sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | stacks 2.68+dfsg-4 (amd64) Sun, 12 Jul 2026 00:03:41 +0000 | +==============================================================================+ Package: stacks Version: 2.68+dfsg-4 Source Version: 2.68+dfsg-4 Distribution: perl-5.44-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 Sun, 12 Jul 2026 00:03:43 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup stacks_2.68+dfsg-4 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup stacks_2.68+dfsg-4 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 12 Jul 2026 00:03:44 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/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 Sun, 12 Jul 2026 00:03:50 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/stacks_2.68+dfsg-4.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 12 Jul 2026 00:03:51 +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-1GCgzd/resolver-AMNG1B/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/stacks-1GCgzd/resolver-AMNG1B/apt_archive ./ InRelease Get:2 copy:/build/stacks-1GCgzd/resolver-AMNG1B/apt_archive ./ Release [609 B] Ign:3 copy:/build/stacks-1GCgzd/resolver-AMNG1B/apt_archive ./ Release.gpg Get:4 copy:/build/stacks-1GCgzd/resolver-AMNG1B/apt_archive ./ Sources [675 B] Get:5 copy:/build/stacks-1GCgzd/resolver-AMNG1B/apt_archive ./ Packages [714 B] Fetched 1998 B in 0s (132 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... Solving dependencies... 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 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 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 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libsparsehash-dev libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev libxml2-16 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 m4-doc apparmor less www-browser libmail-box-perl cwltool Recommended packages: curl | wget | lynx python3:any 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 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 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 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libsparsehash-dev libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf samtools sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 30.5 MB/30.9 MB of archives. After this operation, 123 MB of additional disk space will be used. Get:1 copy:/build/stacks-1GCgzd/resolver-AMNG1B/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [892 B] Get:2 file:/srv/reprepro perl-5.44/main amd64 libldap-dev amd64 2.6.13+dfsg-1+b1 [308 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 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 1.4.21-1 [332 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1 [50.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 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 1.15.1-1 [17.1 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:26 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 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 1.0.22 [216 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-3 [58.3 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-3 [40.3 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-3 [41.3 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-3 [54.1 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-3 [125 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 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 1.2.0-3 [320 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-3 [324 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.21.0-2 [416 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.21.0-2 [17.0 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.25.1-1+b1 [619 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.13-1 [496 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-5 [102 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.4-1 [225 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2+b1 [98.6 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.13-1 [1479 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-3 [14.0 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.69.0-1 [128 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.15.0-1 [94.5 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.22.1-1 [20.9 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.22.1-1 [192 