386_12.9 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.6 debian-archive-keyring_2021.1.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dpkg_1.21.7 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.21.7 dwz_0.14-1 fakeroot_1.28-1 file_1:5.41-3 findutils_4.9.0-2 g++_4:11.2.0-2 g++-11_11.2.0-19 g++-11-i686-linux-gnu_11.2.0-18cross1 g++-i686-linux-gnu_4:11.2.0-2 gcc_4:11.2.0-2 gcc-11_11.2.0-19 gcc-11-base_11.2.0-19 gcc-11-cross-base_11.2.0-18cross1 gcc-11-i686-linux-gnu_11.2.0-18cross1 gcc-11-i686-linux-gnu-base_11.2.0-18cross1 gcc-12-base_12-20220319-1 gcc-12-cross-base_12-20220222-1cross1 gcc-i686-linux-gnu_4:11.2.0-2 gettext_0.21-6 gettext-base_0.21-6 gpgv_2.2.27-3+b1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 help2man_1.49.2 hostname_3.23 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.4.5 libarchive-zip-perl_1.68-1 libasan6_11.2.0-19 libasan6-i386-cross_11.2.0-18cross1 libatomic1_12-20220319-1 libatomic1-i386-cross_12-20220222-1cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38-3 libblkid1_2.38-2 libbz2-1.0_1.0.8-5 libbz2-dev_1.0.8-5 libc-bin_2.33-7 libc-dev-bin_2.33-7 libc6_2.33-7 libc6-dev_2.33-7 libc6-dev-i386-cross_2.33-1cross1 libc6-i386-cross_2.33-1cross1 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcc1-0_12-20220319-1 libcom-err2_1.46.5-2 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3 libctf0_2.38-3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.6 libdebian-dpkgcross-perl_2.6.18+nmu2 libdpkg-perl_1.21.7 libelf1_0.186-1 libexpat1_2.4.8-1 libfakeroot_1.28-1 libffi8_3.4.2-4 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.13.0-1 libfile-which-perl_1.27-1 libgcc-11-dev_11.2.0-19 libgcc-11-dev-i386-cross_11.2.0-18cross1 libgcc-s1_12-20220319-1 libgcc-s1-i386-cross_12-20220222-1cross1 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.3-4+b1 libgomp1_12-20220319-1 libgomp1-i386-cross_12-20220222-1cross1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.19.2-2+b1 libhogweed6_3.7.3-1 libhwasan0_12-20220319-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl23_0.24-2 libitm1_12-20220319-1 libitm1-i386-cross_12-20220222-1cross1 libjansson-dev_2.13.1-1.1 libjansson4_2.13.1-1.1 libk5crypto3_1.19.2-2+b1 libkeyutils1_1.6.1-3 libkrb5-3_1.19.2-2+b1 libkrb5support0_1.19.2-2+b1 liblocale-gettext-perl_1.07-4+b2 liblsan0_12-20220319-1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-3 libmagic1_1:5.41-3 libmount1_2.38-2 libmpc3_1.2.1-2 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncursesw6_6.3-2 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-4 libpcre3_2:8.39-14 libperl5.34_5.34.0-4 libpipeline1_1.5.5-1 libpython3-stdlib_3.10.4-1 libpython3.10-minimal_3.10.4-3 libpython3.10-stdlib_3.10.4-3 libquadmath0_12-20220319-1 libquadmath0-i386-cross_12-20220222-1cross1 libreadline8_8.1.2-1.2 libseccomp2_2.5.3-2 libselinux1_3.3-1+b2 libsemanage-common_3.3-1 libsemanage2_3.3-1+b2 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.38-2 libsqlite3-0_3.38.2-1 libssl1.1_1.1.1n-1 libstdc++-11-dev_11.2.0-19 libstdc++-11-dev-i386-cross_11.2.0-18cross1 libstdc++6_12-20220319-1 libstdc++6-i386-cross_12-20220222-1cross1 libsub-override-perl_0.09-2 libsystemd0_250.4-1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-3 libtsan0_11.2.0-19 libubsan1_12-20220319-1 libubsan1-i386-cross_12-20220222-1cross1 libuchardet0_0.0.7-1 libudev1_250.4-1 libunistring2_1.0-1 libuuid1_2.38-2 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1 libxml-namespacesupport-perl_1.12-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.13+dfsg-1 libxxhash0_0.8.1-1 libyaml-perl_1.30-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.16.18-1 linux-libc-dev-i386-cross_5.15.5-1cross1 login_1:4.11.1+dfsg1-2 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 media-types_7.1.0 mount_2.38-2 ncurses-base_6.3-2 ncurses-bin_6.3-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-4 perl-base_5.34.0-4 perl-modules-5.34_5.34.0-4 po-debconf_1.0.21+nmu1 python3_3.10.4-1 python3-distutils_3.9.12-1 python3-lib2to3_3.9.12-1 python3-minimal_3.10.4-1 python3.10_3.10.4-3 python3.10-minimal_3.10.4-3 readline-common_8.1.2-1.2 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_3.01-1 tar_1.34+dfsg-1 tzdata_2022a-1 ucf_3.0043 util-linux_2.38-2 util-linux-extra_2.38-2 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4 zlib1g-dev_1:1.2.11.dfsg-4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bedops Binary: bedops, bedops-doc Architecture: any all Version: 2.4.40+dfsg-1 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: d2819342382ce8a8d9519971bd5f6f09b46e53f6 13444448 bedops_2.4.40+dfsg.orig.tar.xz b87353f93d1ef742f06ad98e360a6dfa65d2f4ef 10264 bedops_2.4.40+dfsg-1.debian.tar.xz Checksums-Sha256: 014839e322e14715da2b8b6d879ed9600ef6b558c0bf860c04c64d49328dfc71 13444448 bedops_2.4.40+dfsg.orig.tar.xz 81af8570785380e094f2aaaef9f742f3404b70f01980a1d990de2be391633c1c 10264 bedops_2.4.40+dfsg-1.debian.tar.xz Files: e811a862f0a3c82ee3c4285ebec8393a 13444448 bedops_2.4.40+dfsg.orig.tar.xz 6cf3c54a2b54a622c50c2e42bdb0fe6f 10264 bedops_2.4.40+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmF1G4oSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxXgcQAJ4ugqYcEIJUI28KOfybiurOgzRjrR8u aq/V8bdyuKIVylcZTPfhttXBSANEZX00gYIOgLFd1l7yUuOzwdBBoh+HTBjn5GIi 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signature ./bedops_2.4.40+dfsg-1.dsc dpkg-source: info: extracting bedops in /<> dpkg-source: info: unpacking bedops_2.4.40+dfsg.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.40+dfsg-1.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 parallel.patch dpkg-source: info: applying adapt_to_new_sphinx.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-3966b9ef-1c03-4e9b-a6f0-83447e144288 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 2.4.40+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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/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/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/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/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' 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/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' 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/bedextract/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedextract/src' mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../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:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../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:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../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:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../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:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 