sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | stacks 2.68+dfsg-1 (amd64) Sat, 31 Aug 2024 16:02:09 +0000 | +==============================================================================+ Package: stacks Version: 2.68+dfsg-1 Source Version: 2.68+dfsg-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-1b5ff6c9-3b37-4dec-a9aa-b84790c783d8' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup stacks_2.68+dfsg-1 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup stacks_2.68+dfsg-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/stacks-MCL23P/resolver-0prnn7' 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] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://localhost:3142/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/stacks_2.68+dfsg-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/stacks-MCL23P/stacks-2.68+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-MCL23P' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, 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 [682 B] Get:5 copy:/<>/apt_archive ./ Packages [714 B] Fetched 2005 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 libbam-dev libbrotli-dev libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libsparsehash-dev libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf samtools sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-doc krb5-user liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl cwltool Recommended packages: curl | wget | lynx ca-certificates libarchive-cpio-perl krb5-locales libgpm2 publicsuffix libtasn1-doc 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 libbam-dev libbrotli-dev libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libsparsehash-dev libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf samtools sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 37.1 MB of archives. After this operation, 133 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 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 2.40.2-7 [96.8 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] Get:33 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b4 [313 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:41 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.62.1-2 [74.9 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.9.1-2 [470 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.20.0-1+b1 [583 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.6-2 [439 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2 [439 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2 [123 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2 [208 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b2 [98.0 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1 [1316 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.6-2 [1381 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.62.1-2 [115 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.4.0-1 [86.5 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1 [77.4 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b4 [67.7 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.1-7 [2741 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.0-7 [357 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [368 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.9.1-2 [582 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.21-1 [55.8 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-2 [299 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 37.1 MB in 0s (112 MB/s) Selecting previously unselected package sensible-utils. 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Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libfakeroot:amd64 (1.36-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libpsl-dev:amd64 (0.21.2-1.1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... 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 libunbound8:amd64 (1.20.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libssl-dev:amd64 (3.3.1-7) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libnghttp3-dev:amd64 (1.4.0-1) ... Setting up liblzma-dev:amd64 (5.6.2-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... 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 libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b2) ... Setting up libdeflate-dev:amd64 (1.21-1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b4) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2) ... 