sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | stacks 2.68+dfsg-2 (amd64) Tue, 01 Jul 2025 22:35:17 +0000 | +==============================================================================+ Package: stacks Version: 2.68+dfsg-2 Source Version: 2.68+dfsg-2 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Tue, 01 Jul 2025 22:35:19 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup stacks_2.68+dfsg-2 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup stacks_2.68+dfsg-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Tue, 01 Jul 2025 22:35:19 +0000 | +------------------------------------------------------------------------------+ 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 [213 kB] Get:3 http://deb.debian.org/debian unstable InRelease [213 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-2025-07-01-2004.28-F-2025-07-01-2004.28.pdiff [2379 B] 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-2025-07-01-2004.28-F-2025-07-01-2004.28.pdiff [2379 B] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-07-01-2004.28-F-2025-07-01-2004.28.pdiff [2947 B] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-07-01-2004.28-F-2025-07-01-2004.28.pdiff [2947 B] Fetched 559 kB in 7s (80.2 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Tue, 01 Jul 2025 22:35:28 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/stacks_2.68+dfsg-2.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 01 Jul 2025 22:35:28 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), automake, zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), automake, zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/stacks-CKkSHA/resolver-mWSC1t/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/stacks-CKkSHA/resolver-mWSC1t/apt_archive ./ InRelease Get:2 copy:/build/stacks-CKkSHA/resolver-mWSC1t/apt_archive ./ Release [609 B] Ign:3 copy:/build/stacks-CKkSHA/resolver-mWSC1t/apt_archive ./ Release.gpg Get:4 copy:/build/stacks-CKkSHA/resolver-mWSC1t/apt_archive ./ Sources [675 B] Get:5 copy:/build/stacks-CKkSHA/resolver-mWSC1t/apt_archive ./ Packages [714 B] Fetched 1998 B in 0s (99.1 kB/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 comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbam-dev libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev 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 doc-base dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-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 bzip2-doc 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 comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbam-dev libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev 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, 89 newly installed, 0 to remove and 0 not upgraded. Need to get 28.8 MB/29.1 MB of archives. After this operation, 104 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b1 [312 kB] Get:2 copy:/build/stacks-CKkSHA/resolver-mWSC1t/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [892 B] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b1 [25.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b1 [56.7 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:26 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.0-2 [2950 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.21-1 [667 kB] Preconfiguring packages ... Fetched 28.8 MB in 0s (120 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 23091 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... 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Setting up libssl-dev:amd64 (3.5.0-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up debhelper (13.24.2) ... Setting up samtools (1.21-1) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up libhts-dev:amd64 (1.21+ds-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures Tue, 01 Jul 2025 22:35:37 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Tue, 01 Jul 2025 22:35:37 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b3 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b1 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-13_13.4.0-1 cpp-13-x86-64-linux-gnu_13.4.