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libunistring-dev amd64 1.4.2-1 [651 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.22.0-1 [29.8 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.6.3-1 [3025 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-4 [393 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-3+b2 [372 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.21.0-2 [546 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.25-1 [56.7 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds2-1+b2 [1784 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.6+20260608-2 [107 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.4-1 [76.9 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB] Preconfiguring packages ... Fetched 30.5 MB in 0s (107 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 15696 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.47-4_amd64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.47-4_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.47-4) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.47-4_amd64.deb ... Unpacking file (1:5.47-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_1.0-3_amd64.deb ... Unpacking gettext-base (1.0-3) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2+b2_amd64.deb ... 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Setting up libssl-dev:amd64 (3.6.3-1) ... Setting up autopoint (1.0-3) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up libidn2-dev:amd64 (2.3.8-5) ... Setting up autoconf (2.73-2) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up libnghttp3-dev:amd64 (1.15.0-1) ... Setting up liblzma-dev:amd64 (5.8.3-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-4) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2+b1) ... Setting up libdeflate-dev:amd64 (1.25-1) ... Setting up libbrotli-dev:amd64 (1.2.0-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up libp11-kit-dev:amd64 (0.26.4-1) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-3) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libtool (2.5.4-11) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Setting up libngtcp2-dev:amd64 (1.22.1-1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up libpsl-dev:amd64 (0.22.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up libssh2-1-dev:amd64 (1.11.1-4) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up libgnutls28-dev:amd64 (3.8.13-1) ... Setting up libcurl4-gnutls:amd64 (8.21.0-2) ... Setting up libnghttp2-dev:amd64 (1.69.0-1) ... Setting up po-debconf (1.0.22) ... Setting up libcurl3t64-gnutls:amd64 (8.21.0-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libgssrpc4t64:amd64 (1.22.1-3) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-3) ... Setting up libkdb5-10t64:amd64 (1.22.1-3) ... Setting up debhelper (14.3) ... Setting up samtools (1.22.1-1) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-3) ... Setting up krb5-multidev:amd64 (1.22.1-3) ... Setting up libkrb5-dev:amd64 (1.22.1-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.21.0-2) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1+b2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 12 Jul 2026 00:04:04 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 12 Jul 2026 00:04:04 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-7 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gnupg_2.4.9-7 gnupg-l10n_2.4.9-7 gpg_2.4.9-7 gpg-agent_2.4.9-7 gpgconf_2.4.9-7 gpgsm_2.4.9-7 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-3 libacl1_2.4.0-1 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbam-dev_0.1.19+dfsg-6 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbrotli-dev_1.2.0-3 libbrotli1_1.2.0-3 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcc1-0_16.1.0-2 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl3t64-gnutls_8.21.0-2 libcurl4-gnutls_8.21.0-2 libcurl4-gnutls-dev_8.21.0-2 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdeflate-dev_1.25-1 libdeflate0_1.25-1 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.13-stable-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libgssapi-krb5-2_1.22.1-3 libgssrpc4t64_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhts-dev_1.22.1+ds2-1+b2 libhts3t64_1.22.1+ds2-1+b2 libhtscodecs2_1.6.6-1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libidn2-dev_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libk5crypto3_1.22.1-3 libkadm5clnt-mit12_1.22.1-3 libkadm5srv-mit12_1.22.1-3 