sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | cct 1:1.0.3-1 (amd64) Sat, 14 Sep 2024 23:17:27 +0000 | +==============================================================================+ Package: cct Version: 1:1.0.3-1 Source Version: 1:1.0.3-1 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-59eba5cb-6788-4f79-8215-fe914577d85d' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup cct_1.0.3-1 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup cct_1.0.3-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/cct-groCyV/resolver-0H2uGZ' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://localhost:3142/debian sid InRelease [202 kB] Get:3 http://deb.debian.org/debian unstable InRelease [202 kB] Get:4 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian sid/main Sources T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [21.2 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 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://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:7 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] Fetched 570 kB in 6s (89.1 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/cct_1.0.3-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/cct-groCyV/cct-1.0.3' with '<>' I: NOTICE: Log filtering will replace 'build/cct-groCyV' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), debhelper, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), debhelper, 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 [628 B] Get:5 copy:/<>/apt_archive ./ Packages [660 B] Fetched 1897 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 (153 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 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: SHA256 Format: 3.0 (quilt) Source: cct Binary: cct, cct-examples Architecture: all Version: 1:1.0.3-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://stothard.afns.ualberta.ca/downloads/CCT/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/cct Vcs-Git: https://salsa.debian.org/med-team/cct.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), debhelper Package-List: cct deb science optional arch=all cct-examples deb science optional arch=all Checksums-Sha1: 588f561c9cc4faaad979fbf1c225b681d5f978e0 81734736 cct_1.0.3.orig.tar.xz 06ace14e2579172379e7318292881d5a2ca8af49 11652 cct_1.0.3-1.debian.tar.xz Checksums-Sha256: e0f4d56ccf25843530e9386b2daab97ea02bd00b60df348082be3b921dd8edc7 81734736 cct_1.0.3.orig.tar.xz c04e1b0c8f90dbec3a39d0551f4e45ffd07809d1feb04fee0818c7ae204c6159 11652 cct_1.0.3-1.debian.tar.xz Files: 8d4d1b9f70e70a6d01e3d8d8b90c8eda 81734736 cct_1.0.3.orig.tar.xz 3f88301874c53e545f9585c61dd1dcd9 11652 cct_1.0.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHkNZYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEJLA/+LLgT+bQwoSPjRyaAwhB7F4X2NFCZlp7+ D3l1ruKpT5oJXjpORgW4cknpOuaVH+VvZLxCMMNb9/E231ZqvahFOKf1sC0Xv4KN v5UkVaFEmHOKhAnJKwEGhBgha9hnG9i17d9HAJ7hyZ3f/CILAZMjVR1btmjUwK26 Qev/j+J5fn5YHaS2U/iN9M38xD+It0kQKfKpgbapHJAmwwazhNLJIVDPmWNn4uE2 5SLLI+Vd5hll5MqT0uuMCcLDq3EYrNMAsso8I29aR7i39QmgrU1FDvQDQpi7Vd7c mzgJwVFoCEM22qxyysniNbejffYinSuajOs/OULGmN0dJi/FhM7cNAVqb+Ftf13q ihqogWXfF7x0Sbf44RT6ZFbxrXSrK1FnimyLj/8TgHh15oKclU+lRBH9/mr4x9Qa 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space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network cct_1.0.3-1 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network cct_1.0.3-1 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-59eba5cb-6788-4f79-8215-fe914577d85d 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 cct dpkg-buildpackage: info: source version 1:1.0.3-1 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 cct using existing ./cct_1.0.3.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building cct in cct_1.0.3-1.debian.tar.xz dpkg-source: info: building cct in cct_1.0.3-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install mkdir -p debian/cct/usr/bin for scr in debian/cct/usr/share/cct/scripts/*.sh ; do \ binscr=`basename ${scr} .sh` ; \ ln -s /usr/share/cct/scripts/generic debian/cct/usr/bin/${binscr} ; \ done for scr in debian/cct/usr/share/cct/scripts/*.pl ; do \ binscr=`basename ${scr} .pl` ; \ ln -s /usr/share/cct/scripts/generic debian/cct/usr/bin/${binscr} ; \ done ln -s /etc/cct debian/cct/usr/share/cct/conf # Move "hidden" examples into example package for sample in `find debian -type d \( -name "sample_output" -o -name "test_input" \)` ; do \ base=`dirname ${sample} | sed 's#debian/cct#debian/cct-examples#'` ; \ mkdir -p ${base} ; \ mv ${sample} ${base} ; \ done for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/cct/usr/bin/fetch_all_refseq_chloroplast_genomes: No such file or directory grep: debian/cct/usr/bin/create_zoomed_maps: No such file or directory grep: debian/cct/usr/bin/fetch_refseq_bacterial_genomes_by_name: No such file or directory grep: debian/cct/usr/bin/build_blast_atlas: No such file or directory grep: debian/cct/usr/bin/cgview_comparison_tool: No such file or directory grep: debian/cct/usr/bin/build_blast_atlas_all_vs_all: No such file or directory grep: debian/cct/usr/bin/fetch_all_refseq_bacterial_genomes: No such file or directory grep: debian/cct/usr/bin/fetch_genome_by_accession: No such file or directory grep: debian/cct/usr/bin/redraw_maps: No such file or directory grep: debian/cct/usr/bin/process_test_projects: No such file or directory