sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | gff2aplot 2.0-15 (amd64) Sun, 15 Sep 2024 05:25:05 +0000 | +==============================================================================+ Package: gff2aplot Version: 2.0-15 Source Version: 2.0-15 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-d9787043-912a-4d99-9010-93709efdb8e2' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup gff2aplot_2.0-15 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup gff2aplot_2.0-15 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/gff2aplot-NKLiY5/resolver-nmDLjB' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://localhost:3142/debian sid InRelease 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 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/gff2aplot_2.0-15.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/gff2aplot-NKLiY5/gff2aplot-2.0' with '<>' I: NOTICE: Log filtering will replace 'build/gff2aplot-NKLiY5' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [617 B] Get:5 copy:/<>/apt_archive ./ Packages [649 B] Fetched 1875 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After this operation, 75.7 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [876 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.9 MB in 0s (88.9 MB/s) Selecting previously unselected package sensible-utils. 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Processing triggers for libc-bin (2.40-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-4 gcc-13_13.3.0-6 gcc-14_14.2.0-4 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-4 cpp-14-x86-64-linux-gnu_14.2.0-4 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-4 g++-14-x86-64-linux-gnu_14.2.0-4 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-4 gcc-14-base_14.2.0-4 gcc-14-x86-64-linux-gnu_14.2.0-4 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8+b1 gpg_2.2.43-8+b1 gpg-agent_2.2.43-8+b1 gpg-wks-client_2.2.43-8+b1 gpgconf_2.2.43-8+b1 gpgsm_2.2.43-8+b1 gpgv_2.2.43-8+b1 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-4 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-4 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43.1-4 libblkid1_2.40.2-8 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-6 libc-bin_2.40-2 libc-dev-bin_2.40-2 libc-l10n_2.40-2 libc6_2.40-2 libc6-dev_2.40-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-4 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-4 libctf0_2.43.1-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-6 libgcc-14-dev_14.2.0-4 libgcc-s1_14.2.0-4 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-4 libgpg-error0_1.50-3 libgprofng0_2.43.1-4 libhogweed6t64_3.10-1 libhwasan0_14.2.0-4 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.27-1 libitm1_14.2.0-4 libjansson4_2.14-2+b2 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-3+b1 liblsan0_14.2.0-4 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-8 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnpth0t64_1.6-3.1 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-5 libpipeline1_1.5.8-1 libquadmath0_14.2.0-4 libreadline8t64_8.2-5 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-4 libsmartcols1_2.40.2-8 libsqlite3-0_3.46.1-1 libssl3t64_3.3.2-1 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 libsystemd0_256.6-1 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-4 libubsan1_14.2.0-4 libuchardet0_0.0.8-1+b1 libudev1_256.6-1 libunistring5_1.2-1 libuuid1_2.40.2-8 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.10.9-1 locales-all_2.40-2 login_1:4.16.0-2+really2.40.2-8 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pinentry-curses_1.2.1-4+b1 po-debconf_1.0.21+nmu1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.10-2 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-8 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gff2aplot Binary: gff2aplot Architecture: any Version: 2.0-15 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://genome.crg.es/software/gfftools/GFF2APLOT.html Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/gff2aplot Vcs-Git: https://salsa.debian.org/med-team/gff2aplot.git Testsuite: autopkgtest Testsuite-Triggers: ghostscript, graphicsmagick, imagemagick Build-Depends: debhelper-compat (= 13) Package-List: gff2aplot deb science optional arch=any Checksums-Sha1: 469f99901a437f8b539b8b29be9cb0f392d6633b 328439 gff2aplot_2.0.orig.tar.gz 7f336c40811459aceb3ad0fbb2a81048732612a3 20764 gff2aplot_2.0-15.debian.tar.xz Checksums-Sha256: 33798a1f2877fc9d64aaf143c2e5bb909021b1f147c6718e61fbcc96cc65ccc3 328439 gff2aplot_2.0.orig.tar.gz 341ed9d8a0f8cf26c7c28cfad34cdc49e59230d16d8dc6afd3b9ecfd2ad5cbe7 20764 gff2aplot_2.0-15.debian.tar.xz Files: 8b269e236bcbacb1c70e4a3424940dc6 328439 gff2aplot_2.0.orig.tar.gz 53d9a4f53d588d060b186aa6226a687f 20764 gff2aplot_2.0-15.