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.7-21+b1 dpkg_1.22.20 dpkg-dev_1.22.20 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.4.0-1 g++-13-x86-64-linux-gnu_13.4.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.4.0-1 gcc-13-base_13.4.0-1 gcc-13-x86-64-linux-gnu_13.4.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbam-dev_0.1.19+dfsg-6 libbinutils_2.44-3 libblkid1_2.41-5 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcom-err2_1.47.2-3+b1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libcurl3t64-gnutls_8.14.1-2 libcurl4-gnutls-dev_8.14.1-2 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.20 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-13-dev_13.4.0-1 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.9-2 libgnutls-openssl27t64_3.8.9-2 libgnutls28-dev_3.8.9-2 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgpg-error0_1.51-4 libgprofng0_2.44-3 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libhogweed6t64_3.10.1-1 libhts-dev_1.21+ds-1 libhts3t64_1.21+ds-1 libhtscodecs2_1.6.1-2 libhwasan0_14.2.0-19 libidn2-0_2.3.8-2 libidn2-dev_2.3.8-2 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41-5 libldap-2.5-0_2.5.19+dfsg-1 libldap-dev_2.6.10+dfsg-1+b1 libldap2_2.6.10+dfsg-1+b1 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma-dev_5.8.1-1 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncurses6_6.5+20250216-2 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1 libnghttp2-dev_1.64.0-1.1 libnghttp3-9_1.8.0-1 libnghttp3-dev_1.8.0-1 libngtcp2-16_1.11.0-1 libngtcp2-crypto-gnutls-dev_1.11.0-1 libngtcp2-crypto-gnutls8_1.11.0-1 libngtcp2-dev_1.11.0-1 libnpth0t64_1.8-3 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-4 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe1_2.44-3 libsmartcols1_2.41-5 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.46.1-6 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.0-2 libssl3t64_3.5.0-2 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.7-1 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.7-1 libunbound8_1.22.0-1+b1 libunistring5_1.3-2 libuuid1_2.41-5 libxml2_2.12.7+dfsg+really2.9.14-1 libxxhash0_0.8.3-2 libzstd-dev_1.5.7+dfsg-1 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.33-1 locales-all_2.41-9 login_1:4.16.0-2+really2.41-5 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 nettle-dev_3.10.1-1 openssl-provider-legacy_3.5.0-2 passwd_1:4.17.4-2 patch_2.8-2 perl_5.40.1-4 perl-base_5.40.1-4 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-4 pinentry-curses_1.3.1-2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 samtools_1.21-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 usr-is-merged_39+nmu2 util-linux_2.41-5 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Tue, 01 Jul 2025 22:35:37 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: stacks Binary: stacks Architecture: any Version: 2.68+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: 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), automake, 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 a4b257a1997837310253bbae16d2e7b4b9eaee6b 12488 stacks_2.68+dfsg-2.debian.tar.xz Checksums-Sha256: d5277660330547502069d0976869038e9f47946ef7a8e91bf1213dbc0185072c 371032 stacks_2.68+dfsg.orig.tar.xz e07482fc23eb570d9c43a560055b051f88430b001a86a9b40223e3d5dc4e283c 12488 stacks_2.68+dfsg-2.debian.tar.xz Files: 13bbb30a0414696ac59e3d98d1723d00 371032 stacks_2.68+dfsg.orig.tar.xz c534f4ad4dbee58b2bcbb1a06a37472b 12488 stacks_2.68+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmexvEUUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoXEA//VJ/FgP1rvPK6Y2fdIUOsOvsdBFYw l9bEvoCMNQrpB0rtotfJ7HtfU+z1rvh/sydyGLYCXvxHfcyFXZHKh8EzjcxHsTUC aQD+90m2S9X0xUjqZoh6TvMbJsJPB845dJayzCgTu5Zav9VEbMj+smXy81OIQP+0 EH7wrx1Cdyqf8v39Dxrft0ARdi4O5WCXRtay2VR0E1UpDoMQ8yTlR/ooiZVD/yhe xOo1wiripgPVFe/IJGH1Y9IjGD6CDB01pxvJrDfs7WKViMQ0YL1pGSQQxVFDdnPv 4bmpgpS2qCJ+KP+JjIA09VifUta4w6urk2ouXV7KX1w1khPbUAMIrlPpa9LQ3owQ B4MtordioWMMTPw8wafqe8RdI8zb0AdwGAW3vFhw/hhMd0lQYVnLAnF28sW6aN+h Hg9qCNKmm9gtyAyUdv2OymOcq+SO/KbzZsZj+E4yXWLlXFSdj+TY99ArhEfhQI3W A4iVivodaEyh/YxhmQT+cqne43BWmYZW0R0IzFDWf4p8mROxqJNfSKETzEDXiUa8 zIBz+gc9uyCXeSWfliCrEc84kvKFOxd+Whe2E0CF6Z95SNuOp2rIpRVKVEhWGpNJ fnQo3M4gJw/thOxHpwST8MLh2NWJZWtaSvof6LOZq4RGJwuWeQL9nBppEOjfvwml MObsIAsfY1yB3YE= =FAjp -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting stacks in /build/stacks-CKkSHA/stacks-2.68+dfsg dpkg-source: info: unpacking stacks_2.68+dfsg.orig.tar.xz dpkg-source: info: unpacking stacks_2.68+dfsg-2.