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 -ljansson -lz -lbz2 ExtractRows.cpp 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:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 ../../../../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:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 member function ‘void starch::Starch::setCurrentChromosome(char*)’, 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: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); | ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedextract/src' 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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../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:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../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:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../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:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../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:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 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 -ljansson -lz -lbz2 Bedmap.cpp 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:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 ../../../../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:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedmap/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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../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:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../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:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../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:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../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:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 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 -ljansson -lz -lbz2 Bedops.cpp 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:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 ../../../../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:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 member function ‘void starch::Starch::setCurrentChromosome(char*)’, 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++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:261:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:140:11, inlined from ‘void BedOperations::BedPadReader::CleanAll() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:183:28, inlined from ‘static void BedOperations::createWork, Bed::bed_check_iterator >::run(const BedOperations::Input&) [with BedType1 = Bed::BasicCoords; BedType2 = Bed::BasicCoords; unsigned int Sz = 512]’ at Bedops.cpp:401:30: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static void BedOperations::createWork, Bed::bed_check_iterator >::run(const BedOperations::Input&) [with BedType1 = Bed::BasicCoords; BedType2 = 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 member function ‘void starch::Starch::setCurrentChromosome(char*)’, 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++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:261:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:140:11, inlined from ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*>, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’ at Bedops.cpp:1411:39: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*>, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In member function ‘void starch::Starch::setCurrentChromosome(char*)’, 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++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:261:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:140:11, inlined from ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*, std::allocator*> >, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’ at Bedops.cpp:1411:39: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*, std::allocator*> >, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’: ../../../../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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../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:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../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:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../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:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../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:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 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 -ljansson -lz -lbz2 ClosestFeature.cpp 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:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 ../../../../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:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/closestfeats/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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -iquote"/<>/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread convert2bed.c: In function ‘c2b_process_intermediate_bytes_by_lines’: convert2bed.c:6631:103: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 6631 | 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:6631:109: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘long unsigned int’ [-Wformat=] 6631 | 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:6631:115: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘long unsigned int’ [-Wformat=] 6631 | 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 -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../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:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../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:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../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:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../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:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers SortDetails.cpp: In function ‘ChromBedData* initializeChromBedData(char*, double*)’: SortDetails.cpp:250:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ SortDetails.cpp: In function ‘void lexSortBedData(BedData*)’: SortDetails.cpp:1343:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1343 | strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:1342:33: note: length computed here 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘ChromBedData* initializeChromBedData(char*, double*)’, inlined