libkdb5-10t64_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5-dev_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.0-3 libldap-dev_2.6.13+dfsg-1+b1 libldap2_2.6.13+dfsg-1+b1 liblsan0_16.1.0-2 liblz4-1_1.10.0-10 liblzma-dev_5.8.3-1 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncurses6_6.6+20260608-2 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp2-dev_1.69.0-1 libnghttp3-9_1.15.0-1 libnghttp3-dev_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls-dev_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libngtcp2-dev_1.22.1-1 libnpth0t64_1.8-3+b2 libp11-kit-dev_0.26.4-1 libp11-kit0_0.26.4-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc2-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.22.0-1 libpsl5t64_0.22.0-1 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1 libselinux1_3.11-2 libsframe3_2.46.50.20260617-1 libsmartcols1_2.42.2-1 libsparsehash-dev_2.0.4-1 libsqlite3-0_3.53.3-1 libssh2-1-dev_1.11.1-4 libssh2-1t64_1.11.1-4 libssl-dev_3.6.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd-shared_261.1-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libtss2-esys-3.0.2-0t64_4.1.3-6 libtss2-mu-4.0.1-0t64_4.1.3-6 libtss2-rc0t64_4.1.3-6 libtss2-sys1t64_4.1.3-6 libtss2-tcti-cmd0t64_4.1.3-6 libtss2-tcti-device0t64_4.1.3-6 libtss2-tcti-mssim0t64_4.1.3-6 libtss2-tcti-swtpm0t64_4.1.3-6 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunbound8_1.25.1-1+b1 libunistring-dev_1.4.2-1 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libxml2-16_2.15.3+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-3+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mount_2.42.2-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc2-1 perl-base_5.44.0~rc2-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc2-1 pinentry-curses_1.3.3-2 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 samtools_1.22.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 systemd_261.1-2 systemd-tpm_261.1-2 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tpm-udev_4.1.3-6 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sun, 12 Jul 2026 00:04:04 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: stacks Binary: stacks Architecture: any Version: 2.68+dfsg-4 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 5171c790f396dddf0faad57f826f587b054fb7d5 12760 stacks_2.68+dfsg-4.debian.tar.xz Checksums-Sha256: d5277660330547502069d0976869038e9f47946ef7a8e91bf1213dbc0185072c 371032 stacks_2.68+dfsg.orig.tar.xz aebc888f632ad0f28656f2f6b492d9f08fa47b00ddf6d38320edddd5992bcbc8 12760 stacks_2.68+dfsg-4.debian.tar.xz Files: 13bbb30a0414696ac59e3d98d1723d00 371032 stacks_2.68+dfsg.orig.tar.xz 63ef43c270d3ba2f5116240e3adff6c8 12760 stacks_2.68+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEtSLzkVnaB9053AsR9LqqgNsoukwFAmnoMFgACgkQ9LqqgNso ukx7nRAAvyO64zmwCrfomHuSRhlHdM0uosSQVk7aiFflqK+3NCkzxPWVgZ3nPiUu Y/6F1c4yoEQfsQd0eNwpMCI0UZuMuogkzDpVDodvTc6weTeZn56LKG9H7RR3j1/1 JyUY77IxGKkfI20Ck+JyjaHHuDQ3l4wF2mgm00NVwS9Sr4vpC9OPIilWYregtB8q c464yFq5Y3Wnyqwj0vYPiGoAe9yICTjpki81TbYRGRu9+5z3JNE7hQ40GberJn+i WUp2+z/SA1sVmxbPsqGMCOVvflUyoZS+dUU8Y+LjJe2HyXFOjubpVz7eIoB6htg2 glkr+2DzJKMIquRfJEXHCCGTQJVV5PrgDPvj8MFAv9UXoRYpcysKzO4NfYgzywth EEkI3AVlHrmI3RdmrX/qPJvK1Jmfg11ZEUjnMBrPjAiU5Y1pA/XQNgCKcq2jg39N qE00UNLZYPeh2x/3MO9tmradpoQMoOc1w5OIRGem+Vf8m7v1Rqi6swYb5LxpMJ4b xvwP9BXDhGfWt/eMtr80/awRC5Lw5YPeWwC9tdYHMJYLwH9vX3Gc+/1sAkf4/7IR eP6ykeIeHKJNPdXDcFAcqFffHQIbncggmpoHm35ICOejBE6SXZgYKDWwSbrVbib3 8jXkDjg/sOvy7EciGTes7RLk79Oa4pDg5/bLOyX9NCrAxnII8SI= =mEdx -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-4.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./stacks_2.68+dfsg-4.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting stacks in /build/stacks-1GCgzd/stacks-2.68+dfsg dpkg-source: info: unpacking stacks_2.68+dfsg.orig.tar.xz dpkg-source: info: unpacking stacks_2.68+dfsg-4.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 dpkg-source: info: applying fix-build-with-gcc16.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sun, 12 Jul 2026 00:04:06 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network stacks_2.68+dfsg-4 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network stacks_2.68+dfsg-4 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-1GCgzd/stacks-2.68+dfsg SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-9310500b-7d93-4ab3-b63a-bc3cf42869d5 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-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Marcos Talau 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-1GCgzd/stacks-2.68+dfsg' dh_clean rm -f ./constants.php make[1]: Leaving directory '/build/stacks-1GCgzd/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-4.debian.tar.xz dpkg-source: info: building stacks in ../stacks_2.68+dfsg-4.