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmXAyPkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFfeQ/9FZfoiO4smc+53Q0Ezfb3fword/HVh/IR ggXK4Ki8h4AF0PHpAbWgSSD6mn1V3MnPw5yR2etGPeSSmHouK16GTNih1VK1J6Fm k3YtNWiJo5u87yJTpl9MLblhwf1OpBxty4FBVVHIKmOZe39dyKnvP/kidzvLP6OL P68MUqlHUVVqVaZVn/IuSZvAJgYW+XMrIGbgC/AkOHw0My8oZUcizBsUODiVPqQ3 C07LxsWzgxY4IGRzUEBQ+YYWogxxgyG4yXaXrCw9klDKoHKcCdtp2scA4fLKMsgb CbxhCHjt0B/7k+gVIceZYWejymIYF4ANLcTcFyrtQYjTmpfc8LptUIMxvoUC1WXD CX8yO+KyhRWPjj82m10IPXSDc6ZWTa/tszqEdMzaeT6Zuf4UTF/LMaCLhqZDS6cb vQwH+6RBF9Y3zXz4VJx8ux3B22QsgOYUTQi8yl6hWnM4SPiJj0WqW4e3lVp3W7yf bocCC2UBjg63fgJGpjXSt2AjzNf62IZG9flWRtw8l830GSOWt15Eb+q3WhK7dPmO q6LxzyJOhoCfx9SRTQSPq7rqRmJlXstVs/F0V/6bC9kYzf1jlN+ITUCmuf7m5zzL ELprqaA6vyeD2Zgvd7/kj7tNpZ09n9mSKT29OuH5ZCdRR8X/4s1ccCg70SMtO9Cr WLGbwv3ljTw= =Z4Vx -----END PGP SIGNATURE----- gpgv: Signature made Mon Feb 5 11:39:37 2024 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gff2aplot_2.0-15.dsc: no acceptable signature found dpkg-source: info: extracting gff2aplot in /<> dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz dpkg-source: info: unpacking gff2aplot_2.0-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying non_lexical_loop_iterator.patch dpkg-source: info: applying 02-blat2gff.diff dpkg-source: info: applying 03-parseblast.diff dpkg-source: info: applying use-dpkg-buildflags.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying fis-privacy-breach.patch dpkg-source: info: applying perl_5.28.patch dpkg-source: info: applying fix_install_ali2gff.patch dpkg-source: info: applying enhance_sprintf_buffer.patch dpkg-source: info: applying fix_README_used_for_test.patch dpkg-source: info: applying fix_gff_comments.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network gff2aplot_2.0-15 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network gff2aplot_2.0-15 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-d9787043-912a-4d99-9010-93709efdb8e2 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package gff2aplot dpkg-buildpackage: info: source version 2.0-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f src/ali2gff/ali2gff bin/* make[1]: Leaving directory '/<>' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building gff2aplot using existing ./gff2aplot_2.0.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building gff2aplot in gff2aplot_2.0-15.debian.tar.xz dpkg-source: info: building gff2aplot in gff2aplot_2.0-15.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j2 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' ### ### RUNNING MAKEFILE ### ### Finishing PERL script from "src/gff2aplot.pl" -> "bin/gff2aplot.pl" ### Sun Sep 15 05:25:26 UTC 2024 -- debomatic ### ### Finishing PERL script from "src/parseblast.pl" -> "bin/parseblast.pl" ### Finishing PERL script from "src/blat2gff.pl" -> "bin/blat2gff.pl" ### Finishing PERL script from "src/sim2gff.pl" -> "bin/sim2gff.pl" ### Making ALI2GFF... make[2]: Entering directory '/<>/src/ali2gff' ### ### MAKEFILE DONE... ### ali2gff.c: In function ‘main’: ali2gff.c:88:15: warning: variable ‘ptr’ set but not used [-Wunused-but-set-variable] 88 | char *ptr; | ^~~ ali2gff.c: In function ‘processMumfile’: ali2gff.c:527:86: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 527 | if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); | ~^ ~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld ali2gff.c:527:92: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 527 | if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); | ~^ ~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld ali2gff.c:768:86: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 768 | if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); | ~^ ~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld ali2gff.c:768:92: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 768 | if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); | ~^ ~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld ali2gff.c: In function ‘processGFFfile’: ali2gff.c:355:113: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 355 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", xName,yName,source,xb,yb,xe,ye,scores,strands,frames); | ^~ ~~~~~ In file included from /usr/include/stdio.h:970, from ali2gff.h:20, from ali2gff.c:64: In function ‘sprintf’, inlined from ‘processGFFfile’ at ali2gff.c:355:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 25 or more bytes (assuming 4028) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processGFFfile’: ali2gff.c:354:113: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 354 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",xName,yName,source,xb,yb,xe,ye,score ,strands,frames); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘processGFFfile’ at ali2gff.c:354:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 