sbuild (Debian sbuild) 0.88.2 (16 January 2025) on carme.larted.org.uk +==============================================================================+ | stacks 2.68+dfsg-1 (amd64) Wed, 22 Jan 2025 15:07:37 +0000 | +==============================================================================+ Package: stacks Version: 2.68+dfsg-1 Source Version: 2.68+dfsg-1 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Wed, 22 Jan 2025 15:07:38 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup stacks_2.68+dfsg-1 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup stacks_2.68+dfsg-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Wed, 22 Jan 2025 15:07:38 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:2 http://deb.debian.org/debian unstable InRelease [205 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:3 file:/srv/reprepro perl-5.40/main amd64 Packages [8875 B] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian sid InRelease [205 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-22-1421.56-F-2025-01-20-0805.29.pdiff [170 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-22-1421.56-F-2025-01-20-0805.29.pdiff [170 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-22-1421.56-F-2025-01-20-0805.29.pdiff [171 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-22-1421.56-F-2025-01-20-0805.29.pdiff [171 kB] Fetched 878 kB in 8s (114 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2494 kB of archives. After this operation, 4096 B disk space will be freed. Get:1 http://deb.debian.org/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.24 [1114 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 apt amd64 2.9.24 [1380 kB] Fetched 2494 kB in 0s (62.6 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.24_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.24) over (2.9.23) ... Setting up libapt-pkg6.0t64:amd64 (2.9.24) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.24_amd64.deb ... Unpacking apt (2.9.24) over (2.9.23) ... Setting up apt (2.9.24) ... Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Fetch source files Wed, 22 Jan 2025 15:07:50 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/stacks_2.68+dfsg-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 22 Jan 2025 15:07:51 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/stacks-R4bWFK/resolver-qrtCzu/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/stacks-R4bWFK/resolver-qrtCzu/apt_archive ./ InRelease Get:2 copy:/build/stacks-R4bWFK/resolver-qrtCzu/apt_archive ./ Release [609 B] Ign:3 copy:/build/stacks-R4bWFK/resolver-qrtCzu/apt_archive ./ Release.gpg Get:4 copy:/build/stacks-R4bWFK/resolver-qrtCzu/apt_archive ./ Sources [665 B] Get:5 copy:/build/stacks-R4bWFK/resolver-qrtCzu/apt_archive ./ Packages [704 B] Fetched 1978 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils 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 libicu72 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 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 libicu72 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, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 38.0 MB of archives. After this operation, 137 MB of additional disk space will be used. Get:1 copy:/build/stacks-R4bWFK/resolver-qrtCzu/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [884 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get:25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [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 13.24.1 [920 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [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+b6 [302 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [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 [75.5 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 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 8.11.1-1+b1 [360 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 3.8.8-2 [449 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 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 4.19.0-3+b3 [98.9 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+b1 [1317 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.0-2 [2790 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.1-1+b1 [475 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Preconfiguring packages ... Fetched 38.0 MB in 0s (93.8 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_amd64.