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 Tue, 01 Jul 2025 22:35:38 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network stacks_2.68+dfsg-2 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network stacks_2.68+dfsg-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/stacks-CKkSHA/stacks-2.68+dfsg 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-da444494-9fa6-480c-bae6-8e06666305ea SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package stacks dpkg-buildpackage: info: source version 2.68+dfsg-2 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 '/build/stacks-CKkSHA/stacks-2.68+dfsg' dh_clean rm -f ./constants.php make[1]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' 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-2.debian.tar.xz dpkg-source: info: building stacks in stacks_2.68+dfsg-2.dsc debian/rules binary dh binary dh_update_autotools_config 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 '/build/stacks-CKkSHA/stacks-2.68+dfsg' 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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... 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 '/build/stacks-CKkSHA/stacks-2.68+dfsg' dh_auto_build make -j2 make[1]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make all-recursive make[2]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[3]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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 cr 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 ranlib libcore.a rm -f libclean.a ar cr libclean.a src/clean.o src/kmers.o src/file_io.o src/write.o ranlib libclean.a rm -f libpop.a ar cr libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o ranlib libpop.a g++ -g -O2 -ffile-prefix-map=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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=/build/stacks-CKkSHA/stacks-2.68+dfsg=. -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 '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[2]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[1]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' set -e \ ; TAP_DRIVER=$( ls -d1 /usr/share/automake-*/tap-driver.sh | tail -n-1 ) \ ; if [ -e "$TAP_DRIVER" ] \ ; then ln -s "$TAP_DRIVER" 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 '/build/stacks-CKkSHA/stacks-2.68+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' dh_auto_install --no-parallel make -j1 install DESTDIR=/build/stacks-CKkSHA/stacks-2.68\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[3]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[4]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' /usr/bin/mkdir -p '/build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin' /usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin' /usr/bin/mkdir -p '/build/stacks-CKkSHA/stacks-2.68+dfsg/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 '/build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin' make install-data-hook make[5]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' sed -e 's,_VERSION_,2.68,' -e 's,_BINDIR_,/usr/libexec/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl > /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst mv /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl chmod +x /build/stacks-CKkSHA/stacks-2.68+dfsg/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' /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl > /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl.subst mv /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl chmod +x /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.68,' /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.68,' /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-samtools-tview rm -f /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp rm -f /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp chmod +x /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments chmod +x /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-dist-extract chmod +x /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-gdb make[5]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[4]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[3]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[2]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' make[1]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' 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?' $f ; \ done dh_install make[1]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' dh_installdocs dh_installchangelogs dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' dh_link mkdir -p debian/stacks/usr/libexec/debian-med/bin cd debian/stacks/usr/libexec/debian-med/bin && \ for f in `ls /build/stacks-CKkSHA/stacks-2.68+dfsg/debian/stacks/usr/libexec/stacks/bin` ; do \ ln -s ../../stacks/bin/$f ; \ done make[1]: Leaving directory '/build/stacks-CKkSHA/stacks-2.68+dfsg' 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-dbgsym' in '../stacks-dbgsym_2.68+dfsg-2_amd64.deb'. dpkg-deb: building package 'stacks' in '../stacks_2.68+dfsg-2_amd64.deb'. dpkg-genbuildinfo -O../stacks_2.68+dfsg-2_amd64.buildinfo dpkg-genchanges -O../stacks_2.68+dfsg-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-07-01T22:39:48Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 01 Jul 2025 22:39:49 +0000 | +------------------------------------------------------------------------------+ stacks_2.68+dfsg-2_amd64.changes: --------------------------------- Format: 1.8 Date: Sun, 16 Feb 2025 10:54:31 +0100 Source: stacks Binary: stacks stacks-dbgsym Architecture: source amd64 Version: 2.68+dfsg-2 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 Closes: 1095396 Changes: stacks (2.68+dfsg-2) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * Remove Tim Booth since address is bouncing (Thank you for your work on this package, Tim) . [ Étienne Mollier ] * d/control: explicitly build-depend on automake. * d/rules: reinforce the fetch the TAP driver for any automake version. Unfortunately this change is not sufficient to put upstream's super secret test suite on tracks, so it is still disabled for the moment. (Closes: #1095396) * use_debian_packaged_htslib.patch: normalise Last-Update timestamp. Checksums-Sha1: 8588d152a819b50bbc2aca83dedafe8bae2c0cb7 1138 stacks_2.68+dfsg-2.dsc a4b257a1997837310253bbae16d2e7b4b9eaee6b 12488 stacks_2.68+dfsg-2.debian.tar.xz 8c9752c13c2784c3ec7a8d06a439ef090f000bcd 30724856 stacks-dbgsym_2.68+dfsg-2_amd64.deb c3509a2a88f108fdfd7f9ba28450d92d81802c6f 7435 stacks_2.68+dfsg-2_amd64.buildinfo 64080dd1457b4342eff7f949f66f78171b1f8c55 1262588 stacks_2.68+dfsg-2_amd64.deb Checksums-Sha256: d35ffdb05edc13528c412b00b33edf534abb2fa9eb6bf07ae7fe5cdb615e44fc 1138 stacks_2.68+dfsg-2.dsc e07482fc23eb570d9c43a560055b051f88430b001a86a9b40223e3d5dc4e283c 12488 stacks_2.68+dfsg-2.debian.tar.xz 0eae49dbe4e737fef9bcf17fefda5c42b75e38453764f736e110bf9e775b893f 30724856 stacks-dbgsym_2.68+dfsg-2_amd64.deb b2ace00c8c9d77b8321b3a1356ec45bcca2a5a213836e8bbdf64656610e27931 7435 stacks_2.68+dfsg-2_amd64.buildinfo 20c3bf30c560f380badc046b36566fe709c7286a243359791cb625c65bb44345 1262588 stacks_2.68+dfsg-2_amd64.deb Files: 0e921f4c446566278cca817ce24b2d04 1138 science optional stacks_2.68+dfsg-2.dsc c534f4ad4dbee58b2bcbb1a06a37472b 12488 science optional stacks_2.68+dfsg-2.debian.tar.xz 6808b420775752179e7eb3cc2697c772 30724856 debug optional stacks-dbgsym_2.68+dfsg-2_amd64.deb 662f2bc8cf291fd4893c6f50302a5600 7435 science optional stacks_2.68+dfsg-2_amd64.buildinfo b24350c5353b41a70e91b8593b09b6c9 1262588 science optional stacks_2.68+dfsg-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Tue, 01 Jul 2025 22:39:49 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: stacks Binary: stacks stacks-dbgsym Architecture: amd64 source Version: 2.68+dfsg-2 Checksums-Md5: 0e921f4c446566278cca817ce24b2d04 1138 stacks_2.68+dfsg-2.dsc 6808b420775752179e7eb3cc2697c772 30724856 stacks-dbgsym_2.68+dfsg-2_amd64.deb b24350c5353b41a70e91b8593b09b6c9 1262588 stacks_2.68+dfsg-2_amd64.deb Checksums-Sha1: 