grep: debian/cct/usr/bin/process_sample_projects: No such file or directory grep: debian/cct/usr/bin/remove_long_seqs: No such file or directory grep: debian/cct/usr/bin/ncbi_search: No such file or directory grep: debian/cct/usr/bin/convert_vcf_to_features: No such file or directory grep: debian/cct/usr/bin/check_env: No such file or directory grep: debian/cct/usr/bin/fetch_all_refseq_mitochondrial_genomes: No such file or directory grep: debian/cct/usr/bin/build_cog_db: No such file or directory grep: debian/cct/usr/bin/remove_short_seqs: No such file or directory grep: debian/cct/usr/share/cct/conf: No such file or directory make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package cct-examples: substitution variable ${perl:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'cct' in '../cct_1.0.3-1_all.deb'. dpkg-deb: building package 'cct-examples' in '../cct-examples_1.0.3-1_all.deb'. dpkg-genbuildinfo -O../cct_1.0.3-1_amd64.buildinfo dpkg-genchanges -O../cct_1.0.3-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2024-09-14T23:19:22Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ cct_1.0.3-1_amd64.changes: -------------------------- Format: 1.8 Date: Sun, 16 Jan 2022 14:49:39 +0100 Source: cct Binary: cct cct-examples Architecture: source all Version: 1:1.0.3-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: cct - visually comparing bacterial, plasmid, chloroplast, or mitochondr cct-examples - example data for testing the package cct Changes: cct (1:1.0.3-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.0 (routine-update) * Add missing build dependency on dh addon. 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691ae8ea4e70d717c5d2e6c7c07cd5609dd12b948c70d00fd6e6c2d65e9ac097 5193 cct_1.0.3-1_amd64.buildinfo Files: a611d387bd4a9a0f28326ed87b9a2f3a 1089 science optional cct_1.0.3-1.dsc 8d4d1b9f70e70a6d01e3d8d8b90c8eda 81734736 science optional cct_1.0.3.orig.tar.xz 940baee815d36e6c9cdbea8601766c4c 11660 science optional cct_1.0.3-1.debian.tar.xz 934e5ef0d225aed86469485591e5ca46 41893420 science optional cct-examples_1.0.3-1_all.deb 854cf2bf37b23680c4c46e8c0cdbbddb 36332456 science optional cct_1.0.3-1_all.deb 1b8ad2c2fcf0352cb2f284fca7c46a41 5193 science optional cct_1.0.3-1_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: cct Binary: cct cct-examples Architecture: all source Version: 1:1.0.3-1 Checksums-Md5: a611d387bd4a9a0f28326ed87b9a2f3a 1089 cct_1.0.3-1.dsc 934e5ef0d225aed86469485591e5ca46 41893420 cct-examples_1.0.3-1_all.deb 854cf2bf37b23680c4c46e8c0cdbbddb 36332456 cct_1.0.3-1_all.deb Checksums-Sha1: 15d1468df2f30f1233b538b585d7fa3e30104372 1089 cct_1.0.3-1.dsc d26c7c8b827768189a551a31b07ad56bd620d37e 41893420 cct-examples_1.0.3-1_all.deb 4869bdb782ad28ddfb156caf4858a528a4d1507f 36332456 cct_1.0.3-1_all.deb Checksums-Sha256: 0eb3cb1bc37bd281c75f81029e78f9cbd6a083280f204788fe4d5810cbfcb8da 1089 cct_1.0.3-1.dsc 29c7870dca5d64f62f755befed4f210b8c37a9204956ffc4d7b04ef3c1653a1a 41893420 cct-examples_1.0.3-1_all.deb 91b3d1f45d3dcc3e0f8253f0835b60c660cb94eae3342fc0c5fda435ac60dfbe 36332456 cct_1.0.3-1_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 14 Sep 2024 23:19:21 +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 (= 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), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-3), g++ (= 4:14.1.0-2), 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), 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), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-4), 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), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-2), libc-dev-bin (= 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), libelf1t64 (= 0.191-2), 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), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-4), libgprofng0 (= 2.43.1-4), libhwasan0 (= 14.2.0-4), libicu72 (= 72.1-5), libisl23 (= 0.27-1), libitm1 (= 14.2.0-4), libjansson4 (= 2.14-2+b2), liblsan0 (= 14.2.0-4), 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), 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 (= 5.40.0-5), libpipeline1 (= 1.5.8-1), libquadmath0 (= 14.2.0-4), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-4), libsmartcols1 (= 2.40.2-8), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-4), libstdc++6 (= 14.2.0-4), libsystemd0 (= 256.6-1), 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), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.9-1), 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), 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="1642340979" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ cct-examples_1.0.3-1_all.deb ---------------------------- new Debian package, version 2.0. size 41893420 bytes: control archive=4072 bytes. 