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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Setting up libdeflate-dev:amd64 (1.23-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libtool (2.5.4-2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.9.1-1) ... Setting up libngtcp2-dev:amd64 (1.9.1-1) ... 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 (1.21.3-4) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-4) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-4) ... Setting up libkdb5-10t64:amd64 (1.21.3-4) ... Setting up debhelper (13.24.1) ... Setting up samtools (1.20-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-4) ... Setting up krb5-multidev:amd64 (1.21.3-4) ... Setting up libkrb5-dev:amd64 (1.21.3-4) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.1-1+b1) ... Setting up libhts-dev:amd64 (1.20+ds-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Check architectures Wed, 22 Jan 2025 15:08:01 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Wed, 22 Jan 2025 15:08:01 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.11.10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1 (2024-11-23) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.14 g++-13_13.3.0-12 g++-14_14.2.0-14 gcc-13_13.3.0-12 gcc-14_14.2.0-14 libc6-dev_2.40-5 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 linux-libc-dev_6.12.10-1 Package versions: adduser_3.137 apt_2.9.24 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20250108-1 binutils-common_2.43.50.20250108-1 binutils-x86-64-linux-gnu_2.43.50.20250108-1 bsdextrautils_2.40.4-1 bsdutils_1:2.40.4-1 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-13_13.3.0-12 cpp-13-x86-64-linux-gnu_13.3.0-12 cpp-14_14.2.0-14 cpp-14-x86-64-linux-gnu_14.2.0-14 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-11 debconf_1.5.89 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-1 diffutils_1:3.10-2 dirmngr_2.2.46-1+b1 dpkg_1.22.14 dpkg-dev_1.22.14 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.3.0-12 g++-13-x86-64-linux-gnu_13.3.0-12 g++-14_14.2.0-14 g++-14-x86-64-linux-gnu_14.2.0-14 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.3.0-12 gcc-13-base_13.3.0-12 gcc-13-x86-64-linux-gnu_13.3.0-12 gcc-14_14.2.0-14 gcc-14-base_14.2.0-14 gcc-14-x86-64-linux-gnu_14.2.0-14 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 gnupg_2.2.46-1 gnupg-l10n_2.2.46-1 gnupg-utils_2.2.46-1+b1 gpg_2.2.46-1+b1 gpg-agent_2.2.46-1+b1 gpg-wks-client_2.2.46-1+b1 gpgconf_2.2.46-1+b1 gpgsm_2.2.46-1+b1 gpgv_2.2.46-1+b1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-4 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.24 libarchive-zip-perl_1.68-1 libasan8_14.2.0-14 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-14 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b1 libbam-dev_0.1.19+dfsg-6 libbinutils_2.43.50.20250108-1 libblkid1_2.40.4-1 libbrotli-dev_1.1.0-2+b6 libbrotli1_1.1.0-2+b6 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.40-5 libc-dev-bin_2.40-5 libc-l10n_2.40-5 libc6_2.40-5 libc6-dev_2.40-5 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-14 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.43.50.20250108-1 libctf0_2.43.50.20250108-1 libcurl3t64-gnutls_8.11.1-1+b1 libcurl4-gnutls-dev_8.11.1-1+b1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdeflate-dev_1.23-1+b1 libdeflate0_1.23-1+b1 libdpkg-perl_1.22.14 