sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | any2fasta 0.4.2-2 (amd64) Sat, 14 Sep 2024 21:09:55 +0000 | +==============================================================================+ Package: any2fasta Version: 0.4.2-2 Source Version: 0.4.2-2 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-b57cb2f9-8c94-405e-b33c-f50ae8274113' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup any2fasta_0.4.2-2 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup any2fasta_0.4.2-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/any2fasta-dKqRN6/resolver-L0vtVD' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://deb.debian.org/debian unstable InRelease [202 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [17.4 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [17.4 kB] Get:5 http://localhost:3142/debian sid InRelease [202 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [21.2 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [21.2 kB] Fetched 570 kB in 6s (94.2 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 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/any2fasta_0.4.2-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/any2fasta-dKqRN6/any2fasta-0.4.2' with '<>' I: NOTICE: Log filtering will replace 'build/any2fasta-dKqRN6' 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 [880 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 (131 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 22986 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../31-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.36-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up fakeroot (1.36-1) ... 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 (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+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 (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | 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 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+------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network any2fasta_0.4.2-2 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network any2fasta_0.4.2-2 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-b57cb2f9-8c94-405e-b33c-f50ae8274113 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 any2fasta dpkg-buildpackage: info: source version 0.4.2-2 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 dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building any2fasta using existing ./any2fasta_0.4.2.orig.tar.gz dpkg-source: info: building any2fasta in any2fasta_0.4.2-2.debian.tar.xz dpkg-source: info: building any2fasta in any2fasta_0.4.2-2.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'any2fasta' in '../any2fasta_0.4.2-2_all.deb'. dpkg-deb: building package 'any2fasta-examples' in '../any2fasta-examples_0.4.2-2_all.deb'. dpkg-genbuildinfo -O../any2fasta_0.4.2-2_amd64.buildinfo dpkg-genchanges -O../any2fasta_0.4.2-2_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 2024-09-14T21:10:31Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ any2fasta_0.4.2-2_amd64.changes: -------------------------------- Format: 1.8 Date: Sat, 07 Jan 2023 17:02:41 +0100 Source: any2fasta Binary: any2fasta any2fasta-examples Architecture: source all Version: 0.4.2-2 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: any2fasta - convert various sequence formats to FASTA any2fasta-examples - convert various sequence formats to FASTA (example data) Changes: any2fasta (0.4.2-2) unstable; urgency=medium . * Standards-Version: 4.6.2 (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse. 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6509616 any2fasta-examples_0.4.2-2_all.deb 6d7a71254d0bfc9ae4102f6e7fa54ea8edc3539d 6232 any2fasta_0.4.2-2_all.deb Checksums-Sha256: 7ccca571778d1339fc6bdb5423c3cd9916dee6bc8117160aa1bdfb63d49b7f61 1138 any2fasta_0.4.2-2.dsc 7345afc5878efe867285622415a0ba70b9c32bbd57849df63c4600217c4502f9 6509616 any2fasta-examples_0.4.2-2_all.deb 5d5a205de7ba5317232647d833a1354bc6d3d60228545dcf3fe593be7a3abc76 6232 any2fasta_0.4.2-2_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 14 Sep 2024 21:10:31 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: 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 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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), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), 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) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1673107361" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ any2fasta-examples_0.4.2-2_all.deb ---------------------------------- new Debian package, version 2.0. size 6509616 bytes: control archive=1412 bytes. 