sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | bio-rainbow 2.0.4+dfsg-2 (amd64) Mon, 03 Jun 2024 00:01:15 +0000 | +==============================================================================+ Package: bio-rainbow Version: 2.0.4+dfsg-2 Source Version: 2.0.4+dfsg-2 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-2c0d5a64-519b-4698-9b46-99ecf1278776' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bio-rainbow_2.0.4+dfsg-2 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bio-rainbow_2.0.4+dfsg-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/bio-rainbow-nhW4TZ/resolver-ZkUqcK' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB] Hit:3 http://localhost:3142/debian unstable InRelease Hit:4 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/bio-rainbow_2.0.4+dfsg-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/bio-rainbow-nhW4TZ/bio-rainbow-2.0.4+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bio-rainbow-nhW4TZ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), help2man, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), help2man, 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 [627 B] Get:5 copy:/<>/apt_archive ./ Packages [659 B] Fetched 1895 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 help2man intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libicu72 liblocale-gettext-perl 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 help2man intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libicu72 liblocale-gettext-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB/19.3 MB of archives. After this operation, 74.5 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [888 B] Get:2 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:9 file:/srv/reprepro perl-5.40/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get:10 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-7 [95.9 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:12 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:13 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:14 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:15 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:16 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:17 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:20 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:23 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:24 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:25 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get:28 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:29 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:30 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:31 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:33 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] Get:34 http://localhost:3142/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.3 MB in 0s (149 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 21779 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... 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Setting up fakeroot (1.34-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-2) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40.1-7 bsdutils_1:2.40.1-7 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 help2man_1.49.3 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblkid1_2.40.1-7 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 libc-l10n_2.38-12 libc6_2.38-12 libc6-dev_2.38-12 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.15.3 libdpkg-perl_1.22.6 libeatmydata1_131-2 libelf1t64_0.191-1+b1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.2.0-25 libgcc-s1_14.1.0-1 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-4 libgomp1_14.1.0-1 libgpg-error0_1.49-2 libgprofng0_2.42-4 libhogweed6t64_3.9.1-2.2 libhwasan0_14.1.0-1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.1.0-1 libjansson4_2.14-2+b2 libksba8_1.6.6-1 libldap-2.5-0_2.5.17+dfsg-1+b1 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.1.0-1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.1-7 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.9.1-2.2 libnpth0t64_1.6-3.1 libp11-kit0_0.25.3-5 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~rc1-1 