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.1-1 libgcc-13-dev_13.3.0-12 libgcc-14-dev_14.2.0-14 libgcc-s1_14.2.0-14 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_3.8.8-2 libgnutls-openssl27t64_3.8.8-2 libgnutls28-dev_3.8.8-2 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-14 libgpg-error0_1.51-3 libgprofng0_2.43.50.20250108-1 libgssapi-krb5-2_1.21.3-4 libgssrpc4t64_1.21.3-4 libhogweed6t64_3.10-1+b1 libhts-dev_1.20+ds-2 libhts3t64_1.20+ds-2 libhtscodecs2_1.6.1-1 libhwasan0_14.2.0-14 libicu72_72.1-6 libidn2-0_2.3.7-2+b1 libidn2-dev_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-14 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-4 libkadm5clnt-mit12_1.21.3-4 libkadm5srv-mit12_1.21.3-4 libkdb5-10t64_1.21.3-4 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-4 libkrb5-dev_1.21.3-4 libkrb5support0_1.21.3-4 libksba8_1.6.7-2+b1 libldap-2.5-0_2.5.19+dfsg-1 libldap-dev_2.6.9+dfsg-1 libldap2_2.6.9+dfsg-1 liblsan0_14.2.0-14 liblz4-1_1.9.4-4 liblzma-dev_5.6.3-1+b1 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmount1_2.40.4-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libncurses6_6.5-2+b1 libncursesw6_6.5-2+b1 libnettle8t64_3.10-1+b1 libnghttp2-14_1.64.0-1 libnghttp2-dev_1.64.0-1 libnghttp3-9_1.6.0-2 libnghttp3-dev_1.6.0-2 libngtcp2-16_1.9.1-1 libngtcp2-crypto-gnutls-dev_1.9.1-1 libngtcp2-crypto-gnutls8_1.9.1-1 libngtcp2-dev_1.9.1-1 libnpth0t64_1.8-2 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libpcre2-8-0_10.44-5 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-1 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_14.2.0-14 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+dfsg1-8+b1 libsasl2-modules-db_2.1.28+dfsg1-8+b1 libseccomp2_2.5.5-2 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libsframe1_2.43.50.20250108-1 libsmartcols1_2.40.4-1 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.46.1-1 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.4.0-2 libssl3t64_3.4.0-2 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 libsystemd0_257.2-2 libtasn1-6_4.19.0-3+b3 libtasn1-6-dev_4.19.0-3+b3 libtinfo6_6.5-2+b1 libtool_2.5.4-2 libtsan2_14.2.0-14 libubsan1_14.2.0-14 libuchardet0_0.0.8-1+b2 libudev1_257.2-2 libunbound8_1.22.0-1+b1 libunistring5_1.3-1 libuuid1_2.40.4-1 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxxhash0_0.8.3-2 libzstd-dev_1.5.6+dfsg-2 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.10-1 locales-all_2.40-5 login_1:4.16.0-2+really2.40.4-1 login.defs_1:4.16.0-7 m4_1.4.19-5 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 nettle-dev_3.10-1+b1 openssl-provider-legacy_3.4.0-2 passwd_1:4.16.0-7 patch_2.7.6-7 perl_5.40.1-1 perl-base_5.40.1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-1 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_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sqv_1.2.1-5 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 usr-is-merged_39+nmu2 util-linux_2.40.4-1 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Wed, 22 Jan 2025 15:08:01 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: stacks Binary: stacks Architecture: any Version: 2.68+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://creskolab.uoregon.edu/stacks/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/stacks Vcs-Git: https://salsa.debian.org/med-team/stacks.