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 libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up nettle-dev:amd64 (3.10-1) ... Setting up libtool (2.4.7-7) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up libssh2-1-dev:amd64 (1.11.0-7) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.6-2) ... Setting up libnghttp2-dev:amd64 (1.62.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.9.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up debhelper (13.20) ... Setting up libcurl4-gnutls-dev:amd64 (8.9.1-2) ... Setting up samtools (1.20-3) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... 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 any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-3 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_6.10.6-1 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 binutils_2.43.1-3 binutils-common_2.43.1-3 binutils-x86-64-linux-gnu_2.43.1-3 bsdextrautils_2.40.2-7 bsdutils_1:2.40.2-7 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 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 gpg_2.2.43-8 gpg-agent_2.2.43-8 gpg-wks-client_2.2.43-8 gpgconf_2.2.43-8 gpgsm_2.2.43-8 gpgv_2.2.43-8 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 libatomic1_14.2.0-4 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbam-dev_0.1.19+dfsg-6 libbinutils_2.43.1-3 libblkid1_2.40.2-7 libbrotli-dev_1.1.0-2+b4 libbrotli1_1.1.0-2+b4 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 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-3 libctf0_2.43.1-3 libcurl3t64-gnutls_8.9.1-2 libcurl4-gnutls-dev_8.9.1-2 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdeflate-dev_1.21-1 libdeflate0_1.21-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libevent-2.1-7t64_2.1.12-stable-10 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 libgmp-dev_2:6.3.0+dfsg-2+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgmpxx4ldbl_2:6.3.0+dfsg-2+b1 libgnutls-dane0t64_3.8.6-2 libgnutls-openssl27t64_3.8.6-2 libgnutls28-dev_3.8.6-2 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-4 libgpg-error0_1.50-3 libgprofng0_2.43.1-3 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhts-dev_1.20+ds-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.1-1 libhwasan0_14.2.0-4 libicu72_72.1-5 libidn2-0_2.3.7-2 libidn2-dev_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.2.0-4 libjansson4_2.14-2+b2 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 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 liblzma-dev_5.6.2-2 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-7 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncurses6_6.5-2 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnghttp2-14_1.62.1-2 libnghttp2-dev_1.62.1-2 libnghttp3-9_1.4.0-1 libnghttp3-dev_1.4.0-1 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls-dev_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libngtcp2-dev_1.6.0-1 libnpth0t64_1.6-3.1 libp11-kit-dev_0.25.5-2 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_5.40.0-3 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-3 libpsl-dev_0.21.2-1.1 libpsl5t64_0.21.2-1.1 libquadmath0_14.2.0-4 libreadline8t64_8.2-5 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b4 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libsasl2-2_2.1.28+dfsg1-7 libsasl2-modules-db_2.1.28+dfsg1-7 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-3 libsmartcols1_2.40.2-7 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.46.1-1 libssh2-1-dev_1.11.0-7 libssh2-1t64_1.11.0-7 libssl-dev_3.3.1-7 libssl3t64_3.3.1-7 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 libsystemd0_256.5-1 libtasn1-6_4.19.0-3+b2 libtasn1-6-dev_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_256.5-1 libunbound8_1.20.0-1+b1 libunistring5_1.2-1 libuuid1_2.40.2-7 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd-dev_1.5.6+dfsg-1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.10.6-1 locales-all_2.40-2 login_1:4.16.0-2+really2.40.2-7 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240819-3 ncurses-base_6.5-2 ncurses-bin_6.5-2 nettle-dev_3.10-1 openssl-provider-legacy_3.3.1-7 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-3 perl-base_5.40.0-3 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-3 pinentry-curses_1.2.1-4 pkgconf_1.8.1-3 pkgconf-bin_1.8.1-3 po-debconf_1.0.21+nmu1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.10-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-7 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: stacks Binary: stacks Architecture: any Version: 2.68+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://creskolab.uoregon.edu/stacks/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/stacks Vcs-Git: https://salsa.debian.org/med-team/stacks.