8588d152a819b50bbc2aca83dedafe8bae2c0cb7 1138 stacks_2.68+dfsg-2.dsc 8c9752c13c2784c3ec7a8d06a439ef090f000bcd 30724856 stacks-dbgsym_2.68+dfsg-2_amd64.deb 64080dd1457b4342eff7f949f66f78171b1f8c55 1262588 stacks_2.68+dfsg-2_amd64.deb Checksums-Sha256: d35ffdb05edc13528c412b00b33edf534abb2fa9eb6bf07ae7fe5cdb615e44fc 1138 stacks_2.68+dfsg-2.dsc 0eae49dbe4e737fef9bcf17fefda5c42b75e38453764f736e110bf9e775b893f 30724856 stacks-dbgsym_2.68+dfsg-2_amd64.deb 20c3bf30c560f380badc046b36566fe709c7286a243359791cb625c65bb44345 1262588 stacks_2.68+dfsg-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 01 Jul 2025 22:39:48 +0000 Build-Path: /build/stacks-CKkSHA/stacks-2.68+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 13.8), base-passwd (= 3.6.7), bash (= 5.2.37-2+b3), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-5), bsdutils (= 1:2.41-5), build-essential (= 12.12), bzip2 (= 1.0.8-6), comerr-dev (= 2.1-1.47.2-3+b1), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-13 (= 13.4.0-1), cpp-13-x86-64-linux-gnu (= 13.4.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.23.1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.20), dpkg-dev (= 1.22.20), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.4.0-1), gcc-13-base (= 13.4.0-1), gcc-13-x86-64-linux-gnu (= 13.4.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-5), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbam-dev (= 0.1.19+dfsg-6), libbinutils (= 2.44-3), libblkid1 (= 2.41-5), libbrotli-dev (= 1.1.0-2+b7), libbrotli1 (= 1.1.0-2+b7), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-9), libc-dev-bin (= 2.41-9), libc6 (= 2.41-9), libc6-dev (= 2.41-9), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-9), libcc1-0 (= 14.2.0-19), libcom-err2 (= 1.47.2-3+b1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libcurl3t64-gnutls (= 8.14.1-2), libcurl4-gnutls-dev (= 8.14.1-2), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.279), libdebhelper-perl (= 13.24.2), libdeflate-dev (= 1.23-2), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.20), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libffi8 (= 3.4.8-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-13-dev (= 13.4.0-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp-dev (= 2:6.3.0+dfsg-3), libgmp10 (= 2:6.3.0+dfsg-3), libgmpxx4ldbl (= 2:6.3.0+dfsg-3), libgnutls-dane0t64 (= 3.8.9-2), libgnutls-openssl27t64 (= 3.8.9-2), libgnutls28-dev (= 3.8.9-2), libgnutls30t64 (= 3.8.9-2), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libgssapi-krb5-2 (= 1.21.3-5), libgssrpc4t64 (= 1.21.3-5), libhogweed6t64 (= 3.10.1-1), libhts-dev (= 1.21+ds-1), libhts3t64 (= 1.21+ds-1), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 14.2.0-19), libidn2-0 (= 2.3.8-2), libidn2-dev (= 2.3.8-2), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), libk5crypto3 (= 1.21.3-5), libkadm5clnt-mit12 (= 1.21.3-5), libkadm5srv-mit12 (= 1.21.3-5), libkdb5-10t64 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5-dev (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblastlog2-2 (= 2.41-5), libldap-dev (= 2.6.10+dfsg-1+b1), libldap2 (= 2.6.10+dfsg-1+b1), liblsan0 (= 14.2.0-19), liblzma-dev (= 5.8.1-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-5), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libncurses6 (= 6.5+20250216-2), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1.1), libnghttp2-dev (= 1.64.0-1.1), libnghttp3-9 (= 1.8.0-1), libnghttp3-dev (= 1.8.0-1), libngtcp2-16 (= 1.11.0-1), libngtcp2-crypto-gnutls-dev (= 1.11.0-1), libngtcp2-crypto-gnutls8 (= 1.11.0-1), libngtcp2-dev (= 1.11.0-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-4), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libquadmath0 (= 14.2.0-19), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsmartcols1 (= 2.41-5), libsparsehash-dev (= 2.0.3-2), libsqlite3-0 (= 3.46.1-6), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.5.0-2), libssl3t64 (= 3.5.0-2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.7-1), libtasn1-6 (= 4.20.0-2), libtasn1-6-dev (= 4.20.0-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.7-1), libunbound8 (= 1.22.0-1+b1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-5), libxml2 (= 