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: configure.ac: no need to run autopoint (confirmed) autoreconf: running: /usr/bin/autoconf --force configure.ac:28: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:28: You should run autoupdate. ./lib/autoconf/headers.m4:664: AC_HEADER_STDC is expanded from... configure.ac:28: the top level autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing 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' autoreconf: configure.ac: not running make: --make not given autoreconf: Leaving directory '.' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/stacks-1GCgzd/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 whether UID '1002' is supported by ustar format... yes checking whether GID '110' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar 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 x86_64-linux-gnu-g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of x86_64-linux-gnu-g++... none checking for gcc... x86_64-linux-gnu-gcc checking whether the compiler supports GNU C... yes checking whether x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed checking whether x86_64-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-linux-gnu-gcc... none checking whether x86_64-linux-gnu-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 x86_64-linux-gnu-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 whether malloc (0) returns nonnull... yes checking whether realloc (0, 0) returns nonnull... 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-1GCgzd/stacks-2.68+dfsg' dh_auto_build make -j2 make[1]: Entering directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make all-recursive make[2]: Entering directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make[3]: Entering directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/ustacks.o src/ustacks.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/BamI.o src/BamI.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/cmb.o src/cmb.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/constants.o src/constants.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/DNANSeq.o src/DNANSeq.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/DNASeq4.o src/DNASeq4.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/DNASeq.o src/DNASeq.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/gzFasta.o src/gzFasta.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/input.o src/input.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/kmers.o src/kmers.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/locus.o src/locus.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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}} ); | ^ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/models.o src/models.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/mstack.o src/mstack.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/mst.o src/mst.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/nucleotides.o src/nucleotides.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/renz.o src/renz.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/Seq.o src/Seq.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/stacks.o src/stacks.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/utils.o src/utils.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/Vcf.o src/Vcf.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/cstacks.o src/cstacks.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/sstacks.o src/sstacks.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/clean.o src/clean.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/write.o src/write.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/populations.o src/populations.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/bootstrap.o src/bootstrap.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/PopSum.o src/PopSum.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/Hwp.o src/Hwp.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/phasedstacks.o src/phasedstacks.