from ‘int processData(const char**, unsigned int, double, char*, bool, bool)’ at SortDetails.cpp:909:59: SortDetails.cpp:250:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘int processData(const char**, unsigned int, double, char*, bool, bool)’: SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && i686-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 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 ../../../../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:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52, inlined from ‘static bool starch::Starch::isStarch(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56, inlined from ‘static bool starch::Starch::isStarch(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:678:25, 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:92:90: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In member function ‘void starch::Starch::setCurrentChromosome(char*)’, 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: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 member function ‘void starch::Starch::setCurrentChromosome(char*)’, 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 ‘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:267:24, inlined from ‘int checkSort(const char**, unsigned int)’ at CheckSort.cpp:51:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers 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/starch/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/starch/src' mkdir -p objects i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../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:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../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:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../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:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../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:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 mkdir -p ../bin i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 mkdir -p ../bin i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. In file included from /usr/i686-linux-gnu/include/c++/11/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++/11/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++/11/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 ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’: starchcat.c:3123:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3123:78: note: length computed here 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 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++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 rm -rf objects make[4]: Leaving directory '/<>/applications/bed/starch/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-2.4.40\+dfsg/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="2.4.40+dfsg" -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_2.4.40+dfsg-1_i386.deb'. dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.40+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=any -O../bedops_2.4.40+dfsg-1_i386.buildinfo dpkg-genchanges --build=any -O../bedops_2.4.40+dfsg-1_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 2022-04-14T03:26:41Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedops_2.4.40+dfsg-1_i386.changes: ---------------------------------- Format: 1.8 Date: Sun, 24 Oct 2021 13:20:15 +0530 Source: bedops Binary: bedops bedops-dbgsym Built-For-Profiles: cross nocheck Architecture: i386 Version: 2.4.40+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: bedops - high-performance genomic feature operations Closes: 997157 Changes: bedops (2.4.40+dfsg-1) unstable; urgency=medium . * Team Upload. [ Steffen Möller ] * Update metadata - indent plus ref to guix . [ Nilesh Patra ] * Add patch to fix FTBFS with new sphinx (Closes: #997157) Checksums-Sha1: 3b9df60da4b6131ee907d068059a9097f92df560 73308 bedops-dbgsym_2.4.40+dfsg-1_i386.deb 1e5cd588b919a495a5c7e903f1f1ba6b735c781f 5623 bedops_2.4.40+dfsg-1_i386.buildinfo 3c3065679703545a07acc80daf139a7d56c87f38 1437768 bedops_2.4.40+dfsg-1_i386.deb Checksums-Sha256: 6b3e36f12883a9ad9f4dce7bda30536b3d17c1061f87c74f17cd7a0dbcf5bc72 73308 bedops-dbgsym_2.4.40+dfsg-1_i386.deb d9ebf56a57f061cbd57d38e5431da7e01dd4a7113c0a133a3098fd7f1daef932 5623 bedops_2.4.40+dfsg-1_i386.buildinfo 75de39ba05c312f5897a9a3b936444ee6edd254b7cbd6b17a419cb90576bac0a 1437768 bedops_2.4.40+dfsg-1_i386.deb Files: e22480bf201edb5f82d4439420283b42 73308 debug optional bedops-dbgsym_2.4.40+dfsg-1_i386.deb a2f043ab893bb45d39d72f1c31dbce94 5623 science optional bedops_2.4.40+dfsg-1_i386.buildinfo 1acc1c849f6f400f84d6018fcf58e56d 1437768 science optional bedops_2.4.40+dfsg-1_i386.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bedops Binary: bedops bedops-dbgsym Architecture: i386 Version: 2.4.40+dfsg-1 Checksums-Md5: e22480bf201edb5f82d4439420283b42 73308 bedops-dbgsym_2.4.40+dfsg-1_i386.deb 1acc1c849f6f400f84d6018fcf58e56d 1437768 bedops_2.4.40+dfsg-1_i386.deb Checksums-Sha1: 3b9df60da4b6131ee907d068059a9097f92df560 73308 bedops-dbgsym_2.4.40+dfsg-1_i386.deb 3c3065679703545a07acc80daf139a7d56c87f38 1437768 bedops_2.4.40+dfsg-1_i386.deb Checksums-Sha256: 6b3e36f12883a9ad9f4dce7bda30536b3d17c1061f87c74f17cd7a0dbcf5bc72 73308 bedops-dbgsym_2.4.40+dfsg-1_i386.deb 75de39ba05c312f5897a9a3b936444ee6edd254b7cbd6b17a419cb90576bac0a 1437768 bedops_2.4.40+dfsg-1_i386.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Thu, 14 Apr 2022 03:26:40 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2), base-passwd (= 3.5.52), bash (= 5.1-6), binutils (= 2.38-3), binutils-aarch64-linux-gnu (= 2.38-3), binutils-common (= 2.38-3), bsdextrautils (= 2.38-2), bsdutils (= 1:2.38-2), build-essential (= 12.9), bzip2 (= 1.0.8-5), coreutils (= 8.32-4.1), cpp (= 4:11.2.0-2), cpp-11 (= 11.2.0-19), dash (= 0.5.11+git20210903+057cd650a4ed-8), debconf (= 1.5.79), debhelper (= 13.6), debianutils (= 5.7-0.1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.7-5), dpkg (= 1.21.7), dpkg-dev (= 1.21.7), dwz (= 0.14-1), file (= 1:5.41-3), findutils (= 4.9.0-2), g++ (= 4:11.2.0-2), g++-11 (= 11.2.0-19), gcc (= 4:11.2.0-2), gcc-11 (= 11.2.0-19), gcc-11-base (= 11.2.0-19), gcc-12-base (= 12-20220319-1), gettext (= 0.21-6), gettext-base (= 0.21-6), grep (= 3.7-1), groff-base (= 1.22.4-8), gzip (= 1.12-1), help2man (= 1.49.2), hostname (= 3.23), init-system-helpers (= 1.62), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-19), libatomic1 (= 12-20220319-1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.7-1), libaudit1 (= 1:3.0.7-1+b1), libbinutils (= 2.38-3), libblkid1 (= 2.38-2), libbz2-1.0 (= 1.0.8-5), libbz2-dev (= 1.0.8-5), libc-bin (= 2.33-7), libc-dev-bin (= 2.33-7), libc6 (= 2.33-7), libc6-dev (= 2.33-7), libcap-ng0 (= 0.7.9-2.2+b2), libcap2 (= 1:2.44-1), libcc1-0 (= 12-20220319-1), libcom-err2 (= 1.46.5-2), libcrypt-dev (= 1:4.4.27-1.1), libcrypt1 (= 1:4.4.27-1.1), libctf-nobfd0 (= 2.38-3), libctf0 (= 2.38-3), libdb5.3 (= 5.3.28+dfsg1-0.8), libdebconfclient0 (= 0.261), libdebhelper-perl (= 13.6), libdpkg-perl (= 1.21.7), libelf1 (= 0.186-1), libexpat1 (= 2.4.8-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.2.0-19), libgcc-s1 (= 12-20220319-1), libgcrypt20 (= 1.10.1-2), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgmp10 (= 2:6.2.1+dfsg-3), libgomp1 (= 12-20220319-1), libgpg-error0 (= 1.43-3), libgssapi-krb5-2 (= 1.19.2-2+b1), libhwasan0 (= 12-20220319-1), libicu67 (= 67.1-7), libisl23 (= 0.24-2), libitm1 (= 12-20220319-1), libjansson-dev (= 2.13.1-1.1), libjansson4 (= 2.13.1-1.1), libk5crypto3 (= 1.19.2-2+b1), libkeyutils1 (= 1.6.1-3), libkrb5-3 (= 1.19.2-2+b1), libkrb5support0 (= 1.19.2-2+b1), liblocale-gettext-perl (= 1.07-4+b2), liblsan0 (= 12-20220319-1), liblz4-1 (= 1.9.3-2), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-3), libmagic1 (= 1:5.41-3), libmount1 (= 2.38-2), libmpc3 (= 1.2.1-2), libmpdec3 (= 2.5.1-2), libmpfr6 (= 4.1.0-3), libncursesw6 (= 6.3-2), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libpam-modules (= 1.4.0-11), libpam-modules-bin (= 1.4.0-11), libpam-runtime (= 1.4.0-11), libpam0g (= 1.4.0-11), libpcre2-8-0 (= 10.39-4), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-4), libpipeline1 (= 1.5.5-1), libpython3-stdlib (= 3.10.4-1), libpython3.10-minimal (= 3.10.4-3), libpython3.10-stdlib (= 3.10.4-3), libreadline8 (= 8.1.2-1.2), libseccomp2 (= 2.5.3-2), libselinux1 (= 3.3-1+b2), libsigsegv2 (= 2.14-1), libsmartcols1 (= 2.38-2), libsqlite3-0 (= 3.38.2-1), libssl1.1 (= 1.1.1n-1), libstdc++-11-dev (= 11.2.0-19), libstdc++6 (= 12-20220319-1), libsub-override-perl (= 0.09-2), libsystemd0 (= 250.4-1), libtinfo6 (= 6.3-2), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.7-3), libtsan0 (= 11.2.0-19), libubsan1 (= 12-20220319-1), libuchardet0 (= 0.0.7-1), libudev1 (= 250.4-1), libunistring2 (= 1.0-1), libuuid1 (= 2.38-2), libxml2 (= 2.9.13+dfsg-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.16.18-1), login (= 1:4.11.1+dfsg1-2), lsb-base (= 11.1.0), m4 (= 1.4.18-5), make (= 4.3-4.1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3), media-types (= 7.1.0), ncurses-base (= 6.3-2), ncurses-bin (= 6.3-2), patch (= 2.7.6-7), perl (= 5.34.0-4), perl-base (= 5.34.0-4), perl-modules-5.34 (= 5.34.0-4), po-debconf (= 1.0.21+nmu1), python3 (= 3.10.4-1), python3-distutils (= 3.9.12-1), python3-lib2to3 (= 3.9.12-1), python3-minimal (= 3.10.4-1), python3.10 (= 3.10.4-3), python3.10-minimal (= 3.10.4-3), readline-common (= 8.1.2-1.2), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1), tar (= 1.34+dfsg-1), util-linux (= 2.38-2), util-linux-extra (= 2.38-2), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-4), zlib1g-dev (= 1:1.2.11.dfsg-4) 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="1635061815" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedops-dbgsym_2.4.40+dfsg-1_i386.deb ------------------------------------ new Debian package, version 2.0. size 73308 bytes: control archive=536 bytes. 376 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: bedops-dbgsym Source: bedops Version: 2.4.40+dfsg-1 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 88 Depends: bedops (= 2.4.40+dfsg-1) Section: debug Priority: optional Description: debug symbols for bedops Build-Ids: 8f86e9f69d61b12c28518460413f83cd8670b946 drwxr-xr-x root/root 0 2021-10-24 07:50 ./ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/.build-id/8f/ -rw-r--r-- root/root 79828 2021-10-24 07:50 ./usr/lib/debug/.build-id/8f/86e9f69d61b12c28518460413f83cd8670b946.debug drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/ lrwxrwxrwx root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops-dbgsym -> bedops bedops_2.4.40+dfsg-1_i386.deb ----------------------------- new Debian package, version 2.0. size 1437768 bytes: control archive=6148 bytes. 730 bytes, 15 lines control 21485 bytes, 236 lines md5sums Package: bedops Version: 2.4.40+dfsg-1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 10717 Depends: libbz2-1.0, libc6 (>= 2.33), libgcc-s1 (>= 4.2), libjansson4 (>= 2.3), libstdc++6 (>= 11), 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 2021-10-24 07:50 ./ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/bin/ -rwxr-xr-x root/root 4711 2021-10-24 07:50 ./usr/bin/bam2bed -rwxr-xr-x root/root 4501 2021-10-24 07:50 ./usr/bin/bam2bed_gnuParallel -rwxr-xr-x root/root 5022 2021-10-24 07:50 ./usr/bin/bam2bed_sge -rwxr-xr-x root/root 5021 2021-10-24 07:50 ./usr/bin/bam2bed_slurm -rwxr-xr-x root/root 5842 2021-10-24 07:50 ./usr/bin/bam2starch -rwxr-xr-x root/root 4507 2021-10-24 07:50 ./usr/bin/bam2starch_gnuParallel -rwxr-xr-x root/root 5076 2021-10-24 07:50 ./usr/bin/bam2starch_sge -rwxr-xr-x root/root 5014 2021-10-24 07:50 ./usr/bin/bam2starch_slurm -rwxr-xr-x root/root 247868 2021-10-24 07:50 ./usr/bin/bedextract -rwxr-xr-x root/root 8394908 2021-10-24 07:50 ./usr/bin/bedmap -rwxr-xr-x root/root 534656 2021-10-24 07:50 ./usr/bin/bedops -rwxr-xr-x root/root 112452 2021-10-24 07:50 ./usr/bin/bedops-starch -rwxr-xr-x root/root 305240 2021-10-24 07:50 ./usr/bin/closest-features -rwxr-xr-x root/root 145736 2021-10-24 07:50 ./usr/bin/convert2bed -rwxr-xr-x root/root 3773 2021-10-24 07:50 ./usr/bin/gff2bed -rwxr-xr-x root/root 4904 2021-10-24 07:50 ./usr/bin/gff2starch -rwxr-xr-x root/root 3532 2021-10-24 07:50 ./usr/bin/gtf2bed -rwxr-xr-x root/root 4663 2021-10-24 07:50 ./usr/bin/gtf2starch -rwxr-xr-x root/root 3773 2021-10-24 07:50 ./usr/bin/gvf2bed -rwxr-xr-x root/root 4904 2021-10-24 07:50 ./usr/bin/gvf2starch -rwxr-xr-x root/root 3976 2021-10-24 07:50 ./usr/bin/psl2bed -rwxr-xr-x root/root 5107 2021-10-24 07:50 ./usr/bin/psl2starch -rwxr-xr-x root/root 3776 2021-10-24 07:50 ./usr/bin/rmsk2bed -rwxr-xr-x root/root 4907 2021-10-24 07:50 ./usr/bin/rmsk2starch -rwxr-xr-x root/root 4711 2021-10-24 07:50 ./usr/bin/sam2bed -rwxr-xr-x root/root 5842 2021-10-24 07:50 ./usr/bin/sam2starch -rwxr-xr-x root/root 260192 2021-10-24 07:50 ./usr/bin/sort-bed -rwxr-xr-x root/root 10163 2021-10-24 07:50 ./usr/bin/starch-diff -rwxr-xr-x root/root 210772 2021-10-24 07:50 ./usr/bin/starchcat -rwxr-xr-x root/root 4299 2021-10-24 07:50 ./usr/bin/starchcluster_gnuParallel -rwxr-xr-x root/root 4810 2021-10-24 07:50 ./usr/bin/starchcluster_sge -rwxr-xr-x root/root 4716 2021-10-24 07:50 ./usr/bin/starchcluster_slurm -rwxr-xr-x root/root 116484 2021-10-24 07:50 ./usr/bin/starchstrip -rwxr-xr-x root/root 157328 2021-10-24 07:50 ./usr/bin/unstarch -rwxr-xr-x root/root 32686 2021-10-24 07:50 ./usr/bin/update-sort-bed-migrate-candidates -rwxr-xr-x root/root 