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev Package-List: stacks deb science optional arch=any Checksums-Sha1: 84d9fefcc2da0bdeedd86d7dc994ef5b84012806 371032 stacks_2.68+dfsg.orig.tar.xz 2ae2f8bb561ab10fd538b4a2aeae7efc6975709d 12224 stacks_2.68+dfsg-1.debian.tar.xz Checksums-Sha256: d5277660330547502069d0976869038e9f47946ef7a8e91bf1213dbc0185072c 371032 stacks_2.68+dfsg.orig.tar.xz e82a33ae713b469deb6894e91356092ad49b37154665af8112dcde78f93bebaf 12224 stacks_2.68+dfsg-1.debian.tar.xz Files: 13bbb30a0414696ac59e3d98d1723d00 371032 stacks_2.68+dfsg.orig.tar.xz f668530ee6a2d621c2db77deee8e7dc9 12224 stacks_2.68+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbS6dEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoV8BAAngn3fAqKfwZK8rxd+k8/0qpElpLX ioQsk/rGfA37Ds8kNitjOUZveZFfVGa6Q1XB687gjWTHHcovoU8XpJD06zUvtCwe MQwK1wl7LPzK/m+9wPPHXh7RF5uqeKsWCspBTdlC+5Ei4B2azoYkEzyh1gcltwMF i7lNDMa4kt4A/06AfroqewGRAg0f8oRWBkOIqBO78l7cicT1tE/k1FrFCXpmn1qk v9Tz78uy/8YAGCqlAicAtqo+CCq0yJmsTW92jTD6AHx0EcwWhBYUZ9PdpOJnuNar JPKjlNDkPquwVrZ5s6jOX5lRk6adhFxCdugm3YXzvpIXghNmlcbVOfzqtzVkiRa0 +BdMzNsaOwkwEYiPdaI2Y6Gi68KsSFV52WGUC61s9Uk0sTWuuOo4i23YaGbNWtyX X50Kz0gKXlaFZJWt5scW0ntMRoCi79Ad8VQcMRl/B7zjbEZgkM9XolGdciQ5Z1O4 nSuE7Eiz/TRKbI5HHbpH23VJoqOty3CQiIrri4VCFKFtgJqJBWlMmZUIx7S2ftaP K/nCCxJgBB3dKI+mNTZmfM52Lsy7ayYfVSaABdEJSP62UIj12SB3TvdtzJtzFAWi 6F9lL9kpE8EeX80imGVJ0/RA25UE8JEB68j3TC5QgSGH32ZeZoyVYJFeWVS3aPjk 2rqDe7ayCe+sj+I= =L+YB -----END PGP SIGNATURE----- gpgv: Signature made Sat Aug 31 10:00:49 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting stacks in /<> dpkg-source: info: unpacking stacks_2.68+dfsg.orig.tar.xz dpkg-source: info: unpacking stacks_2.68+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying RisR.patch dpkg-source: info: applying script-exe-paths dpkg-source: info: applying use_debian_packaged_htslib.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying change_program_exit_to_success.patch dpkg-source: info: applying offer_help_option_for_stacks_gdb.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network stacks_2.68+dfsg-1 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network stacks_2.68+dfsg-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-1b5ff6c9-3b37-4dec-a9aa-b84790c783d8 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 stacks dpkg-buildpackage: info: source version 2.68+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -f ./constants.php make[1]: Leaving directory '/<>' dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building stacks using existing ./stacks_2.68+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building stacks in stacks_2.68+dfsg-1.debian.tar.xz dpkg-source: info: building stacks in stacks_2.68+dfsg-1.dsc debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead dh_autoreconf configure.ac:28: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:28: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:28: the top level configure.ac:20: installing 'config/ar-lib' configure.ac:15: installing 'config/compile' configure.ac:7: installing 'config/install-sh' configure.ac:7: installing 'config/missing' Makefile.am: installing 'config/depcomp' parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-sparsehash --enable-bam \ --with-bam-include-path=/usr/include/samtools \ --with-bam-lib-path=/usr/lib ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking whether g++ supports C++11 features by default... yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for gcc option to support OpenMP... -fopenmp checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for clock_gettime... yes checking for functional regular expressions... yes checking for gawk... (cached) mawk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/<>' dh_auto_build make -j2 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/ustacks.o src/ustacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/aln_utils.o src/aln_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/BamI.o src/BamI.