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev Package-List: stacks deb science optional arch=any Checksums-Sha1: 84d9fefcc2da0bdeedd86d7dc994ef5b84012806 371032 stacks_2.68+dfsg.orig.tar.xz 2ae2f8bb561ab10fd538b4a2aeae7efc6975709d 12224 stacks_2.68+dfsg-1.debian.tar.xz Checksums-Sha256: d5277660330547502069d0976869038e9f47946ef7a8e91bf1213dbc0185072c 371032 stacks_2.68+dfsg.orig.tar.xz e82a33ae713b469deb6894e91356092ad49b37154665af8112dcde78f93bebaf 12224 stacks_2.68+dfsg-1.debian.tar.xz Files: 13bbb30a0414696ac59e3d98d1723d00 371032 stacks_2.68+dfsg.orig.tar.xz f668530ee6a2d621c2db77deee8e7dc9 12224 stacks_2.68+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbS6dEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoV8BAAngn3fAqKfwZK8rxd+k8/0qpElpLX ioQsk/rGfA37Ds8kNitjOUZveZFfVGa6Q1XB687gjWTHHcovoU8XpJD06zUvtCwe MQwK1wl7LPzK/m+9wPPHXh7RF5uqeKsWCspBTdlC+5Ei4B2azoYkEzyh1gcltwMF i7lNDMa4kt4A/06AfroqewGRAg0f8oRWBkOIqBO78l7cicT1tE/k1FrFCXpmn1qk v9Tz78uy/8YAGCqlAicAtqo+CCq0yJmsTW92jTD6AHx0EcwWhBYUZ9PdpOJnuNar JPKjlNDkPquwVrZ5s6jOX5lRk6adhFxCdugm3YXzvpIXghNmlcbVOfzqtzVkiRa0 +BdMzNsaOwkwEYiPdaI2Y6Gi68KsSFV52WGUC61s9Uk0sTWuuOo4i23YaGbNWtyX X50Kz0gKXlaFZJWt5scW0ntMRoCi79Ad8VQcMRl/B7zjbEZgkM9XolGdciQ5Z1O4 nSuE7Eiz/TRKbI5HHbpH23VJoqOty3CQiIrri4VCFKFtgJqJBWlMmZUIx7S2ftaP K/nCCxJgBB3dKI+mNTZmfM52Lsy7ayYfVSaABdEJSP62UIj12SB3TvdtzJtzFAWi 6F9lL9kpE8EeX80imGVJ0/RA25UE8JEB68j3TC5QgSGH32ZeZoyVYJFeWVS3aPjk 2rqDe7ayCe+sj+I= =L+YB -----END PGP SIGNATURE----- gpgv: Signature made Sat Aug 31 10:00:49 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting stacks in /build/stacks-R4bWFK/stacks-2.68+dfsg dpkg-source: info: unpacking stacks_2.68+dfsg.orig.tar.xz dpkg-source: info: unpacking stacks_2.68+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying RisR.patch dpkg-source: info: applying script-exe-paths dpkg-source: info: applying use_debian_packaged_htslib.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying change_program_exit_to_success.patch dpkg-source: info: applying offer_help_option_for_stacks_gdb.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Wed, 22 Jan 2025 15:08:02 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network stacks_2.68+dfsg-1 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network stacks_2.68+dfsg-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/stacks-R4bWFK/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-128e6a72-a1f6-43ab-a275-7fd2842932f4 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-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' dh_clean rm -f ./constants.php make[1]: Leaving directory '/build/stacks-R4bWFK/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-1.debian.tar.xz dpkg-source: info: building stacks in stacks_2.68+dfsg-1.dsc debian/rules binary dh binary dh_update_autotools_config 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-R4bWFK/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 build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking whether g++ supports C++11 features by default... yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for gcc option to support OpenMP... -fopenmp checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for clock_gettime... yes checking for functional regular expressions... yes checking for gawk... (cached) mawk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' dh_auto_build make -j2 make[1]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make all-recursive make[2]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make[3]: Entering directory '/build/stacks-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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 cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcore.a rm -f libclean.a ar cru libclean.a src/clean.o src/kmers.o src/file_io.o src/write.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libclean.a rm -f libpop.a ar cru libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpop.a g++ -g -O2 -ffile-prefix-map=/build/stacks-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/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-R4bWFK/stacks-2.68+dfsg' make[2]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make[1]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' if [ -e /usr/share/automake-1.16/tap-driver.sh ] ; then \ ln -s /usr/share/automake-1.16/tap-driver.sh tests/tap-driver.sh ; \ else \ echo "Make sure /usr/share/automake-*/tap-driver.sh exists