20701 2021-10-24 07:50 ./usr/bin/update-sort-bed-slurm -rwxr-xr-x root/root 22682 2021-10-24 07:50 ./usr/bin/update-sort-bed-starch-slurm -rwxr-xr-x root/root 4675 2021-10-24 07:50 ./usr/bin/vcf2bed -rwxr-xr-x root/root 5806 2021-10-24 07:50 ./usr/bin/vcf2starch -rwxr-xr-x root/root 4598 2021-10-24 07:50 ./usr/bin/wig2bed -rwxr-xr-x root/root 5729 2021-10-24 07:50 ./usr/bin/wig2starch drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/ -rw-r--r-- root/root 267 2021-10-24 07:33 ./usr/share/doc/bedops/README.Debian -rw-r--r-- root/root 1618 2021-10-24 07:50 ./usr/share/doc/bedops/changelog.Debian.gz -rw-r--r-- root/root 22054 2021-07-27 21:43 ./usr/share/doc/bedops/changelog.gz -rw-r--r-- root/root 1156 2021-10-24 07:33 ./usr/share/doc/bedops/copyright drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/ -rw-r--r-- root/root 954 2021-07-27 21:43 ./usr/share/doc/bedops/tests/Makefile drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/bedops/ -rw-r--r-- root/root 2166 2021-10-24 07:50 ./usr/share/doc/bedops/tests/bedops/Makefile.gz drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/ -rw-r--r-- root/root 197 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001.expected -rw-r--r-- root/root 44 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001a.test -rw-r--r-- root/root 53 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001b.test -rw-r--r-- root/root 24 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chrom.001.expected -rw-r--r-- root/root 26 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.complement.001.expected -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.difference.001.expected -rw-r--r-- root/root 23 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.ec.001a.test -rw-r--r-- root/root 69 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.element-of.001.expected -rw-r--r-- root/root 91 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001.expected -rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001a.test -rw-r--r-- root/root 104 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001b.test -rw-r--r-- root/root 37 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.expected -rw-r--r-- root/root 111 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.test -rw-r--r-- root/root 368 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.named-pipe.001.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.not-element-of.001.expected -rw-r--r-- root/root 148 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001.expected -rw-r--r-- root/root 39 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001a.test -rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001b.test -rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001c.test -rw-r--r-- root/root 257 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.stdin.001.expected -rw-r--r-- root/root 130 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.symdiff.001.expected -rw-r--r-- root/root 134 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.expected -rw-r--r-- root/root 126 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.test -rw-r--r-- root/root 171 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.chop.002.expected -rw-r--r-- root/root 20 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.chrom.002.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.complement.002.expected -rw-r--r-- root/root 2172 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002.expected -rw-r--r-- root/root 3033 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002a.test -rw-r--r-- root/root 2941 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002b.test -rw-r--r-- root/root 18 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.element-of.002.expected -rw-r--r-- root/root 13 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.expected -rw-r--r-- root/root 26 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.test -rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.merge.002.expected -rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.not-element-of.002.expected -rw-r--r-- root/root 376 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002.expected -rw-r--r-- root/root 48 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002a.test -rw-r--r-- root/root 49 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002b.test -rw-r--r-- root/root 101 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002c.test -rw-r--r-- root/root 39 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002d.test -rw-r--r-- root/root 131 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002e.test -rw-r--r-- root/root 118 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.symdiff.002.expected -rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.union.002.expected -rw-r--r-- root/root 368 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.chop.003.expected -rw-r--r-- root/root 24 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.chrom.003.expected -rw-r--r-- root/root 61 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.complement.003.expected -rw-r--r-- root/root 3794 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.difference.003.expected -rw-r--r-- root/root 42 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.element-of.003.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.intersection.003.expected -rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.expected -rw-r--r-- root/root 46 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.test -rw-r--r-- root/root 21 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003.expected -rw-r--r-- root/root 63 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003a.test -rw-r--r-- root/root 42 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003b.test -rw-r--r-- root/root 153 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.expected -rw-r--r-- root/root 398 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.test -rw-r--r-- root/root 22 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003.expected -rw-r--r-- root/root 18 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003a.test -rw-r--r-- root/root 29 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003b.test -rw-r--r-- root/root 9 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003c.test -rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003d.test -rw-r--r-- root/root 355 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.expected -rw-r--r-- root/root 360 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.test -rw-r--r-- root/root 257 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.chop.004.expected -rw-r--r-- root/root 24 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.chrom.004.expected -rw-r--r-- root/root 111 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004.expected -rw-r--r-- root/root 46 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004a.test -rw-r--r-- root/root 132 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004b.test -rw-r--r-- root/root 94 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004c.test -rw-r--r-- root/root 30 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004.expected -rw-r--r-- root/root 30 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004a.test -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004b.test -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004.expected -rw-r--r-- root/root 92 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004a.test -rw-r--r-- root/root 23 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004b.test -rw-r--r-- root/root 49 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004.expected -rw-r--r-- root/root 103 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004a.test -rw-r--r-- root/root 85 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004b.test -rw-r--r-- root/root 47 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004c.test -rw-r--r-- root/root 72 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.merge.004.expected -rw-r--r-- root/root 117 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.expected -rw-r--r-- root/root 117 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.test -rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.symdiff.004.expected -rw-r--r-- root/root 22 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.expected -rw-r--r-- root/root 32 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.test -rw-r--r-- root/root 385 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.expected -rw-r--r-- root/root 87 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.test -rw-r--r-- root/root 20 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.expected -rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.test -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.difference.005.expected -rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.expected -rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.test -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.symdiff.005.expected -rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.union.005.expected -rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.complement.006.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.difference.006.expected -rw-r--r-- root/root 41 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006.expected -rw-r--r-- root/root 37 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006a.test -rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006b.test -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006c.test -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.union.006.expected -rw-r--r-- root/root 9 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.complement.007.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.difference.007.expected -rw-r--r-- root/root 55 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007.expected -rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007a.test -rw-r--r-- root/root 69 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007b.test -rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.union.007.expected -rw-r--r-- root/root 79 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.complement.008.expected -rw-r--r-- root/root 197 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.merge.008.expected -rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.union.008.expected -rw-r--r-- root/root 175 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.complement.009.expected -rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.merge.009.expected -rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.expected -rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.test drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/conversion/ -rw-r--r-- root/root 1159 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/Makefile.gz drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/ -rw-r--r-- root/root 398 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 352 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 368 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 322 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 102 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 102 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.expected -rw-r--r-- root/root 60 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.wig -rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 49 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.expected -rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.wig -rw-r--r-- root/root 170 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 85 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 34 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.expected -rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.wig -rw-r--r-- root/root 155 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 82 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.expected -rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.wig -rw-r--r-- root/root 538 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.expected -rw-r--r-- root/root 454 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.wig -rw-r--r-- root/root 583 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.002.expected -rw-r--r-- root/root 700 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.003.expected -rw-r--r-- root/root 763 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.004.expected -rw-r--r-- root/root 493 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.expected -rw-r--r-- root/root 421 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.wig -rw-r--r-- root/root 538 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.002.expected -rw-r--r-- root/root 652 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.003.expected -rw-r--r-- root/root 715 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.004.expected drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/ -rw-r--r-- root/root 1078 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/Makefile.gz drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/data/ -rw-r--r-- root/root 1935 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.expected -rw-r--r-- root/root 2813 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.test.gz -rw-r--r-- root/root 772 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1.001.test -rw-r--r-- root/root 1166 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1andChr2.001.expected -rw-r--r-- root/root 772 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr2.001.test -rw-r--r-- root/root 764 