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/catalog_utils.o src/catalog_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/cmb.o src/cmb.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/constants.o src/constants.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/DNANSeq.o src/DNANSeq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/DNASeq4.o src/DNASeq4.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/DNASeq.o src/DNASeq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/gzFasta.o src/gzFasta.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/input.o src/input.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/kmers.o src/kmers.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/locus.o src/locus.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/log_utils.o src/log_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/MetaPopInfo.o src/MetaPopInfo.cc src/MetaPopInfo.cc: In member function ‘void MetaPopInfo::fill_pop_indexes(std::map >&) const’: src/MetaPopInfo.cc:427:30: warning: narrowing conversion of ‘i’ from ‘std::size_t’ {aka ‘long unsigned int’} to ‘int’ [-Wnarrowing] 427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} ); | ^ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/models.o src/models.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/mstack.o src/mstack.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/mst.o src/mst.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/nucleotides.o src/nucleotides.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/renz.o src/renz.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/Seq.o src/Seq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/sql_utilities.o src/sql_utilities.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/stacks.o src/stacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/utils.o src/utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/Vcf.o src/Vcf.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/cstacks.o src/cstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/sstacks.o src/sstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/process_radtags.o src/process_radtags.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/clean.o src/clean.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/file_io.o src/file_io.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/write.o src/write.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/process_shortreads.o src/process_shortreads.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/kmer_filter.o src/kmer_filter.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/clone_filter.o src/clone_filter.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/populations.o src/populations.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/bootstrap.o src/bootstrap.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/export_formats.o src/export_formats.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/mapping_utils.o src/mapping_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/PopSum.o src/PopSum.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/Hwp.o src/Hwp.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/phasedstacks.o src/phasedstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/tsv2bam.o src/tsv2bam.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/gstacks.o src/gstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/debruijn.o src/debruijn.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/SuffixTree.o src/SuffixTree.cc rm -f libcore.a ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcore.a rm -f libclean.a ar cru libclean.a src/clean.o src/kmers.o src/file_io.o src/write.