2.12.7+dfsg+really2.9.14-1), libzstd-dev (= 1.5.7+dfsg-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.33-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), nettle-dev (= 3.10.1-1), openssl-provider-legacy (= 3.5.0-2), patch (= 2.8-2), perl (= 5.40.1-4), perl-base (= 5.40.1-4), perl-modules-5.40 (= 5.40.1-4), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), samtools (= 1.21-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41-5), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) 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="1739699671" +------------------------------------------------------------------------------+ | Package contents Tue, 01 Jul 2025 22:39:49 +0000 | +------------------------------------------------------------------------------+ stacks-dbgsym_2.68+dfsg-2_amd64.deb ----------------------------------- new Debian package, version 2.0. size 30724856 bytes: control archive=1088 bytes. 786 bytes, 12 lines control 1249 bytes, 12 lines md5sums Package: stacks-dbgsym Source: stacks Version: 2.68+dfsg-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 32151 Depends: stacks (= 2.68+dfsg-2) Section: debug Priority: optional Description: debug symbols for stacks Build-Ids: 06ce64250fcb371b696561e21f5dec770dc29821 07439570f66641222f161efde7cd25bce7aabbeb 3a1353f215a9611d9ab39e32728a7de083640d47 45cbbe83705ff765fbfb2133fc6b3a2247ef1bff 5548c0c77b84dd90d181fa35d6ce159b5d6f8c2a 6fbcdb02344fb9d80cb698ab75758dfe2caa1f0f 8cbfcc1bd135490245f471b3e46b1516a9401288 b085116c3eda24516e524c884005d33fafe76acd bf4ad6a4e26eca4ab6175918e309055aa251404b c04f51cd288ad1d68d384719e623180c3e95985d d766d74879ec4b7a1c32354d587ac6a0291e4c3e drwxr-xr-x root/root 0 2025-02-16 09:54 ./ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/06/ -rw-r--r-- root/root 1631512 2025-02-16 09:54 ./usr/lib/debug/.build-id/06/ce64250fcb371b696561e21f5dec770dc29821.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/07/ -rw-r--r-- root/root 2234648 2025-02-16 09:54 ./usr/lib/debug/.build-id/07/439570f66641222f161efde7cd25bce7aabbeb.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/3a/ -rw-r--r-- root/root 5246504 2025-02-16 09:54 ./usr/lib/debug/.build-id/3a/1353f215a9611d9ab39e32728a7de083640d47.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/45/ -rw-r--r-- root/root 1039592 2025-02-16 09:54 ./usr/lib/debug/.build-id/45/cbbe83705ff765fbfb2133fc6b3a2247ef1bff.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/55/ -rw-r--r-- root/root 2141112 2025-02-16 09:54 ./usr/lib/debug/.build-id/55/48c0c77b84dd90d181fa35d6ce159b5d6f8c2a.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/6f/ -rw-r--r-- root/root 6009552 2025-02-16 09:54 ./usr/lib/debug/.build-id/6f/bcdb02344fb9d80cb698ab75758dfe2caa1f0f.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/8c/ -rw-r--r-- root/root 2788328 2025-02-16 09:54 ./usr/lib/debug/.build-id/8c/bfcc1bd135490245f471b3e46b1516a9401288.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/b0/ -rw-r--r-- root/root 3147072 2025-02-16 09:54 ./usr/lib/debug/.build-id/b0/85116c3eda24516e524c884005d33fafe76acd.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/bf/ -rw-r--r-- root/root 2440984 2025-02-16 09:54 ./usr/lib/debug/.build-id/bf/4ad6a4e26eca4ab6175918e309055aa251404b.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/c0/ -rw-r--r-- root/root 2056976 2025-02-16 09:54 ./usr/lib/debug/.build-id/c0/4f51cd288ad1d68d384719e623180c3e95985d.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.build-id/d7/ -rw-r--r-- root/root 2728544 2025-02-16 09:54 ./usr/lib/debug/.build-id/d7/66d74879ec4b7a1c32354d587ac6a0291e4c3e.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 1429792 2025-02-16 09:54 ./usr/lib/debug/.dwz/x86_64-linux-gnu/stacks.debug drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/share/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/share/doc/stacks-dbgsym -> stacks stacks_2.68+dfsg-2_amd64.deb ---------------------------- new Debian package, version 2.0. size 1262588 bytes: control archive=1608 bytes. 