1464 bytes, 37 lines control 1029 bytes, 13 lines md5sums Package: any2fasta-examples Source: any2fasta Version: 0.4.2-2 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 6373 Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/tseemann/any2fasta Description: convert various sequence formats to FASTA (example data) Established tools like readseq and seqret from EMBOSS, both create mangled IDs containing | or . characters, and there is no way to fix this behaviour. This resultes in inconsitences between .gbk and .fna versions of files in pipelines. . This script uses only core Perl modules, has no other dependencies like Bioperl or Biopython, and runs very quickly. . It supports the following input formats: . 1. Genbank flat file, typically .gb, .gbk, .gbff (starts with LOCUS) 2. EMBL flat file, typically .embl, (starts with ID) 3. GFF with sequence, typically .gff, .gff3 (starts with ##gff) 4. FASTA DNA, typically .fasta, .fa, .fna, .ffn (starts with >) 5. FASTQ DNA, typically .fastq, .fq (starts with @) 6. CLUSTAL alignments, typically .clw, .clu (starts with CLUSTAL or MUSCLE) 7. STOCKHOLM alignments, typically .sth (starts with # STOCKHOLM) 8. GFA assembly graph, typically .gfa (starts with ^[A-Z]\t) . Files may be compressed with: . 1. gzip, typically .gz 2. bzip2, typically .bz2 3. zip, typically .zip . This package contains some example data for testing. drwxr-xr-x root/root 0 2023-01-07 16:02 ./ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/share/ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/share/doc/any2fasta-examples/ -rw-r--r-- root/root 278 2023-01-07 16:02 ./usr/share/doc/any2fasta-examples/README.test -rw-r--r-- root/root 268 2023-01-07 16:02 ./usr/share/doc/any2fasta-examples/changelog.Debian.gz -rw-r--r-- root/root 871 2023-01-07 16:02 ./usr/share/doc/any2fasta-examples/copyright -rw-r--r-- root/root 573 2023-01-07 16:02 ./usr/share/doc/any2fasta-examples/run-unit-test drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/share/doc/any2fasta/ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/share/doc/any2fasta/examples/ -rw-r--r-- root/root 619 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.clw -rw-r--r-- root/root 3610 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.embl -rw-r--r-- root/root 17854 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.fna.gz -rw-r--r-- root/root 176153 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.fq.gz -rw-r--r-- root/root 3071491 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.gbk.gz -rw-r--r-- root/root 1570339 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.gfa.gz -rw-r--r-- root/root 1665133 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.gff.gz -rw-r--r-- root/root 1960 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.noseq.gff -rw-r--r-- root/root 1106 2018-10-18 04:07 ./usr/share/doc/any2fasta/examples/test.sth any2fasta_0.4.2-2_all.deb ------------------------- new Debian package, version 2.0. size 6232 bytes: control archive=1136 bytes. 1381 bytes, 35 lines control 266 bytes, 4 lines md5sums Package: any2fasta Version: 0.4.2-2 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 21 Depends: perl:any Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/tseemann/any2fasta Description: convert various sequence formats to FASTA Established tools like readseq and seqret from EMBOSS, both create mangled IDs containing | or . characters, and there is no way to fix this behaviour. This resultes in inconsitences between .gbk and .fna versions of files in pipelines. . This script uses only core Perl modules, has no other dependencies like Bioperl or Biopython, and runs very quickly. . It supports the following input formats: . 1. Genbank flat file, typically .gb, .gbk, .gbff (starts with LOCUS) 2. EMBL flat file, typically .embl, (starts with ID) 3. GFF with sequence, typically .gff, .gff3 (starts with ##gff) 4. FASTA DNA, typically .fasta, .fa, .fna, .ffn (starts with >) 5. FASTQ DNA, typically .fastq, .fq (starts with @) 6. CLUSTAL alignments, typically .clw, .clu (starts with CLUSTAL or MUSCLE) 7. STOCKHOLM alignments, typically .sth (starts with # STOCKHOLM) 8. GFA assembly graph, typically .gfa (starts with ^[A-Z]\t) . Files may be compressed with: . 1. gzip, typically .gz 2. bzip2, typically .bz2 3. zip, typically .zip drwxr-xr-x root/root 0 2023-01-07 16:02 ./ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/bin/ -rwxr-xr-x root/root 7724 2023-01-07 16:02 ./usr/bin/any2fasta drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/share/ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-01-07 16:02 ./usr/share/doc/any2fasta/ -rw-r--r-- root/root 3840 2018-10-18 04:07 ./usr/share/doc/any2fasta/README.md -rw-r--r-- root/root 268 2023-01-07 16:02 ./usr/share/doc/any2fasta/changelog.Debian.gz -rw-r--r-- root/root 871 2023-01-07 16:02 ./usr/share/doc/any2fasta/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 36008 Build-Time: 20 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 6 Job: /srv/debomatic/incoming/any2fasta_0.4.2-2.dsc Machine Architecture: amd64 Package: any2fasta Package-Time: 36 Source-Version: 0.4.2-2 Space: 36008 Status: successful Version: 0.4.2-2 -------------------------------------------------------------------------------- Finished at 2024-09-14T21:10:31Z Build needed 00:00:36, 36008k disk space