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libclean.a rm -f libpop.a ar cru libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpop.a g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -Wl,-z,relro -Wl,-z,now -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o -lhts libcore.a -lz -lgomp make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' if [ -e /usr/share/automake-1.16/tap-driver.sh ] ; then \ ln -s /usr/share/automake-1.16/tap-driver.sh tests/tap-driver.sh ; \ else \ echo "Make sure /usr/share/automake-*/tap-driver.sh exists and is linked" ; \ false ; \ fi # dh_auto_test rm tests/tap-driver.sh # FIXME: Does not work even after this trick. See # https://groups.google.com/forum/#!msg/stacks-users/TA2tMEqb4Mg/pQy4fUCYi9kJ true make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install --no-parallel make -j1 install DESTDIR=/<>/stacks-2.68\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' /usr/bin/mkdir -p '/<>/debian/stacks/usr/bin' /usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/<>/debian/stacks/usr/bin' /usr/bin/mkdir -p '/<>/debian/stacks/usr/bin' /usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-private-alleles scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/<>/debian/stacks/usr/bin' make install-data-hook make[5]: Entering directory '/<>' sed -e 's,_VERSION_,2.68,' -e 's,_BINDIR_,/usr/libexec/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<>/debian/stacks/usr/bin/denovo_map.pl > /<>/debian/stacks/usr/bin/denovo_map.pl.subst mv /<>/debian/stacks/usr/bin/denovo_map.pl.subst /<>/debian/stacks/usr/bin/denovo_map.pl chmod +x /<>/debian/stacks/usr/bin/denovo_map.pl sed -e 's,_VERSION_,2.68,' -e 's,_BINDIR_,/usr/libexec/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<>/debian/stacks/usr/bin/ref_map.pl > /<>/debian/stacks/usr/bin/ref_map.pl.subst mv /<>/debian/stacks/usr/bin/ref_map.pl.subst /<>/debian/stacks/usr/bin/ref_map.pl chmod +x /<>/debian/stacks/usr/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.68,' /<>/debian/stacks/usr/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.68,' /<>/debian/stacks/usr/bin/stacks-samtools-tview rm -f /<>/debian/stacks/usr/bin/stacks-integrate-alignments.bkp rm -f /<>/debian/stacks/usr/bin/stacks-samtools-tview.bkp chmod +x /<>/debian/stacks/usr/bin/stacks-integrate-alignments chmod +x /<>/debian/stacks/usr/bin/stacks-dist-extract chmod +x /<>/debian/stacks/usr/bin/stacks-gdb make[5]: Leaving directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' mkdir -p debian/stacks/usr/libexec/stacks mv debian/stacks/usr/bin debian/stacks/usr/libexec/stacks cd debian/stacks/usr/libexec/stacks/bin && \ for f in *.pl ; do \ ln -s "$f" "`basename $f .pl`" ; \ sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $f ; \ done dh_install make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_perl debian/rules override_dh_link make[1]: Entering directory '/<>' dh_link mkdir -p debian/stacks/usr/libexec/debian-med/bin cd debian/stacks/usr/libexec/debian-med/bin && \ for f in `ls /<>/debian/stacks/usr/libexec/stacks/bin` ; do \ ln -s ../../stacks/bin/$f ; \ done make[1]: Leaving directory '/<>' 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 dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'stacks' in '../stacks_2.68+dfsg-1_amd64.deb'. dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.68+dfsg-1_amd64.deb'. dpkg-genbuildinfo -O../stacks_2.68+dfsg-1_amd64.buildinfo dpkg-genchanges -O../stacks_2.68+dfsg-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 2024-08-31T16:05:27Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ stacks_2.68+dfsg-1_amd64.changes: --------------------------------- Format: 1.8 Date: Sat, 31 Aug 2024 11:24:11 +0200 Source: stacks Binary: stacks stacks-dbgsym Architecture: source amd64 Version: 2.68+dfsg-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: stacks - pipeline for building loci from short-read DNA sequences Changes: stacks (2.68+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version 2.68+dfsg * d/patches/*: unfuzz. Checksums-Sha1: b73792dbd1c67f1fef805700d532abf52ea03167 1158 stacks_2.68+dfsg-1.dsc 84d9fefcc2da0bdeedd86d7dc994ef5b84012806 371032 stacks_2.68+dfsg.orig.tar.xz 2ae2f8bb561ab10fd538b4a2aeae7efc6975709d 12224 stacks_2.68+dfsg-1.debian.tar.xz a325c48bd1d55250c4d3de62c8d7bd32d56116fe 30799144 stacks-dbgsym_2.68+dfsg-1_amd64.deb 422cd4106d3c1882cdc8331117e7bbdd7b52f387 7130 stacks_2.68+dfsg-1_amd64.buildinfo 9aaa9c736b866b989f22b8a00fff6a33c9ad6762 1258976 stacks_2.68+dfsg-1_amd64.deb Checksums-Sha256: 7dc157d052af08c5103397e70a87870daeccdf3d13c332d0ea5eea4ce0adecc4 1158 stacks_2.68+dfsg-1.dsc d5277660330547502069d0976869038e9f47946ef7a8e91bf1213dbc0185072c 371032 stacks_2.68+dfsg.orig.tar.xz e82a33ae713b469deb6894e91356092ad49b37154665af8112dcde78f93bebaf 12224 stacks_2.68+dfsg-1.debian.tar.xz 696aea5b86c35979995e4b661c34e8cdbf6a46d2694f23e69e8a2f51e8524030 30799144 