2034) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processGFFfile’: ali2gff.c:351:113: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 351 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", xName,yName,source,xb,yb,xe,ye,scores,strands,frames,cptr); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘processGFFfile’ at ali2gff.c:351:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 25 or more bytes (assuming 4028) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processGFFfile’: ali2gff.c:350:113: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 350 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",xName,yName,source,xb,yb,xe,ye,score ,strands,frames,cptr); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘processGFFfile’ at ali2gff.c:350:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 2034) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processGFFfile’: ali2gff.c:300:113: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 300 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", yName,xName,source,yb,xb,ye,xe,scores,strands,frames); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘processGFFfile’ at ali2gff.c:300:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 25 or more bytes (assuming 4028) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processGFFfile’: ali2gff.c:299:113: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 299 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",yName,xName,source,yb,xb,ye,xe,score,strands,frames); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘processGFFfile’ at ali2gff.c:299:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 2034) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processGFFfile’: ali2gff.c:296:113: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 296 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", yName,xName,source,yb,xb,ye,xe,scores,strands,frames,cptr); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘processGFFfile’ at ali2gff.c:296:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 25 or more bytes (assuming 4028) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processGFFfile’: ali2gff.c:295:113: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 295 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",yName,xName,source,yb,xb,ye,xe,score,strands,frames,cptr); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘processGFFfile’ at ali2gff.c:295:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 2034) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processMumfile’: ali2gff.c:732:40: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized] 732 | score = (score - errCount)/score; // match percentage | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:420:15: note: ‘score’ was declared here 420 | float score; | ^~~~~ ali2gff.c:840:67: warning: ‘fxb’ may be used uninitialized [-Wmaybe-uninitialized] 840 | fxe = fxb + flen - 1; | ~~~~^~~~~~ ali2gff.c:421:27: note: ‘fxb’ was declared here 421 | unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps | ^~~ ali2gff.c:841:67: warning: ‘fyb’ may be used uninitialized [-Wmaybe-uninitialized] 841 | fye = fyb + flen - 1; | ~~~~^~~~~~ ali2gff.c:421:37: note: ‘fyb’ was declared here 421 | unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps | ^~~ ali2gff.c: In function ‘processSimfile’: ali2gff.c:1064:36: warning: ‘xseqLen_4’ may be used uninitialized [-Wmaybe-uninitialized] 1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:997:27: note: ‘xseqLen_4’ was declared here 997 | unsigned long int xseqLen_4; /* length of x sequence -5 */ | ^~~~~~~~~ ali2gff.c:1064:62: warning: ‘yseqLen_4’ may be used uninitialized [-Wmaybe-uninitialized] 1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:998:27: note: ‘yseqLen_4’ was declared here 998 | unsigned long int yseqLen_4; /* length of y sequence -5 */ | ^~~~~~~~~ ali2gff.c: In function ‘main’: ali2gff.c:135:9: warning: ‘__builtin_strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation] 135 | strncpy(infile,argv[1],MAXSTRING); | ^ make[2]: Leaving directory '/<>/src/ali2gff' mkdir -p ./bin cp ./src/ali2gff/ali2gff \ ./bin/ali2gff mode of 'bin/gff2aplot.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/parseblast.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/blat2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/sim2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) make[1]: Leaving directory '/<>' dh_auto_test make -j2 test make[1]: Entering directory '/<>' ### SORRY !!! Tests were not implemented yet... make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/<>' for script in `find bin -name "*.pl"` ; do mv $script bin/`basename $script .pl` ; done make[1]: Leaving directory '/<>' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples # Fix path names, silence GS find debian/*/usr/share/doc/*/examples -name README -exec sed -i \ -e 's?