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/tsv2bam.o src/tsv2bam.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/gstacks.o src/gstacks.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o src/debruijn.o src/debruijn.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/stacks-1GCgzd/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-1GCgzd/stacks-2.68+dfsg' make[2]: Leaving directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make[1]: Leaving directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/stacks-1GCgzd/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-1GCgzd/stacks-2.68+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' dh_auto_install --no-parallel make -j1 install DESTDIR=/build/stacks-1GCgzd/stacks-2.68\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make[3]: Entering directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make[4]: Entering directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' /usr/bin/mkdir -p '/build/stacks-1GCgzd/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-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin' /usr/bin/mkdir -p '/build/stacks-1GCgzd/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-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin' make install-data-hook make[5]: Entering directory '/build/stacks-1GCgzd/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-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl > /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst mv /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl chmod +x /build/stacks-1GCgzd/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-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl > /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl.subst mv /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl chmod +x /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.68,' /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.68,' /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-samtools-tview rm -f /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp rm -f /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp chmod +x /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments chmod +x /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-dist-extract chmod +x /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-gdb make[5]: Leaving directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make[4]: Leaving directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make[3]: Leaving directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make[2]: Leaving directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' make[1]: Leaving directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/stacks-1GCgzd/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?' $f ; \ done dh_install make[1]: Leaving directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' dh_installdocs dh_installchangelogs dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/stacks-1GCgzd/stacks-2.68+dfsg' dh_link mkdir -p debian/stacks/usr/libexec/debian-med/bin cd debian/stacks/usr/libexec/debian-med/bin && \ for f in `ls /build/stacks-1GCgzd/stacks-2.68+dfsg/debian/stacks/usr/libexec/stacks/bin` ; do \ ln -s ../../stacks/bin/$f ; \ done make[1]: Leaving directory '/build/stacks-1GCgzd/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' in '../stacks_2.68+dfsg-4_amd64.deb'. dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.68+dfsg-4_amd64.deb'. dpkg-genbuildinfo -O../stacks_2.68+dfsg-4_amd64.buildinfo dpkg-genchanges -O../stacks_2.68+dfsg-4_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 2026-07-12T00:07:43Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 12 Jul 2026 00:07:43 +0000 | +------------------------------------------------------------------------------+ stacks_2.68+dfsg-4_amd64.changes: --------------------------------- Format: 1.8 Date: Tue, 21 Apr 2026 22:57:02 -0300 Source: stacks Binary: stacks stacks-dbgsym Architecture: source amd64 Version: 2.68+dfsg-4 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Marcos Talau Description: stacks - pipeline for building loci from short-read DNA sequences Closes: 1133636 Changes: stacks (2.68+dfsg-4) unstable; urgency=medium . * Team upload. * debian/patches/fix-build-with-gcc16.patch: New. Fix FTBFS with gcc-16. (Closes: #1133636) Checksums-Sha1: 88ecb74ad7b9e7016dc9565d7b21efef3eb28396 1138 stacks_2.68+dfsg-4.dsc 