stacks-dbgsym_2.68+dfsg-1_amd64.deb dfef6aac59ae1bce260eb4387b46fb7183ebd0eafe97805e44fc98e961ae327b 7130 stacks_2.68+dfsg-1_amd64.buildinfo 6a5fbd17a9a9c3db1f91ac1834ea7d5d061b31743f5720f845254cbc1ee55fac 1258976 stacks_2.68+dfsg-1_amd64.deb Files: 6621878051ed173a2d9d8744c60a6b43 1158 science optional stacks_2.68+dfsg-1.dsc 13bbb30a0414696ac59e3d98d1723d00 371032 science optional stacks_2.68+dfsg.orig.tar.xz f668530ee6a2d621c2db77deee8e7dc9 12224 science optional stacks_2.68+dfsg-1.debian.tar.xz 576796a3b328ede42f667b35cc5fc4e8 30799144 debug optional stacks-dbgsym_2.68+dfsg-1_amd64.deb cd9ef4f8272b1867461353a80d0bb87c 7130 science optional stacks_2.68+dfsg-1_amd64.buildinfo e88e3fe6addb319555b241af38c451d7 1258976 science optional stacks_2.68+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: stacks Binary: stacks stacks-dbgsym Architecture: amd64 source Version: 2.68+dfsg-1 Checksums-Md5: 6621878051ed173a2d9d8744c60a6b43 1158 stacks_2.68+dfsg-1.dsc 576796a3b328ede42f667b35cc5fc4e8 30799144 stacks-dbgsym_2.68+dfsg-1_amd64.deb e88e3fe6addb319555b241af38c451d7 1258976 stacks_2.68+dfsg-1_amd64.deb Checksums-Sha1: b73792dbd1c67f1fef805700d532abf52ea03167 1158 stacks_2.68+dfsg-1.dsc a325c48bd1d55250c4d3de62c8d7bd32d56116fe 30799144 stacks-dbgsym_2.68+dfsg-1_amd64.deb 9aaa9c736b866b989f22b8a00fff6a33c9ad6762 1258976 stacks_2.68+dfsg-1_amd64.deb Checksums-Sha256: 7dc157d052af08c5103397e70a87870daeccdf3d13c332d0ea5eea4ce0adecc4 1158 stacks_2.68+dfsg-1.dsc 696aea5b86c35979995e4b661c34e8cdbf6a46d2694f23e69e8a2f51e8524030 30799144 stacks-dbgsym_2.68+dfsg-1_amd64.deb 6a5fbd17a9a9c3db1f91ac1834ea7d5d061b31743f5720f845254cbc1ee55fac 1258976 stacks_2.68+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 31 Aug 2024 16:05:27 +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), binutils (= 2.43.1-3), binutils-common (= 2.43.1-3), binutils-x86-64-linux-gnu (= 2.43.1-3), bsdextrautils (= 2.40.2-7), bsdutils (= 1:2.40.2-7), 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), libbam-dev (= 0.1.19+dfsg-6), libbinutils (= 2.43.1-3), libblkid1 (= 2.40.2-7), libbrotli-dev (= 1.1.0-2+b4), libbrotli1 (= 1.1.0-2+b4), 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), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-3), libctf0 (= 2.43.1-3), libcurl3t64-gnutls (= 8.9.1-2), libcurl4-gnutls-dev (= 8.9.1-2), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdeflate-dev (= 1.21-1), libdeflate0 (= 1.21-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libevent-2.1-7t64 (= 2.1.12-stable-10), 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), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp-dev (= 2:6.3.0+dfsg-2+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgmpxx4ldbl (= 2:6.3.0+dfsg-2+b1), libgnutls-dane0t64 (= 3.8.6-2), libgnutls-openssl27t64 (= 3.8.6-2), libgnutls28-dev (= 3.8.6-2), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-4), libgprofng0 (= 2.43.1-3), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhts-dev (= 1.20+ds-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.1-1), libhwasan0 (= 14.2.0-4), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libidn2-dev (= 2.3.7-2), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-4), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), libldap-2.5-0 (= 2.5.18+dfsg-3+b1), liblsan0 (= 14.2.0-4), liblzma-dev (= 5.6.2-2), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-7), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncurses6 (= 6.5-2), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.62.1-2), libnghttp2-dev (= 1.62.1-2), libnghttp3-9 (= 1.4.0-1), libnghttp3-dev (= 1.4.0-1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls-dev (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libngtcp2-dev (= 1.6.0-1), libp11-kit-dev (= 0.25.5-2), 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), libperl5.40 (= 5.40.0-3), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-3), libpsl-dev (= 0.21.2-1.1), libpsl5t64 (= 0.21.2-1.1), libquadmath0 (= 14.2.0-4), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b4), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-7), libsasl2-modules-db (= 2.1.28+dfsg1-7), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-3), libsmartcols1 (= 2.40.2-7), libsparsehash-dev (= 2.0.3-2), libssh2-1-dev (= 1.11.0-7), libssh2-1t64 (= 1.11.0-7), libssl-dev (= 