^$BIN/\([0-9a-z]\+\)\.pl?\1?' \ -e 's?^$BIN/\([0-9a-z]\+\) ?\1 ?' \ -e 's?^GS=.*;?GS="gs -q" ;?' \{\} \; make[1]: Leaving directory '/<>' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gff2aplot' in '../gff2aplot_2.0-15_amd64.deb'. dpkg-deb: building package 'gff2aplot-dbgsym' in '../gff2aplot-dbgsym_2.0-15_amd64.deb'. dpkg-genbuildinfo -O../gff2aplot_2.0-15_amd64.buildinfo dpkg-genchanges -O../gff2aplot_2.0-15_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-09-15T05:25:32Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gff2aplot_2.0-15_amd64.changes: ------------------------------- Format: 1.8 Date: Mon, 05 Feb 2024 12:09:38 +0100 Source: gff2aplot Binary: gff2aplot gff2aplot-dbgsym Architecture: source amd64 Version: 2.0-15 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gff2aplot - pair-wise alignment-plots for genomic sequences in PostScript Closes: 1044834 Changes: gff2aplot (2.0-15) unstable; urgency=medium . * Fix clean target Closes: #1044834 * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 307f1a1e9442c1773b4dd26d5a839c21cbe03b1b 1136 gff2aplot_2.0-15.dsc 7f336c40811459aceb3ad0fbb2a81048732612a3 20764 gff2aplot_2.0-15.debian.tar.xz fe213fa9bbef8e17be24773e97c73da33a31c7a8 24928 gff2aplot-dbgsym_2.0-15_amd64.deb 584e6312affbc176ce2c037c072115df78516ef9 5254 gff2aplot_2.0-15_amd64.buildinfo c2721ce32a908ae6e64728163bd115fcc8accdc6 244080 gff2aplot_2.0-15_amd64.deb Checksums-Sha256: 3dc3e45f64cd26fbf1683b1805f93f2da0a7f2b544e8db7beab19a951d230530 1136 gff2aplot_2.0-15.dsc 341ed9d8a0f8cf26c7c28cfad34cdc49e59230d16d8dc6afd3b9ecfd2ad5cbe7 20764 gff2aplot_2.0-15.debian.tar.xz 0aa9558967ed05cbfa31de58eea18d4c6ed7ba0b246226fa926bc5bb52a21af4 24928 gff2aplot-dbgsym_2.0-15_amd64.deb 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+------------------------------------------------------------------------------+ gff2aplot-dbgsym_2.0-15_amd64.deb --------------------------------- new Debian package, version 2.0. size 24928 bytes: control archive=536 bytes. 375 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: gff2aplot-dbgsym Source: gff2aplot Version: 2.0-15 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 39 Depends: gff2aplot (= 2.0-15) Section: debug Priority: optional Description: debug symbols for gff2aplot Build-Ids: e0ca621910e1567b92ae801f10d98b9c9166a015 drwxr-xr-x root/root 0 2024-02-05 11:09 ./ drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/ drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/lib/ drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/lib/debug/.build-id/e0/ -rw-r--r-- root/root 29088 2024-02-05 11:09 ./usr/lib/debug/.build-id/e0/ca621910e1567b92ae801f10d98b9c9166a015.debug drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/share/ drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-02-05 11:09 ./usr/share/doc/gff2aplot-dbgsym -> gff2aplot gff2aplot_2.0-15_amd64.deb -------------------------- new Debian package, version 2.0. size 244080 bytes: control archive=3408 bytes. 2843 bytes, 49 lines control 5626 bytes, 66 lines md5sums Package: gff2aplot Version: 2.0-15 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1447 Depends: libc6 (>= 2.34), perl:any Recommends: graphicsmagick | imagemagick, ghostscript Suggests: postscript-viewer, gff2ps Section: science Priority: optional Homepage: https://genome.crg.es/software/gfftools/GFF2APLOT.html Description: pair-wise alignment-plots for genomic sequences in PostScript A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot: * Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets. * All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file. * Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement. * All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients. * Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes. * The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error. * gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape. * You can draw different alignments on same alignment plot and distinguish them by using different colors for each. * Shape dictionary has been expanded, so that further feature shapes are now available (see manual). * Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. 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Build-Space: 5240 Build-Time: 8 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 8 Job: /srv/debomatic/incoming/gff2aplot_2.0-15.dsc Machine Architecture: amd64 Package: gff2aplot Package-Time: 27 Source-Version: 2.0-15 Space: 5240 Status: successful Version: 2.0-15 -------------------------------------------------------------------------------- Finished at 2024-09-15T05:25:32Z Build needed 00:00:27, 5240k disk space