and is linked" ; \ false ; \ fi # dh_auto_test rm tests/tap-driver.sh # FIXME: Does not work even after this trick. See # https://groups.google.com/forum/#!msg/stacks-users/TA2tMEqb4Mg/pQy4fUCYi9kJ true make[1]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' dh_auto_install --no-parallel make -j1 install DESTDIR=/build/stacks-R4bWFK/stacks-2.68\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make[3]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make[4]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' /usr/bin/mkdir -p '/build/stacks-R4bWFK/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-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin' /usr/bin/mkdir -p '/build/stacks-R4bWFK/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-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin' make install-data-hook make[5]: Entering directory '/build/stacks-R4bWFK/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-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl > /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst mv /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl chmod +x /build/stacks-R4bWFK/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-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl > /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl.subst mv /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl chmod +x /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.68,' /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.68,' /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-samtools-tview rm -f /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp rm -f /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp chmod +x /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments chmod +x /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-dist-extract chmod +x /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-gdb make[5]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make[4]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make[3]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make[2]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' make[1]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/stacks-R4bWFK/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?' $f ; \ done dh_install make[1]: Leaving directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' dh_installdocs dh_installchangelogs dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/stacks-R4bWFK/stacks-2.68+dfsg' dh_link mkdir -p debian/stacks/usr/libexec/debian-med/bin cd debian/stacks/usr/libexec/debian-med/bin && \ for f in `ls /build/stacks-R4bWFK/stacks-2.68+dfsg/debian/stacks/usr/libexec/stacks/bin` ; do \ ln -s ../../stacks/bin/$f ; \ done make[1]: Leaving directory '/build/stacks-R4bWFK/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-1_amd64.deb'. dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.68+dfsg-1_amd64.deb'. dpkg-genbuildinfo -O../stacks_2.68+dfsg-1_amd64.buildinfo dpkg-genchanges -O../stacks_2.68+dfsg-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2025-01-22T15:12:20Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 22 Jan 2025 15:12:21 +0000 | +------------------------------------------------------------------------------+ stacks_2.68+dfsg-1_amd64.changes: --------------------------------- Format: 1.8 Date: Sat, 31 Aug 2024 11:24:11 +0200 Source: stacks Binary: stacks stacks-dbgsym Architecture: source amd64 Version: 2.68+dfsg-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: stacks - pipeline for building loci from short-read DNA sequences Changes: stacks (2.68+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version 2.68+dfsg * d/patches/*: unfuzz. Checksums-Sha1: b73792dbd1c67f1fef805700d532abf52ea03167 1158 stacks_2.68+dfsg-1.dsc 84d9fefcc2da0bdeedd86d7dc994ef5b84012806 371032 stacks_2.68+dfsg.orig.tar.xz 