3.3.1-7), libssl3t64 (= 3.3.1-7), libstdc++-14-dev (= 14.2.0-4), libstdc++6 (= 14.2.0-4), libsystemd0 (= 256.5-1), libtasn1-6 (= 4.19.0-3+b2), libtasn1-6-dev (= 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 (= 256.5-1), libunbound8 (= 1.20.0-1+b1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-7), libxml2 (= 2.12.7+dfsg-3+b1), libzstd-dev (= 1.5.6+dfsg-1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.6-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240819-3), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), nettle-dev (= 3.10-1), openssl-provider-legacy (= 3.3.1-7), patch (= 2.7.6-7), perl (= 5.40.0-3), perl-base (= 5.40.0-3), perl-modules-5.40 (= 5.40.0-3), pkgconf (= 1.8.1-3), pkgconf-bin (= 1.8.1-3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.10-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.2-7), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 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="1725096251" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ stacks-dbgsym_2.68+dfsg-1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 30799144 bytes: control archive=1112 bytes. 786 bytes, 12 lines control 1249 bytes, 12 lines md5sums Package: stacks-dbgsym Source: stacks Version: 2.68+dfsg-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 31337 Depends: stacks (= 2.68+dfsg-1) Section: debug Priority: optional Description: debug symbols for stacks Build-Ids: 0239c1a85ac15f99c988c6a4374344b95b175781 24f80fbeca407ec92d644f344c029a42f6f03a6b 33fad40630332e36f2cd5aef70d2b5bd51fd952b 3dd967fd46e37f4a3394ba6e1b40bb5a109433ad 73395b39f44baaffc73b510589d7db23aa2e94e7 98b236c416cae0f4ce6d43f0f605af978ca276ce 9aa90f59e1c5c5712db297b43328a4de24d48719 ae92b7bab17334ebc93af6198f12dc6ac1546939 c0fe1fa449e2b19f64d4426827228a084afeeb50 d5479553938fdbd3a2ea76186b01a81d4dd11eec efcdd7b8bd1384cee97fbe66d056a2c5dfd6713a drwxr-xr-x root/root 0 2024-08-31 09:24 ./ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/02/ -rw-r--r-- root/root 993608 2024-08-31 09:24 ./usr/lib/debug/.build-id/02/39c1a85ac15f99c988c6a4374344b95b175781.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/24/ -rw-r--r-- root/root 2646008 2024-08-31 09:24 ./usr/lib/debug/.build-id/24/f80fbeca407ec92d644f344c029a42f6f03a6b.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/33/ -rw-r--r-- root/root 1571096 2024-08-31 09:24 ./usr/lib/debug/.build-id/33/fad40630332e36f2cd5aef70d2b5bd51fd952b.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/3d/ -rw-r--r-- root/root 5101264 2024-08-31 09:24 ./usr/lib/debug/.build-id/3d/d967fd46e37f4a3394ba6e1b40bb5a109433ad.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/73/ -rw-r--r-- root/root 2373728 2024-08-31 09:24 ./usr/lib/debug/.build-id/73/395b39f44baaffc73b510589d7db23aa2e94e7.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/98/ -rw-r--r-- root/root 5892688 2024-08-31 09:24 ./usr/lib/debug/.build-id/98/b236c416cae0f4ce6d43f0f605af978ca276ce.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/9a/ -rw-r--r-- root/root 2082072 2024-08-31 09:24 ./usr/lib/debug/.build-id/9a/a90f59e1c5c5712db297b43328a4de24d48719.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/ae/ -rw-r--r-- root/root 3074064 2024-08-31 09:24 ./usr/lib/debug/.build-id/ae/92b7bab17334ebc93af6198f12dc6ac1546939.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/c0/ -rw-r--r-- root/root 1997864 2024-08-31 09:24 ./usr/lib/debug/.build-id/c0/fe1fa449e2b19f64d4426827228a084afeeb50.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/d5/ -rw-r--r-- root/root 2168448 2024-08-31 09:24 ./usr/lib/debug/.build-id/d5/479553938fdbd3a2ea76186b01a81d4dd11eec.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/ef/ -rw-r--r-- root/root 2707280 2024-08-31 09:24 ./usr/lib/debug/.build-id/ef/cdd7b8bd1384cee97fbe66d056a2c5dfd6713a.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 1451968 2024-08-31 09:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/stacks.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/share/doc/stacks-dbgsym -> stacks stacks_2.68+dfsg-1_amd64.deb ---------------------------- new Debian package, version 2.0. size 1258976 bytes: control archive=1608 bytes. 