992 bytes, 20 lines control 1796 bytes, 25 lines md5sums Package: stacks Version: 2.68+dfsg-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 6169 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 2025-02-16 09:54 ./ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/bin/ -rwxr-xr-x root/root 775 2024-08-31 09:15 ./usr/bin/stacks drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/libexec/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/ lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/cstacks -> ../../stacks/bin/cstacks lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/gstacks -> ../../stacks/bin/gstacks lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/populations -> ../../stacks/bin/populations lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/ref_map -> ../../stacks/bin/ref_map lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/sstacks -> ../../stacks/bin/sstacks lrwxrwxrwx root/root 0 2025-02-16 09:54 ./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 2025-02-16 09:54 ./usr/libexec/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/stacks-private-alleles -> ../../stacks/bin/stacks-private-alleles lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/debian-med/bin/ustacks -> ../../stacks/bin/ustacks drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/libexec/stacks/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/libexec/stacks/bin/ -rwxr-xr-x root/root 418424 2025-02-16 09:54 ./usr/libexec/stacks/bin/clone_filter -rwxr-xr-x root/root 503800 2025-02-16 09:54 ./usr/libexec/stacks/bin/cstacks lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/stacks/bin/denovo_map -> denovo_map.pl -rwxr-xr-x root/root 32933 2025-02-16 09:54 ./usr/libexec/stacks/bin/denovo_map.pl -rwxr-xr-x root/root 867976 2025-02-16 09:54 ./usr/libexec/stacks/bin/gstacks -rwxr-xr-x root/root 287256 2025-02-16 09:54 ./usr/libexec/stacks/bin/kmer_filter -rwxr-xr-x root/root 381208 2025-02-16 09:54 ./usr/libexec/stacks/bin/phasedstacks -rwxr-xr-x root/root 1191384 2025-02-16 09:54 ./usr/libexec/stacks/bin/populations -rwxr-xr-x root/root 589336 2025-02-16 09:54 ./usr/libexec/stacks/bin/process_radtags -rwxr-xr-x root/root 423384 2025-02-16 09:54 ./usr/libexec/stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2025-02-16 09:54 ./usr/libexec/stacks/bin/ref_map -> ref_map.pl -rwxr-xr-x root/root 15395 2025-02-16 09:54 ./usr/libexec/stacks/bin/ref_map.pl -rwxr-xr-x root/root 458648 2025-02-16 09:54 ./usr/libexec/stacks/bin/sstacks -rwxr-xr-x root/root 1040 2025-02-16 09:54 ./usr/libexec/stacks/bin/stacks-count-reads-per-sample-per-locus -rwxr-xr-x root/root 7331 2025-02-16 09:54 ./usr/libexec/stacks/bin/stacks-dist-extract -rwxr-xr-x root/root 1244 2025-02-16 09:54 ./usr/libexec/stacks/bin/stacks-gdb -rwxr-xr-x root/root 1773 2025-02-16 09:54 ./usr/libexec/stacks/bin/stacks-hist2d-loci-samples-coverage -rwxr-xr-x root/root 22320 2025-02-16 09:54 ./usr/libexec/stacks/bin/stacks-integrate-alignments -rwxr-xr-x root/root 40422 2025-02-16 09:54 ./usr/libexec/stacks/bin/stacks-private-alleles -rwxr-xr-x root/root 3037 2025-02-16 09:54 ./usr/libexec/stacks/bin/stacks-samtools-tview -rwxr-xr-x root/root 482728 2025-02-16 09:54 ./usr/libexec/stacks/bin/tsv2bam -rwxr-xr-x root/root 500504 2025-02-16 09:54 ./usr/libexec/stacks/bin/ustacks drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/share/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-02-16 09:54 ./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 1728 2025-02-16 09:54 ./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 Tue, 01 Jul 2025 22:39:50 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 01 Jul 2025 22:39:50 +0000 | +------------------------------------------------------------------------------+ Purging /build/stacks-CKkSHA Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 01 Jul 2025 22:39:51 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 395620 Build-Time: 250 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 9 Job: /srv/debomatic/incoming/stacks_2.68+dfsg-2.dsc Machine Architecture: amd64 Package: stacks Package-Time: 271 Source-Version: 2.68+dfsg-2 Space: 395620 Status: successful Version: 2.68+dfsg-2 -------------------------------------------------------------------------------- Finished at 2025-07-01T22:39:48Z Build needed 00:04:31, 395620k disk space