5171c790f396dddf0faad57f826f587b054fb7d5 12760 stacks_2.68+dfsg-4.debian.tar.xz 504664afabbd320790393f794ca37251b31c4168 30885788 stacks-dbgsym_2.68+dfsg-4_amd64.deb 9775fdcb77f5e918aeca2a262819c8786f4a60e8 7339 stacks_2.68+dfsg-4_amd64.buildinfo 422e2362f614cfc1c563065866612503ad1d3624 1272864 stacks_2.68+dfsg-4_amd64.deb Checksums-Sha256: 37f06184d973df75caecdb01bdb851be1a28f80c51ca5686559cbd4c3ca13a2a 1138 stacks_2.68+dfsg-4.dsc aebc888f632ad0f28656f2f6b492d9f08fa47b00ddf6d38320edddd5992bcbc8 12760 stacks_2.68+dfsg-4.debian.tar.xz c8f3cea45b0ec85258d8afaf3704bd55d952b627a8a255a6867982d961f9498e 30885788 stacks-dbgsym_2.68+dfsg-4_amd64.deb 876a58758bed16c9367f21321bfc2b9a4ecf2a4eb1b49445ea5eb62572e6d91b 7339 stacks_2.68+dfsg-4_amd64.buildinfo a9e8d0f10ac45d7675e0b2fd9094a274a7fa1daa9919f2a1eb8c714be2538e9a 1272864 stacks_2.68+dfsg-4_amd64.deb Files: 48e3abda65f14ab3c5dea210149dd34a 1138 science optional stacks_2.68+dfsg-4.dsc 63ef43c270d3ba2f5116240e3adff6c8 12760 science optional stacks_2.68+dfsg-4.debian.tar.xz 307beab840dab5cdeef94fd639270053 30885788 debug optional stacks-dbgsym_2.68+dfsg-4_amd64.deb 198817d532703cdff8f1962f586bb69e 7339 science optional stacks_2.68+dfsg-4_amd64.buildinfo 94403a4707dcfb73986e3f3468f1faf1 1272864 science optional stacks_2.68+dfsg-4_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 12 Jul 2026 00:07:43 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: stacks Binary: stacks stacks-dbgsym Architecture: amd64 source Version: 2.68+dfsg-4 Checksums-Md5: 48e3abda65f14ab3c5dea210149dd34a 1138 stacks_2.68+dfsg-4.dsc 307beab840dab5cdeef94fd639270053 30885788 stacks-dbgsym_2.68+dfsg-4_amd64.deb 94403a4707dcfb73986e3f3468f1faf1 1272864 stacks_2.68+dfsg-4_amd64.deb Checksums-Sha1: 88ecb74ad7b9e7016dc9565d7b21efef3eb28396 1138 stacks_2.68+dfsg-4.dsc 504664afabbd320790393f794ca37251b31c4168 30885788 stacks-dbgsym_2.68+dfsg-4_amd64.deb 422e2362f614cfc1c563065866612503ad1d3624 1272864 stacks_2.68+dfsg-4_amd64.deb Checksums-Sha256: 37f06184d973df75caecdb01bdb851be1a28f80c51ca5686559cbd4c3ca13a2a 1138 stacks_2.68+dfsg-4.dsc c8f3cea45b0ec85258d8afaf3704bd55d952b627a8a255a6867982d961f9498e 30885788 stacks-dbgsym_2.68+dfsg-4_amd64.deb a9e8d0f10ac45d7675e0b2fd9094a274a7fa1daa9919f2a1eb8c714be2538e9a 1272864 stacks_2.68+dfsg-4_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 12 Jul 2026 00:07:42 +0000 Build-Path: /build/stacks-1GCgzd/stacks-2.68+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-3), gettext-base (= 1.0-3), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-3), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbam-dev (= 0.1.19+dfsg-6), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbrotli-dev (= 1.2.0-3), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcc1-0 (= 16.1.0-2), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl3t64-gnutls (= 8.21.0-2), libcurl4-gnutls (= 8.21.0-2), libcurl4-gnutls-dev (= 8.21.0-2), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdeflate-dev (= 1.25-1), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.13-stable-1), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgnutls-dane0t64 (= 3.8.13-1), libgnutls28-dev (= 3.8.13-1), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgssapi-krb5-2 (= 1.22.1-3), libgssrpc4t64 (= 1.22.1-3), libhogweed6t64 (= 3.10.2-1+b1), libhts-dev (= 1.22.1+ds2-1+b2), libhts3t64 (= 1.22.1+ds2-1+b2), libhtscodecs2 (= 1.6.6-1), libhwasan0 (= 16.1.0-2), libidn2-0 (= 2.3.8-5), libidn2-dev (= 2.3.8-5), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), libk5crypto3 (= 1.22.1-3), libkadm5clnt-mit12 (= 1.22.1-3), libkadm5srv-mit12 (= 1.22.1-3), libkdb5-10t64 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5-dev (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap-dev (= 2.6.13+dfsg-1+b1), libldap2 (= 2.6.13+dfsg-1+b1), liblsan0 (= 16.1.0-2), liblzma-dev (= 5.8.3-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libncurses6 (= 6.6+20260608-2), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp2-dev (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libnghttp3-dev (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-gnutls-dev (= 1.22.1-1), libngtcp2-crypto-gnutls8 (= 1.22.1-1), libngtcp2-dev (= 1.22.1-1), libp11-kit-dev (= 0.26.4-1), libp11-kit0 (= 0.26.4-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc2-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.22.0-1), libpsl5t64 (= 0.22.0-1), libquadmath0 (= 16.1.0-2), librtmp-dev (= 2.6-1), librtmp1 (= 2.6-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.1-1), libselinux1 (= 3.11-2), libsframe3 (= 2.46.50.20260617-1), libsmartcols1 (= 2.42.2-1), libsparsehash-dev (= 2.0.4-1), libssh2-1-dev (= 1.11.1-4), libssh2-1t64 (= 1.11.1-4), libssl-dev (= 3.6.3-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd0 (= 261.1-2), libtasn1-6 (= 4.21.0-2+b1), libtasn1-6-dev (= 4.21.0-2+b1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunbound8 (= 1.25.1-1+b1), libunistring-dev (= 1.4.2-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libxml2-16 (= 2.15.3+dfsg-1), libzstd-dev (= 1.5.7+dfsg-3+b2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc2-1), perl-base (= 5.44.0~rc2-1), perl-modules-5.44 (= 5.44.0~rc2-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.4-1), samtools (= 1.22.1-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1776823022" +------------------------------------------------------------------------------+ | Package contents Sun, 12 Jul 2026 00:07:43 +0000 | +------------------------------------------------------------------------------+ stacks-dbgsym_2.68+dfsg-4_amd64.deb ----------------------------------- new Debian package, version 2.0. size 30885788 bytes: control archive=1100 bytes. 786 bytes, 12 lines control 1249 bytes, 12 lines md5sums Package: stacks-dbgsym Source: stacks Version: 2.68+dfsg-4 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 32307 Depends: stacks (= 2.68+dfsg-4) Section: debug Priority: optional Description: debug symbols for stacks Build-Ids: 158875fc614a8c7f375ae73a48b1ecf1e0c2637c 15dc61a8d061d96f9d8862b96325574e002523ac 28e304f11138c67d3a870e1450b005aa66b761c7 3801d46d92ea067b7c5e9e9a096172eeb1c0c933 4627856b1487593ce63650acf1d61e011dea8992 5f1d13b263ca8a59396ae411eb2a2cdef843ba95 7edce48fc4746f716654bda0c4b85635cff111fb 95427a81ef31e890e576384a978900704fd8cb6d ac35b38f71002a42c8965506ff7227466cdbdb01 c7fdeb53061885d574faaa2513a3dc7c2c509def dea797f448cd768c4928e72ae16ad2b3e3955370 drwxr-xr-x root/root 0 2026-04-22 01:57 ./ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/15/ -rw-r--r-- root/root 5220616 2026-04-22 01:57 ./usr/lib/debug/.build-id/15/8875fc614a8c7f375ae73a48b1ecf1e0c2637c.debug -rw-r--r-- root/root 1083248 2026-04-22 01:57 ./usr/lib/debug/.build-id/15/dc61a8d061d96f9d8862b96325574e002523ac.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/28/ -rw-r--r-- root/root 2510512 2026-04-22 01:57 ./usr/lib/debug/.build-id/28/e304f11138c67d3a870e1450b005aa66b761c7.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/38/ -rw-r--r-- root/root 2007944 2026-04-22 01:57 ./usr/lib/debug/.build-id/38/01d46d92ea067b7c5e9e9a096172eeb1c0c933.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/46/ -rw-r--r-- root/root 2784088 2026-04-22 01:57 ./usr/lib/debug/.build-id/46/27856b1487593ce63650acf1d61e011dea8992.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/5f/ -rw-r--r-- root/root 2679816 2026-04-22 01:57 ./usr/lib/debug/.build-id/5f/1d13b263ca8a59396ae411eb2a2cdef843ba95.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/7e/ -rw-r--r-- root/root 1673632 2026-04-22 01:57 ./usr/lib/debug/.build-id/7e/dce48fc4746f716654bda0c4b85635cff111fb.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/95/ -rw-r--r-- root/root 2216792 2026-04-22 01:57 ./usr/lib/debug/.build-id/95/427a81ef31e890e576384a978900704fd8cb6d.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/ac/ -rw-r--r-- root/root 2332216 2026-04-22 01:57 ./usr/lib/debug/.build-id/ac/35b38f71002a42c8965506ff7227466cdbdb01.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/c7/ -rw-r--r-- root/root 5996560 2026-04-22 01:57 ./usr/lib/debug/.build-id/c7/fdeb53061885d574faaa2513a3dc7c2c509def.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.build-id/de/ -rw-r--r-- root/root 3118744 2026-04-22 01:57 ./usr/lib/debug/.build-id/de/a797f448cd768c4928e72ae16ad2b3e3955370.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 1430544 2026-04-22 01:57 ./usr/lib/debug/.dwz/x86_64-linux-gnu/stacks.debug drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/share/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/share/doc/stacks-dbgsym -> stacks stacks_2.68+dfsg-4_amd64.deb ---------------------------- new Debian package, version 2.0. size 1272864 bytes: control archive=1608 bytes. 