992 bytes, 20 lines control 1796 bytes, 25 lines md5sums Package: stacks Version: 2.68+dfsg-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 6153 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 14), zlib1g (>= 1:1.2.6), samtools, libdbi-perl, bsdextrautils, python3 Recommends: libspreadsheet-writeexcel-perl, littler Suggests: gdb Provides: stacks-web Section: science Priority: optional Homepage: https://creskolab.uoregon.edu/stacks/ Description: pipeline for building loci from short-read DNA sequences Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. . Note that this package installs Stacks such that all commands must be run as: $ stacks drwxr-xr-x root/root 0 2024-08-31 09:24 ./ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/bin/ -rwxr-xr-x root/root 775 2024-08-31 09:15 ./usr/bin/stacks drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/ lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/cstacks -> ../../stacks/bin/cstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/gstacks -> ../../stacks/bin/gstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/populations -> ../../stacks/bin/populations lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/ref_map -> ../../stacks/bin/ref_map lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/sstacks -> ../../stacks/bin/sstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-count-reads-per-sample-per-locus -> ../../stacks/bin/stacks-count-reads-per-sample-per-locus lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-private-alleles -> ../../stacks/bin/stacks-private-alleles lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/ustacks -> ../../stacks/bin/ustacks drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/stacks/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/stacks/bin/ -rwxr-xr-x root/root 414328 2024-08-31 09:24 ./usr/libexec/stacks/bin/clone_filter -rwxr-xr-x root/root 503800 2024-08-31 09:24 ./usr/libexec/stacks/bin/cstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/stacks/bin/denovo_map -> denovo_map.pl -rwxr-xr-x root/root 32933 2024-08-31 09:24 ./usr/libexec/stacks/bin/denovo_map.pl -rwxr-xr-x root/root 863880 2024-08-31 09:24 ./usr/libexec/stacks/bin/gstacks -rwxr-xr-x root/root 287256 2024-08-31 09:24 ./usr/libexec/stacks/bin/kmer_filter -rwxr-xr-x root/root 381208 2024-08-31 09:24 ./usr/libexec/stacks/bin/phasedstacks -rwxr-xr-x root/root 1187288 2024-08-31 09:24 ./usr/libexec/stacks/bin/populations -rwxr-xr-x root/root 589336 2024-08-31 09:24 ./usr/libexec/stacks/bin/process_radtags -rwxr-xr-x root/root 423384 2024-08-31 09:24 ./usr/libexec/stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/stacks/bin/ref_map -> ref_map.pl -rwxr-xr-x root/root 15395 2024-08-31 09:24 ./usr/libexec/stacks/bin/ref_map.pl -rwxr-xr-x root/root 454552 2024-08-31 09:24 ./usr/libexec/stacks/bin/sstacks -rwxr-xr-x root/root 1040 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-count-reads-per-sample-per-locus -rwxr-xr-x root/root 7331 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-dist-extract -rwxr-xr-x root/root 1244 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-gdb -rwxr-xr-x root/root 1773 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-hist2d-loci-samples-coverage -rwxr-xr-x root/root 22320 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-integrate-alignments -rwxr-xr-x root/root 40422 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-private-alleles -rwxr-xr-x root/root 3037 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-samtools-tview -rwxr-xr-x root/root 482728 2024-08-31 09:24 ./usr/libexec/stacks/bin/tsv2bam -rwxr-xr-x root/root 500504 2024-08-31 09:24 ./usr/libexec/stacks/bin/ustacks drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/doc/stacks/ -rw-r--r-- root/root 1451 2024-08-31 09:15 ./usr/share/doc/stacks/README.Debian -rw-r--r-- root/root 1430 2024-08-31 09:24 ./usr/share/doc/stacks/changelog.Debian.gz -rw-r--r-- root/root 32538 2024-08-23 15:56 ./usr/share/doc/stacks/changelog.gz -rw-r--r-- root/root 1730 2024-08-31 09:15 ./usr/share/doc/stacks/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 397064 Build-Time: 185 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 5 Job: /srv/debomatic/incoming/stacks_2.68+dfsg-1.dsc Machine Architecture: amd64 Package: stacks Package-Time: 198 Source-Version: 2.68+dfsg-1 Space: 397064 Status: successful Version: 2.68+dfsg-1 -------------------------------------------------------------------------------- Finished at 2024-08-31T16:05:27Z Build needed 00:03:18, 397064k disk space