libpipeline1_1.5.7-2 libquadmath0_14.1.0-1 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b3 libsepol2_3.5-2+b1 libsframe1_2.42-4 libsmartcols1_2.40.1-7 libsqlite3-0_3.46.0-1 libssl3t64_3.2.1-3 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 libsystemd0_256~rc3-7 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-1 libubsan1_14.1.0-1 libuchardet0_0.0.8-1+b1 libudev1_256~rc3-7 libunistring5_1.2-1 libuuid1_2.40.1-7 libxml2_2.12.7+dfsg-2 libxxhash0_0.8.2-2+b1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.12-1 locales-all_2.38-12 login_1:4.13+dfsg1-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.13+dfsg1-4 patch_2.7.6-7 perl_5.40.0~rc1-1 perl-base_5.40.0~rc1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0~rc1-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.1-7 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bio-rainbow Binary: bio-rainbow Architecture: any Version: 2.0.4+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Pranav Ballaney Homepage: http://sourceforge.net/projects/bio-rainbow/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/bio-rainbow Vcs-Git: https://salsa.debian.org/med-team/bio-rainbow.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), help2man Package-List: bio-rainbow deb science optional arch=any Checksums-Sha1: 69aa7e1ad4254ee1f2aa3f4d62bb49be724654aa 58808 bio-rainbow_2.0.4+dfsg.orig.tar.xz 0167f4b007285a9c2f54f313a7a1c475aaebc0d5 14012 bio-rainbow_2.0.4+dfsg-2.debian.tar.xz Checksums-Sha256: a4e77785f8b5419d8d40aaa0b3b3fe48d3892793dec60049ca5074e43fe46b5e 58808 bio-rainbow_2.0.4+dfsg.orig.tar.xz 2ff6db13165339d6b52e13eea6ab32700a48c662d9409062a18cebe156836a36 14012 bio-rainbow_2.0.4+dfsg-2.debian.tar.xz Files: 9dcb2fb4e52a73ffe32c61f97921c8e0 58808 bio-rainbow_2.0.4+dfsg.orig.tar.xz cb7bb50a5910620b126226506cc13922 14012 bio-rainbow_2.0.4+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl9CvWsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG0WRAAjkL/JGdzH8Lv124xrTFM+K7v1nXRx+4S kjbW3pVRURp6XgXFRiJ47x1nknjpS6h7AO2MLQ1zLJ27CyIFdRsZSliH8T3afxIE wn17QfCIwmbYP8S/LMo0viD5xuB5C2LVj9Zncn1M05qacdecUgayX62YVOavQcyz V7CYc5ohABV7Fdq+0GKttEIOy/WSstj3vquHogjA7x0CI+THxPcpUhkmndx7aMFV gEJUm981/Y92LUkqGNHGZp9NGyq9EVHuOQYVZ/1pQI5R5iLJvBXDOYugM0NTRW+d asxNiLY3W0kpYQTkLcrk1kjJFA4EjUzT1Wq1ZZvXso+agEh8V+32ZuJmAIA6D163 YCYpwlk8/dpoOlnWqBv8tue9nm431troD1rHjyVg/1QdlQjvmmrpNPd8NdH7aFw8 X7P4ShZwU0EhAW0ysJi96R49ZpN6AnLNgP4O99EYj2eDe7im9OyOaF/EwXAWCwOf CO9g4d8Cms3WsCmSQySavDjqjgPBF/9yFwuya4PBmbjtOac5p/6wpHMlVUO2c/Uc RpRGvm8awZu7S0d4izN9ouHSOLdfekKZjxscHrLFNCgWK0EdnRuyPJGiCcDtFkgM ZadBsADFHUyO9+AzhE49D5Z3sDU3/nn+m3JEcwE38oLDHUQglaPsZtJybg38hHYz eyvo4OggmpE= =e4K2 -----END PGP SIGNATURE----- gpgv: Signature made Sun Aug 23 19:03:07 2020 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 ./bio-rainbow_2.0.4+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting bio-rainbow in /<> dpkg-source: info: unpacking bio-rainbow_2.0.4+dfsg.orig.tar.xz tar: Ignoring unknown extended header keyword 'LIBARCHIVE.creationtime' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' dpkg-source: info: unpacking bio-rainbow_2.0.4+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_hardening.patch dpkg-source: info: applying rename_binary.patch dpkg-source: info: applying spelling.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bio-rainbow_2.0.4+dfsg-2 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bio-rainbow_2.0.4+dfsg-2 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-2c0d5a64-519b-4698-9b46-99ecf1278776 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 bio-rainbow dpkg-buildpackage: info: source version 2.0.4+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pranav Ballaney dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/<>' rm -f *.o *.gcda *.gcno *.gcov gmon.out bio-rainbow rbasm ezmsim rbmergetag *.exe make[1]: Leaving directory '/<>' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bio-rainbow using existing ./bio-rainbow_2.0.4+dfsg.orig.tar.xz tar: Ignoring unknown extended header keyword 'LIBARCHIVE.creationtime' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' tar: Ignoring unknown extended header keyword 'SCHILY.dev' tar: Ignoring unknown extended header keyword 'SCHILY.ino' tar: Ignoring unknown extended header keyword 'SCHILY.nlink' dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bio-rainbow in bio-rainbow_2.0.4+dfsg-2.debian.tar.xz dpkg-source: info: building bio-rainbow in bio-rainbow_2.0.4+dfsg-2.