1558 bytes, 30 lines control 14888 bytes, 128 lines md5sums Package: cct-examples Source: cct Version: 1:1.0.3-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 101295 Depends: bioperl, cgview Section: science Priority: optional Homepage: http://stothard.afns.ualberta.ca/downloads/CCT/ Description: example data for testing the package cct The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation. . This package provides the data which can be used as example. These are the same data as used in autopkgtest. drwxr-xr-x root/root 0 2022-01-16 13:49 ./ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/assign_cogs/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/ -rw-r--r-- root/root 202 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_1.gff -rw-r--r-- root/root 1496 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_1b.gff -rw-r--r-- root/root 826 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_2.gff -rw-r--r-- root/root 1401 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_2b.gff drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/test_input/ -rw-r--r-- root/root 14693 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/test_input/sample_1.gbk -rw-r--r-- root/root 5869 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/test_input/sample_2.fna drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/cgview_xml_builder/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/ -rw-r--r-- root/root 38162 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/R_denitrificans.cogs -rw-r--r-- root/root 8823242 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/R_denitrificans.gbk -rw-r--r-- root/root 80 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/labels_to_show.txt -rw-r--r-- root/root 13715306 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/prokka_multicontig.gbk drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/convert_vcf_to_features/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/ -rw-r--r-- root/root 164 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_20 -rw-r--r-- root/root 164 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_20.tab -rw-r--r-- root/root 132 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_21 -rw-r--r-- root/root 132 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_21.tab -rw-r--r-- root/root 164 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_single_chromosome_20 -rw-r--r-- root/root 164 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_single_chromosome_20.tab drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/ -rw-r--r-- root/root 1563 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/input_multiple_chromosomes.vcf -rw-r--r-- root/root 1353 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/input_single_chromosome.vcf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/get_cds/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/ -rw-r--r-- root/root 1525633 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/R_denitrificans.cds.faa -rw-r--r-- root/root 4140742 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/R_denitrificans.cds.fna -rw-r--r-- root/root 2329771 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/prokka_multicontig.cds.faa -rw-r--r-- root/root 6252922 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/prokka_multicontig.cds.fna drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/test_input/ -rw-r--r-- root/root 8823242 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/test_input/R_denitrificans.gbk -rw-r--r-- root/root 13715306 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/test_input/prokka_multicontig.gbk drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/get_orfs/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/ -rw-r--r-- root/root 77986 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/R_denitrificans.orfs.faa -rw-r--r-- root/root 228506 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/R_denitrificans.orfs.fna -rw-r--r-- root/root 181045 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/prokka_multicontig.orfs.faa -rw-r--r-- root/root 530920 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/prokka_multicontig.orfs.fna drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/test_input/ -rw-r--r-- root/root 8823242 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/test_input/R_denitrificans.gbk -rw-r--r-- root/root 13715306 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/test_input/prokka_multicontig.gbk drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/local_blast_client/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/ -rw-r--r-- root/root 1500 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastn.txt -rw-r--r-- root/root 1380 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastp.txt -rw-r--r-- root/root 2537 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastx.txt -rw-r--r-- root/root 1582 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_tblastn.txt -rw-r--r-- root/root 6262 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_tblastx.txt drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/ -rw-r--r-- root/root 2997 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/test_dna_database.fasta -rw-r--r-- root/root 1365 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/test_input_dna.fasta -rw-r--r-- root/root 406 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/test_input_protein.fasta -rw-r--r-- root/root 1019 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/test_protein_database.fasta drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/ncbi_search/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/sample_output/ -rw-r--r-- root/root 276500 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/sample_output/NC_009933.gbk -rw-r--r-- root/root 8301 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/sample_output/NC_009934.gbk -rw-r--r-- root/root 284801 