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.expected -rw-r--r-- root/root 2851 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.test.gz -rw-r--r-- root/root 218 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.expected -rw-r--r-- root/root 2254 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.test.gz -rw-r--r-- root/root 109 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/README -rw-r--r-- root/root 426 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/hg38.bed -rw-r--r-- root/root 1516 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/generate_random_intervals.sh drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/man/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/man/man1/ -rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/bam2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/bam2starch.1.gz -rw-r--r-- root/root 354 2021-10-24 07:50 ./usr/share/man/man1/bedextract.1.gz -rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/bedmap.1.gz -rw-r--r-- root/root 371 2021-10-24 07:50 ./usr/share/man/man1/bedops-starch.1.gz -rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/bedops.1.gz -rw-r--r-- root/root 463 2021-10-24 07:50 ./usr/share/man/man1/closest-features.1.gz -rw-r--r-- root/root 356 2021-10-24 07:50 ./usr/share/man/man1/convert2bed.1.gz -rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/gff2bed.1.gz -rw-r--r-- root/root 354 2021-10-24 07:50 ./usr/share/man/man1/gff2starch.1.gz -rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/gtf2bed.1.gz -rw-r--r-- root/root 353 2021-10-24 07:50 ./usr/share/man/man1/gtf2starch.1.gz -rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/gvf2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/gvf2starch.1.gz -rw-r--r-- root/root 346 2021-10-24 07:50 ./usr/share/man/man1/psl2bed.1.gz -rw-r--r-- root/root 354 2021-10-24 07:50 ./usr/share/man/man1/psl2starch.1.gz -rw-r--r-- root/root 349 2021-10-24 07:50 ./usr/share/man/man1/rmsk2bed.1.gz -rw-r--r-- root/root 356 2021-10-24 07:50 ./usr/share/man/man1/rmsk2starch.1.gz -rw-r--r-- root/root 346 2021-10-24 07:50 ./usr/share/man/man1/sam2bed.1.gz -rw-r--r-- root/root 354 2021-10-24 07:50 ./usr/share/man/man1/sam2starch.1.gz -rw-r--r-- root/root 352 2021-10-24 07:50 ./usr/share/man/man1/sort-bed.1.gz -rw-r--r-- root/root 719 2021-10-24 07:50 ./usr/share/man/man1/starch-diff.1.gz -rw-r--r-- root/root 351 2021-10-24 07:50 ./usr/share/man/man1/starchcat.1.gz -rw-r--r-- root/root 354 2021-10-24 07:50 ./usr/share/man/man1/starchstrip.1.gz -rw-r--r-- root/root 349 2021-10-24 07:50 ./usr/share/man/man1/unstarch.1.gz -rw-r--r-- root/root 1764 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz -rw-r--r-- root/root 1329 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-slurm.1.gz -rw-r--r-- root/root 1383 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz -rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/vcf2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/vcf2starch.1.gz -rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/wig2bed.1.gz -rw-r--r-- root/root 356 2021-10-24 07:50 ./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 [657 B] Fetched 2191 B in 0s (51.0 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 libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-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-someutils-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 libnet-ipv6addr-perl libnet-netmask-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxs-parse-keyword-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 libbusiness-isbn-perl libwww-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg liblist-someutils-xs-perl libmath-base85-perl libsocket6-perl libpackage-stash-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 libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-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-someutils-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 libnet-ipv6addr-perl libnet-netmask-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils sbuild-build-depends-lintian-dummy:i386 t1utils unzip 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. Need to get 6628 kB of archives. After this operation, 20.6 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://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 2.2.27-3+b1 [540 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.27-3+b1 [884 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+b1 [69.2 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-1+b4 [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+b3 [15.8 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-1+b4 [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 0.31-1 [24.2 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+b4 [44.2 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libb-hooks-endofscope-perl all 0.26-1 [19.6 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+b8 [36.4 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 libclone-perl arm64 0.45-1+b2 [15.3 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 libconfig-tiny-perl all 2.28-1 [17.3 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-1+b2 [25.2 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libconst-fast-perl all 0.014-1.1 [8552 B] Get:29 http://mirror.einval.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.27-1+b1 [127 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 libiterator-perl all 0.03+ds1-1.1 [18.4 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-2+b1 [36.9 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.02-1 [34.6 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libnet-netmask-perl all 2.0001-1 [32.2 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-1+b6 [103 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libdevel-size-perl arm64 0.83-1+b3 [25.8 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.04-1+b4 [26.7 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libnumber-compare-perl all 0.03-2 [7448 B] Get:51 http://mirror.einval.org/debian sid/main arm64 libtext-glob-perl all 0.11-2 [8992 B] Get:52 http://mirror.einval.org/debian sid/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libio-prompt-tiny-perl all 0.003-1 [9150 B] Get:58 http://mirror.einval.org/debian sid/main arm64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.005004-3 [60.5 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:70 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b2 [171 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-1+b4 [11.9 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-1+b2 [13.5 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.122-1 [56.0 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.19-1+b8 [17.0 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.009-1+b1 [11.9 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.634-1+b1 [46.4 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 4.023+ds-1 [95.0 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 4.023+ds-1 [97.9 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libsort-versions-perl all 1.62-1 [11.0 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.22-1 [50.3 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libsyntax-keyword-try-perl arm64 0.27-1 [28.2 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-1+b3 [27.2 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-4+b9 [8660 B] Get:86 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.13-1+b1 [13.4 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.9-1+b1 [194 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-1+b4 [74.7 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b3 [19.8 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.10-1 [91.0 kB] Get:93 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get:94 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.83+ds-1+b1 [34.4 kB] Get:95 http://mirror.einval.org/debian sid/main arm64 lzip arm64 1.23-3 [86.6 kB] Get:96 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:97 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:98 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:99 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-26 [165 kB] Get:100 http://mirror.einval.org/debian sid/main arm64 lintian all 2.114.0 [1382 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6628 kB in 0s (38.1 MB/s) Selecting previously unselected package diffstat. (Reading database ... 19796 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_2.2.27-3+b1_arm64.deb ... Unpacking gpgconf (2.2.27-3+b1) ... Selecting previously unselected package gpg. Preparing to unpack .../03-gpg_2.2.27-3+b1_arm64.deb ... Unpacking gpg (2.2.27-3+b1) ... 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+b1_arm64.deb ... Unpacking libapt-pkg-perl (0.1.40+b1) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../06-libb-hooks-op-check-perl_0.22-1+b4_arm64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b4) ... 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+b3_arm64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b3) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../09-libparams-classify-perl_0.015-1+b4_arm64.deb ... Unpacking libparams-classify-perl (0.015-1+b4) ... 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. Preparing to unpack .../11-libtry-tiny-perl_0.31-1_all.deb ... Unpacking libtry-tiny-perl (0.31-1) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../12-libmodule-implementation-perl_0.09-1.1_all.deb ... Unpacking libmodule-implementation-perl (0.09-1.1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../13-libsub-exporter-progressive-perl_0.001013-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-1) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../14-libvariable-magic-perl_0.62-1+b4_arm64.deb ... Unpacking libvariable-magic-perl (0.62-1+b4) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../15-libb-hooks-endofscope-perl_0.26-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.26-1) ... Selecting previously unselected package libcapture-tiny-perl. 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Unpacking libconfig-tiny-perl (2.28-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../22-libparams-util-perl_1.102-1+b2_arm64.deb ... Unpacking libparams-util-perl (1.102-1+b2) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../23-libsub-install-perl_0.928-1.1_all.deb ... Unpacking libsub-install-perl (0.928-1.1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../24-libdata-optlist-perl_0.112-1_all.deb ... Unpacking libdata-optlist-perl (0.112-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../25-libsub-exporter-perl_0.988-1_all.deb ... Unpacking libsub-exporter-perl (0.988-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../26-libconst-fast-perl_0.014-1.1_all.deb ... Unpacking libconst-fast-perl (0.014-1.1) ... Selecting previously unselected package libcpanel-json-xs-perl:arm64. 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Setting up lzip (1.23-3) ... update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up t1utils (1.41-4) ... Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.62-1+b4) ... Setting up libb-hooks-op-check-perl (0.22-1+b4) ... Setting up liblist-moreutils-xs-perl (0.430-2+b1) ... Setting up libparams-util-perl (1.102-1+b2) ... Setting up libtime-duration-perl (1.21-1) ... Setting up libtext-xslate-perl:arm64 (3.5.9-1+b1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl (0.26-1+b2) ... Setting up libsyntax-keyword-try-perl (0.27-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:arm64 (0.634-1+b1) ... Setting up libpath-tiny-perl (0.122-1) ... Setting up lzop (1.04-2) ... Setting up gpgconf (2.2.27-3+b1) ... 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+b8) ... Setting up libsort-versions-perl (1.62-1) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libterm-readkey-perl (2.38-1+b3) ... Setting up libfont-ttf-perl (1.06-1.1) ... Setting up libtext-levenshteinxs-perl (0.03-4+b9) ... Setting up libperlio-gzip-perl (0.19-1+b8) ... Setting up libhtml-html5-entities-perl (0.004-1.1) ... Setting up libsereal-decoder-perl (4.023+ds-1) ... Setting up libmarkdown2:arm64 (2.2.7-2) ... Setting up liburi-perl (5.10-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up gpg (2.2.27-3+b1) ... Setting up libdata-validate-ip-perl (0.30-1) ... Setting up libemail-address-xs-perl (1.04-1+b4) ... Setting up libfile-basedir-perl (0.09-1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libtext-markdown-discount-perl:arm64 (0.13-1+b1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl (0.008-1+b3) ... Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libsub-exporter-perl (0.988-1) ... 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+b4) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libconst-fast-perl (0.014-1.1) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.114.0) ... Setting up sbuild-build-depends-lintian-dummy:i386 (0.invalid.0) ... Processing triggers for man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.33-7) ... 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: 56540 Build-Time: 1997 Distribution: unstable Foreign Architectures: i386 Host Architecture: i386 Install-Time: 44 Job: bedops_2.4.40+dfsg-1 Lintian: pass Machine Architecture: arm64 Package: bedops Package-Time: 2072 Source-Version: 2.4.40+dfsg-1 Space: 56540 Status: successful Version: 2.4.40+dfsg-1 -------------------------------------------------------------------------------- Finished at 2022-04-14T03:26:41Z Build needed 00:34:32, 56540k disk space