992 bytes, 20 lines control 1796 bytes, 25 lines md5sums Package: stacks Version: 2.68+dfsg-4 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 6253 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 2026-04-22 01:57 ./ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/bin/ -rwxr-xr-x root/root 775 2026-04-22 01:42 ./usr/bin/stacks drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/libexec/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/ lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/cstacks -> ../../stacks/bin/cstacks lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/gstacks -> ../../stacks/bin/gstacks lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/populations -> ../../stacks/bin/populations lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/ref_map -> ../../stacks/bin/ref_map lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/sstacks -> ../../stacks/bin/sstacks lrwxrwxrwx root/root 0 2026-04-22 01:57 ./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 2026-04-22 01:57 ./usr/libexec/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/stacks-private-alleles -> ../../stacks/bin/stacks-private-alleles lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/debian-med/bin/ustacks -> ../../stacks/bin/ustacks drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/libexec/stacks/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/libexec/stacks/bin/ -rwxr-xr-x root/root 422520 2026-04-22 01:57 ./usr/libexec/stacks/bin/clone_filter -rwxr-xr-x root/root 516088 2026-04-22 01:57 ./usr/libexec/stacks/bin/cstacks lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/stacks/bin/denovo_map -> denovo_map.pl -rwxr-xr-x root/root 32933 2026-04-22 01:57 ./usr/libexec/stacks/bin/denovo_map.pl -rwxr-xr-x root/root 872072 2026-04-22 01:57 ./usr/libexec/stacks/bin/gstacks -rwxr-xr-x root/root 291352 2026-04-22 01:57 ./usr/libexec/stacks/bin/kmer_filter -rwxr-xr-x root/root 393496 2026-04-22 01:57 ./usr/libexec/stacks/bin/phasedstacks -rwxr-xr-x root/root 1191384 2026-04-22 01:57 ./usr/libexec/stacks/bin/populations -rwxr-xr-x root/root 605720 2026-04-22 01:57 ./usr/libexec/stacks/bin/process_radtags -rwxr-xr-x root/root 427480 2026-04-22 01:57 ./usr/libexec/stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2026-04-22 01:57 ./usr/libexec/stacks/bin/ref_map -> ref_map.pl -rwxr-xr-x root/root 15395 2026-04-22 01:57 ./usr/libexec/stacks/bin/ref_map.pl -rwxr-xr-x root/root 470936 2026-04-22 01:57 ./usr/libexec/stacks/bin/sstacks -rwxr-xr-x root/root 1040 2026-04-22 01:57 ./usr/libexec/stacks/bin/stacks-count-reads-per-sample-per-locus -rwxr-xr-x root/root 7331 2026-04-22 01:57 ./usr/libexec/stacks/bin/stacks-dist-extract -rwxr-xr-x root/root 1244 2026-04-22 01:57 ./usr/libexec/stacks/bin/stacks-gdb -rwxr-xr-x root/root 1773 2026-04-22 01:57 ./usr/libexec/stacks/bin/stacks-hist2d-loci-samples-coverage -rwxr-xr-x root/root 22320 2026-04-22 01:57 ./usr/libexec/stacks/bin/stacks-integrate-alignments -rwxr-xr-x root/root 40422 2026-04-22 01:57 ./usr/libexec/stacks/bin/stacks-private-alleles -rwxr-xr-x root/root 3037 2026-04-22 01:57 ./usr/libexec/stacks/bin/stacks-samtools-tview -rwxr-xr-x root/root 495016 2026-04-22 01:57 ./usr/libexec/stacks/bin/tsv2bam -rwxr-xr-x root/root 504600 2026-04-22 01:57 ./usr/libexec/stacks/bin/ustacks drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/share/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-04-22 01:57 ./usr/share/doc/stacks/ -rw-r--r-- root/root 1451 2026-04-22 01:42 ./usr/share/doc/stacks/README.Debian -rw-r--r-- root/root 1254 2026-04-22 01:57 ./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 2026-04-22 01:42 ./usr/share/doc/stacks/copyright +------------------------------------------------------------------------------+ | Post Build Sun, 12 Jul 2026 00:07:44 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 12 Jul 2026 00:07:44 +0000 | +------------------------------------------------------------------------------+ Purging /build/stacks-1GCgzd Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 12 Jul 2026 00:07:45 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 404600 Build-Time: 217 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 13 Job: /srv/debomatic/incoming/stacks_2.68+dfsg-4.dsc Machine Architecture: amd64 Package: stacks Package-Time: 242 Source-Version: 2.68+dfsg-4 Space: 404600 Status: successful Version: 2.68+dfsg-4 -------------------------------------------------------------------------------- Finished at 2026-07-12T00:07:43Z Build needed 00:04:02, 404600k disk space