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/sample_output/combined.gbk drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/ -rw-r--r-- root/root 1696 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output1.fasta -rw-r--r-- root/root 1059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output2.fasta -rw-r--r-- root/root 1059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output3.fasta -rw-r--r-- root/root 1059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq.fasta -rw-r--r-- root/root 2059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi.fasta -rw-r--r-- root/root 3357 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi_s100_v5.fasta -rw-r--r-- root/root 2059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi_v5.fasta -rw-r--r-- root/root 1696 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_s100_v5.fasta -rw-r--r-- root/root 1059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_v5.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/ -rw-r--r-- root/root 1034 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/test_seq.fasta -rw-r--r-- root/root 2068 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/test_seq_multi.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/ -rw-r--r-- root/root 383 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/match_end_of_orf.fasta -rw-r--r-- root/root 392 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/match_end_of_orf_rev_comp.fasta -rw-r--r-- root/root 324 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/match_start_of_orf.fasta -rw-r--r-- root/root 333 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/match_start_of_orf_rev_comp.fasta -rw-r--r-- root/root 667 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/reference_genome/ -rw-r--r-- root/root 16317 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/comparison_genomes/ -rw-r--r-- root/root 392 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/comparison_genomes/match_end_of_orf.fasta -rw-r--r-- root/root 324 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/comparison_genomes/match_start_of_orf.fasta -rw-r--r-- root/root 7997 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/reference_genome/ -rw-r--r-- root/root 16317 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/comparison_genomes/ -rw-r--r-- root/root 392 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/comparison_genomes/match_end_of_orf.fasta -rw-r--r-- root/root 324 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/comparison_genomes/match_start_of_orf.fasta -rw-r--r-- root/root 660 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/reference_genome/ -rw-r--r-- root/root 16317 2022-01-06 22:27 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new Debian package, version 2.0. size 36332456 bytes: control archive=3008 bytes. 182 bytes, 5 lines conffiles 1567 bytes, 26 lines control 5454 bytes, 66 lines md5sums Package: cct Version: 1:1.0.3-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 35963 Depends: perl:any, bioperl, cgview, ncbi-blast+-legacy, imagemagick | graphicsmagick, liberror-perl, libtie-ixhash-perl, libwww-perl Section: science Priority: optional Homepage: http://stothard.afns.ualberta.ca/downloads/CCT/ Description: visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation. drwxr-xr-x root/root 0 2022-01-16 13:49 ./ drwxr-xr-x root/root 0 2022-01-16 13:49 ./etc/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./etc/cct/ -rw-r--r-- root/root 1512 2022-01-16 13:49 ./etc/cct/global_settings.conf -rw-r--r-- root/root 7302 2022-01-06 22:27 ./etc/cct/project_settings.conf -rw-r--r-- root/root 7315 2022-01-06 22:27 ./etc/cct/project_settings_cds_vs_cds.conf -rw-r--r-- root/root 7330 2022-01-06 22:27 ./etc/cct/project_settings_dna_vs_dna.conf -rw-r--r-- root/root 7313 2022-01-06 22:27 ./etc/cct/project_settings_multi.conf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/bin/ lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/build_blast_atlas -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/build_blast_atlas_all_vs_all -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 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./usr/bin/fetch_refseq_bacterial_genomes_by_name -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/ncbi_search -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/process_sample_projects -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/process_test_projects -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/redraw_maps -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/remove_long_seqs -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/remove_short_seqs -> ../share/cct/scripts/generic drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/ lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/share/cct/conf -> /etc/cct drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ 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+------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 488892 Build-Time: 97 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 4 Job: /srv/debomatic/incoming/cct_1.0.3-1.dsc Machine Architecture: amd64 Package: cct Package-Time: 115 Source-Version: 1:1.0.3-1 Space: 488892 Status: successful Version: 1:1.0.3-1 -------------------------------------------------------------------------------- Finished at 2024-09-14T23:19:22Z Build needed 00:01:55, 488892k disk space