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 '/<>' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 main.c -o main.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 divide.c -o divide.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 file_reader.c -o file_reader.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 asm_R2.c -o asm_R2.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 mergectg.c -o mergectg.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 cluster.c -o cluster.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 ezmsim.c -o ezmsim.o ezmsim.c: In function ‘LR_main’: ezmsim.c:440:33: warning: this statement may fall through [-Wimplicit-fallthrough=] 440 | case 'z': cut = strdup(optarg); | ^~~~~~~~~~~~~~ ezmsim.c:441:17: note: here 441 | case 'p': pos = atoi(optarg); | ^~~~ ezmsim.c: In function ‘EF_main’: ezmsim.c:707:33: warning: this statement may fall through [-Wimplicit-fallthrough=] 707 | case 'z': cut = strdup(optarg); | ^~~~~~~~~~~~~~ ezmsim.c:708:17: note: here 708 | case 'p': pos = atoi(optarg); | ^~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 rbasm_main.c -o rbasm_main.o At top level: cc1: note: unrecognized command-line option ‘-Wno-self-assign’ may have been intended to silence earlier diagnostics gcc -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -o bio-rainbow main.o divide.o file_reader.o asm_R2.o mergectg.o cluster.o -lm gcc -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -o ezmsim ezmsim.o -lm gcc -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -o rbasm asm_R2.o rbasm_main.o file_reader.o -lm make[1]: Leaving directory '/<>' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bio-rainbow/ dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/<>' # dh_installman is messing up .sh extension as language extension dh_install debian/mans/*.1 usr/share/man/man1 make[1]: Leaving directory '/<>' dh_lintian 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 'bio-rainbow' in '../bio-rainbow_2.0.4+dfsg-2_amd64.deb'. dpkg-deb: building package 'bio-rainbow-dbgsym' in '../bio-rainbow-dbgsym_2.0.4+dfsg-2_amd64.deb'. dpkg-genbuildinfo -O../bio-rainbow_2.0.4+dfsg-2_amd64.buildinfo dpkg-genchanges -O../bio-rainbow_2.0.4+dfsg-2_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 2024-06-03T00:01:37Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bio-rainbow_2.0.4+dfsg-2_amd64.changes: --------------------------------------- Format: 1.8 Date: Sun, 23 Aug 2020 05:32:47 +0530 Source: bio-rainbow Binary: bio-rainbow bio-rainbow-dbgsym Architecture: source amd64 Version: 2.0.4+dfsg-2 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pranav Ballaney Description: bio-rainbow - clustering and assembling short reads for bioinformatics Changes: bio-rainbow (2.0.4+dfsg-2) unstable; urgency=medium . [ Steffen Möller ] * Updated bio.tools ref * Added ref to conda . [ Pranav Ballaney ] * Install data for autopkgtests * Add autopkgtests * Install docs * Add Pranav Ballaney to Uploaders * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Remove trailing whitespace in debian/rules (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) Checksums-Sha1: b7031815225c5846773b5778140b4f5f23c25ed1 1186 bio-rainbow_2.0.4+dfsg-2.dsc d3e1d65747b7bacc0f33b6f8339b640d5a44696f 14020 bio-rainbow_2.0.4+dfsg-2.debian.tar.xz b53432628b358574f380f754df2d4c0460fe3217 176364 bio-rainbow-dbgsym_2.0.4+dfsg-2_amd64.deb 40db2f3daaca164301ac9785579ccceaba304c84 5319 bio-rainbow_2.0.4+dfsg-2_amd64.buildinfo b6e26ce1c2b9e8c9088d19d8a97f99d1ed8448a3 59916 bio-rainbow_2.0.4+dfsg-2_amd64.deb Checksums-Sha256: 04d9e35d886f55cd5d3e2d96518d60d2e2463d79c2335596cc68c52657985306 1186 bio-rainbow_2.0.4+dfsg-2.dsc 0099b9151c1fa68aa01f6116d968055705fca9bd4161ddfba7ebc1596516f6a9 14020 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+------------------------------------------------------------------------------+ Format: 1.0 Source: bio-rainbow Binary: bio-rainbow bio-rainbow-dbgsym Architecture: amd64 source Version: 2.0.4+dfsg-2 Checksums-Md5: 397abaf24d0e1880eb219f526657b0b8 1186 bio-rainbow_2.0.4+dfsg-2.dsc 78574dae4251ad95bf064848f5784bc1 176364 bio-rainbow-dbgsym_2.0.4+dfsg-2_amd64.deb c37203c572c48e55eb46d6137ef8bc6f 59916 bio-rainbow_2.0.4+dfsg-2_amd64.deb Checksums-Sha1: b7031815225c5846773b5778140b4f5f23c25ed1 1186 bio-rainbow_2.0.4+dfsg-2.dsc b53432628b358574f380f754df2d4c0460fe3217 176364 bio-rainbow-dbgsym_2.0.4+dfsg-2_amd64.deb b6e26ce1c2b9e8c9088d19d8a97f99d1ed8448a3 59916 bio-rainbow_2.0.4+dfsg-2_amd64.deb Checksums-Sha256: 04d9e35d886f55cd5d3e2d96518d60d2e2463d79c2335596cc68c52657985306 1186 bio-rainbow_2.0.4+dfsg-2.dsc 79d6eca05293fbd3060945a4f7c5724e1b22aa223a53bdaab1faea98a2563fd1 176364 bio-rainbow-dbgsym_2.0.4+dfsg-2_amd64.deb 51b5663c9c377d9669dca590504cb1dbb56f6a9dd08a5e0c877be0d3a9f67521 59916 bio-rainbow_2.0.4+dfsg-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 03 Jun 2024 00:01:37 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13.2), base-passwd (= 3.6.3), bash (= 5.2.21-2+b1), binutils (= 2.42-4), binutils-common (= 2.42-4), binutils-x86-64-linux-gnu (= 2.42-4), bsdextrautils (= 2.40.1-7), bsdutils (= 1:2.40.1-7), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), grep (= 3.11-4), groff-base (= 1.23.0-4), gzip (= 1.12-1.1), help2man (= 1.49.3), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.1.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-4), libblkid1 (= 2.40.1-7), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), libc6-dev (= 2.38-12), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.1.0-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4), libctf0 (= 2.42-4), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.15.3), libdpkg-perl (= 1.22.6), libelf1t64 (= 0.191-1+b1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.2.0-25), libgcc-s1 (= 14.1.0-1), libgdbm-compat4t64 (= 1.23-5.1+b1), libgdbm6t64 (= 1.23-5.1+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.1.0-1), libgprofng0 (= 2.42-4), libhwasan0 (= 14.1.0-1), libicu72 (= 72.1-4+b1), libisl23 (= 0.26-3+b2), libitm1 (= 14.1.0-1), libjansson4 (= 2.14-2+b2), liblocale-gettext-perl (= 1.07-7+b1), liblsan0 (= 14.1.0-1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.1-7), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), 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), libperl5.40 (= 5.40.0~rc1-1), libpipeline1 (= 1.5.7-2), libquadmath0 (= 14.1.0-1), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2+b2), libsframe1 (= 2.42-4), libsmartcols1 (= 2.40.1-7), libssl3t64 (= 3.2.1-3), libstdc++-13-dev (= 13.2.0-25), libstdc++6 (= 14.1.0-1), libsystemd0 (= 256~rc3-7), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.1.0-1), libubsan1 (= 14.1.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256~rc3-7), libunistring5 (= 1.2-1), libuuid1 (= 2.40.1-7), libxml2 (= 2.12.7+dfsg-2), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.12-1), login (= 1:4.13+dfsg1-4), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), patch (= 2.7.6-7), perl (= 5.40.0~rc1-1), perl-base (= 5.40.0~rc1-1), perl-modules-5.40 (= 5.40.0~rc1-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.09-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.1-7), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1598140967" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bio-rainbow-dbgsym_2.0.4+dfsg-2_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 176364 bytes: control archive=692 bytes. 478 bytes, 12 lines control 406 bytes, 4 lines md5sums Package: bio-rainbow-dbgsym Source: bio-rainbow Version: 2.0.4+dfsg-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 208 Depends: bio-rainbow (= 2.0.4+dfsg-2) Section: debug Priority: optional Description: debug symbols for bio-rainbow Build-Ids: 1deb3020e136438951ae3e344167a0728863f252 34d12e5464286bda5dd4414f8b380e8611fbc884 f615e7a365a7ffa5f7e59f7f61a6ed155b486dbb drwxr-xr-x root/root 0 2020-08-23 00:02 ./ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/lib/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/lib/debug/.build-id/1d/ -rw-r--r-- root/root 25592 2020-08-23 00:02 ./usr/lib/debug/.build-id/1d/eb3020e136438951ae3e344167a0728863f252.debug drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/lib/debug/.build-id/34/ -rw-r--r-- root/root 115408 2020-08-23 00:02 ./usr/lib/debug/.build-id/34/d12e5464286bda5dd4414f8b380e8611fbc884.debug drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/lib/debug/.build-id/f6/ -rw-r--r-- root/root 49760 2020-08-23 00:02 ./usr/lib/debug/.build-id/f6/15e7a365a7ffa5f7e59f7f61a6ed155b486dbb.debug drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 6520 2020-08-23 00:02 ./usr/lib/debug/.dwz/x86_64-linux-gnu/bio-rainbow.debug drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-08-23 00:02 ./usr/share/doc/bio-rainbow-dbgsym -> bio-rainbow bio-rainbow_2.0.4+dfsg-2_amd64.deb ---------------------------------- new Debian package, version 2.0. size 59916 bytes: control archive=1704 bytes. 1361 bytes, 26 lines control 1642 bytes, 23 lines md5sums Package: bio-rainbow Version: 2.0.4+dfsg-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 186 Depends: libc6 (>= 2.34), perl:any Section: science Priority: optional Homepage: http://sourceforge.net/projects/bio-rainbow/ Description: clustering and assembling short reads for bioinformatics Efficient tool for clustering and assembling short reads, especially for RAD. . Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top-down manner. long a guided tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, it is shown that Rainbow is more competent than the other tools in dealing with RAD-seq data. drwxr-xr-x root/root 0 2020-08-23 00:02 ./ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/bin/ -rwxr-xr-x root/root 80120 2020-08-23 00:02 ./usr/bin/bio-rainbow -rwxr-xr-x root/root 27200 2020-08-23 00:02 ./usr/bin/ezmsim -rwxr-xr-x root/root 39152 2020-08-23 00:02 ./usr/bin/rbasm -rwxr-xr-x root/root 427 2015-07-27 18:28 ./usr/bin/select_all_rbcontig.pl -rwxr-xr-x root/root 535 2015-07-27 18:28 ./usr/bin/select_best_rbcontig.pl -rwxr-xr-x root/root 1597 2015-07-27 18:28 ./usr/bin/select_best_rbcontig_plus_read1.pl -rwxr-xr-x root/root 872 2015-07-27 18:28 ./usr/bin/select_sec_rbcontig.pl drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/ -rw-r--r-- root/root 86 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/README.Debian -rw-r--r-- root/root 731 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/README.test -rw-r--r-- root/root 1932 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/README.txt.gz -rw-r--r-- root/root 717 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/changelog.Debian.gz -rw-r--r-- root/root 1869 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/copyright drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/examples/ -rw-r--r-- root/root 3321 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/examples/R.1.fastq.gz -rw-r--r-- root/root 3568 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/examples/R.2.fastq.gz -rw-r--r-- root/root 842 2020-08-23 00:02 ./usr/share/doc/bio-rainbow/run-unit-test drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 121 2020-08-23 00:02 ./usr/share/lintian/overrides/bio-rainbow drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/man/ drwxr-xr-x root/root 0 2020-08-23 00:02 ./usr/share/man/man1/ -rw-r--r-- root/root 928 2020-08-23 00:02 ./usr/share/man/man1/bio-rainbow.1.gz -rw-r--r-- root/root 405 2020-08-23 00:02 ./usr/share/man/man1/ezmsim.1.gz -rw-r--r-- root/root 439 2020-08-23 00:02 ./usr/share/man/man1/rbasm.1.gz -rw-r--r-- root/root 315 2020-08-23 00:02 ./usr/share/man/man1/select_all_rbcontig.pl.1.gz -rw-r--r-- root/root 316 2020-08-23 00:02 ./usr/share/man/man1/select_best_rbcontig.pl.1.gz -rw-r--r-- root/root 348 2020-08-23 00:02 ./usr/share/man/man1/select_best_rbcontig_plus_read1.pl.1.gz -rw-r--r-- root/root 317 2020-08-23 00:02 ./usr/share/man/man1/select_sec_rbcontig.pl.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 2772 Build-Time: 10 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 5 Job: /srv/debomatic/incoming/bio-rainbow_2.0.4+dfsg-2.dsc Machine Architecture: amd64 Package: bio-rainbow Package-Time: 22 Source-Version: 2.0.4+dfsg-2 Space: 2772 Status: successful Version: 2.0.4+dfsg-2 -------------------------------------------------------------------------------- Finished at 2024-06-03T00:01:37Z Build needed 00:00:22, 2772k disk space