2ae2f8bb561ab10fd538b4a2aeae7efc6975709d 12224 stacks_2.68+dfsg-1.debian.tar.xz 6d9c3e0eb7ac393c4ed1ca2fe860988b1b42178c 30736540 stacks-dbgsym_2.68+dfsg-1_amd64.deb c5968286070cccbfe5a49c61a8dae30ee5507159 7543 stacks_2.68+dfsg-1_amd64.buildinfo 93109c432349937261c3da821d5862a7ea489153 1261044 stacks_2.68+dfsg-1_amd64.deb Checksums-Sha256: 7dc157d052af08c5103397e70a87870daeccdf3d13c332d0ea5eea4ce0adecc4 1158 stacks_2.68+dfsg-1.dsc d5277660330547502069d0976869038e9f47946ef7a8e91bf1213dbc0185072c 371032 stacks_2.68+dfsg.orig.tar.xz e82a33ae713b469deb6894e91356092ad49b37154665af8112dcde78f93bebaf 12224 stacks_2.68+dfsg-1.debian.tar.xz 450e19f9c9566f12c9bd878a76f462816317d4f76d6e9e7f03babb561b4c7488 30736540 stacks-dbgsym_2.68+dfsg-1_amd64.deb 4730a2eb44f4b6ec7858c004296bff5d3c1086dcd4a07983295398932013d86d 7543 stacks_2.68+dfsg-1_amd64.buildinfo 2cf8b1f9714f6876f6e130f0d6956f5ef50815c09c921065c3152941d00f68cb 1261044 stacks_2.68+dfsg-1_amd64.deb Files: 6621878051ed173a2d9d8744c60a6b43 1158 science optional stacks_2.68+dfsg-1.dsc 13bbb30a0414696ac59e3d98d1723d00 371032 science optional stacks_2.68+dfsg.orig.tar.xz f668530ee6a2d621c2db77deee8e7dc9 12224 science optional stacks_2.68+dfsg-1.debian.tar.xz 6abc88bccbc48336437aab6430154494 30736540 debug optional stacks-dbgsym_2.68+dfsg-1_amd64.deb 0a5026a2aeb605135e2429b1bb0f7de8 7543 science optional stacks_2.68+dfsg-1_amd64.buildinfo 9d5ccb4d65adc9c1d58faf9b1c0421b9 1261044 science optional stacks_2.68+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Wed, 22 Jan 2025 15:12:21 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: stacks Binary: stacks stacks-dbgsym Architecture: amd64 source Version: 2.68+dfsg-1 Checksums-Md5: 6621878051ed173a2d9d8744c60a6b43 1158 stacks_2.68+dfsg-1.dsc 6abc88bccbc48336437aab6430154494 30736540 stacks-dbgsym_2.68+dfsg-1_amd64.deb 9d5ccb4d65adc9c1d58faf9b1c0421b9 1261044 stacks_2.68+dfsg-1_amd64.deb Checksums-Sha1: b73792dbd1c67f1fef805700d532abf52ea03167 1158 stacks_2.68+dfsg-1.dsc 6d9c3e0eb7ac393c4ed1ca2fe860988b1b42178c 30736540 stacks-dbgsym_2.68+dfsg-1_amd64.deb 93109c432349937261c3da821d5862a7ea489153 1261044 stacks_2.68+dfsg-1_amd64.deb Checksums-Sha256: 7dc157d052af08c5103397e70a87870daeccdf3d13c332d0ea5eea4ce0adecc4 1158 stacks_2.68+dfsg-1.dsc 450e19f9c9566f12c9bd878a76f462816317d4f76d6e9e7f03babb561b4c7488 30736540 stacks-dbgsym_2.68+dfsg-1_amd64.deb 2cf8b1f9714f6876f6e130f0d6956f5ef50815c09c921065c3152941d00f68cb 1261044 stacks_2.68+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 22 Jan 2025 15:12:20 +0000 Build-Path: /build/stacks-R4bWFK/stacks-2.68+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.23.1-1), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.6), bash (= 5.2.37-1), binutils (= 2.43.50.20250108-1), binutils-common (= 2.43.50.20250108-1), binutils-x86-64-linux-gnu (= 2.43.50.20250108-1), bsdextrautils (= 2.40.4-1), bsdutils (= 1:2.40.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), comerr-dev (= 2.1-1.47.2-1), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-12), cpp-13-x86-64-linux-gnu (= 13.3.0-12), cpp-14 (= 14.2.0-14), cpp-14-x86-64-linux-gnu (= 14.2.0-14), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-11), debconf (= 1.5.89), debhelper (= 13.24.1), debianutils (= 5.21), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-1), diffutils (= 1:3.10-2), dpkg (= 1.22.14), dpkg-dev (= 1.22.14), dwz (= 0.15-1+b1), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-14), g++-14-x86-64-linux-gnu (= 14.2.0-14), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.3.0-12), gcc-13-base (= 13.3.0-12), gcc-13-x86-64-linux-gnu (= 13.3.0-12), gcc-14 (= 14.2.0-14), gcc-14-base (= 14.2.0-14), gcc-14-x86-64-linux-gnu (= 14.2.0-14), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-4), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-14), libatomic1 (= 14.2.0-14), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b1), libbam-dev (= 0.1.19+dfsg-6), libbinutils (= 2.43.50.20250108-1), libblkid1 (= 2.40.4-1), libbrotli-dev (= 1.1.0-2+b6), libbrotli1 (= 1.1.0-2+b6), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.40-5), libc-dev-bin (= 2.40-5), libc6 (= 2.40-5), libc6-dev (= 2.40-5), libcap-ng0 (= 0.8.5-4), libcap2 (= 1:2.66-5+b1), libcc1-0 (= 14.2.0-14), libcom-err2 (= 1.47.2-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.43.50.20250108-1), libctf0 (= 2.43.50.20250108-1), libcurl3t64-gnutls (= 8.11.1-1+b1), libcurl4-gnutls-dev (= 8.11.1-1+b1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.277), libdebhelper-perl (= 13.24.1), libdeflate-dev (= 1.23-1+b1), libdeflate0 (= 1.23-1+b1), libdpkg-perl (= 1.22.14), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.1-1), libgcc-13-dev (= 13.3.0-12), libgcc-14-dev (= 14.2.0-14), libgcc-s1 (= 14.2.0-14), 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 (= 3.8.8-2), libgnutls-openssl27t64 (= 3.8.8-2), libgnutls28-dev (= 3.8.8-2), libgnutls30t64 (= 3.8.8-2), libgomp1 (= 14.2.0-14), libgprofng0 (= 2.43.50.20250108-1), libgssapi-krb5-2 (= 1.21.3-4), libgssrpc4t64 (= 1.21.3-4), libhogweed6t64 (= 3.10-1+b1), libhts-dev (= 1.20+ds-2), libhts3t64 (= 1.20+ds-2), libhtscodecs2 (= 1.6.1-1), libhwasan0 (= 14.2.0-14), libicu72 (= 72.1-6), libidn2-0 (= 2.3.7-2+b1), libidn2-dev (= 2.3.7-2+b1), libisl23 (= 0.27-1), libitm1 (= 14.2.0-14), libjansson4 (= 2.14-2+b3), libk5crypto3 (= 1.21.3-4), libkadm5clnt-mit12 (= 1.21.3-4), libkadm5srv-mit12 (= 1.21.3-4), libkdb5-10t64 (= 1.21.3-4), libkeyutils1 (= 1.6.3-4), libkrb5-3 (= 1.21.3-4), libkrb5-dev (= 1.21.3-4), libkrb5support0 (= 1.21.3-4), libldap-dev (= 2.6.9+dfsg-1), libldap2 (= 2.6.9+dfsg-1), liblsan0 (= 14.2.0-14), liblzma-dev (= 5.6.3-1+b1), liblzma5 (= 5.6.3-1+b1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.40.4-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.1-1+b2), libncurses6 (= 6.5-2+b1), libnettle8t64 (= 3.10-1+b1), libnghttp2-14 (= 1.64.0-1), libnghttp2-dev (= 1.64.0-1), libnghttp3-9 (= 1.6.0-2), libnghttp3-dev (= 1.6.0-2), libngtcp2-16 (= 1.9.1-1), libngtcp2-crypto-gnutls-dev (= 1.9.1-1), libngtcp2-crypto-gnutls8 (= 1.9.1-1), libngtcp2-dev (= 1.9.1-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7+b1), libpcre2-8-0 (= 10.44-5), libperl5.40 (= 5.40.1-1), 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 (= 14.2.0-14), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-8+b1), libsasl2-modules-db (= 2.1.28+dfsg1-8+b1), libseccomp2 (= 2.5.5-2), libselinux1 (= 3.7-3+b1), libsframe1 (= 2.43.50.20250108-1), libsmartcols1 (= 2.40.4-1), libsparsehash-dev (= 2.0.3-2), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.4.0-2), libssl3t64 (= 3.4.0-2), libstdc++-14-dev (= 14.2.0-14), libstdc++6 (= 14.2.0-14), libsystemd0 (= 257.2-2), libtasn1-6 (= 4.19.0-3+b3), libtasn1-6-dev (= 4.19.0-3+b3), libtinfo6 (= 6.5-2+b1), libtool (= 2.5.4-2), libtsan2 (= 14.2.0-14), libubsan1 (= 14.2.0-14), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.2-2), libunbound8 (= 1.22.0-1+b1), libunistring5 (= 1.3-1), libuuid1 (= 2.40.4-1), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libzstd-dev (= 1.5.6+dfsg-2), libzstd1 (= 1.5.6+dfsg-2), linux-libc-dev (= 6.12.10-1), m4 (= 1.4.19-5), make (= 4.4.1-1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), nettle-dev (= 3.10-1+b1), openssl-provider-legacy (= 3.4.0-2), patch (= 2.7.6-7), perl (= 5.40.1-1), perl-base (= 5.40.1-1), perl-modules-5.40 (= 5.40.1-1), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.13-1), tar (= 1.35+dfsg-3.1), util-linux (= 2.40.4-1), xz-utils (= 5.6.3-1+b1), 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="1725096251" +------------------------------------------------------------------------------+ | Package contents Wed, 22 Jan 2025 15:12:21 +0000 | +------------------------------------------------------------------------------+ stacks-dbgsym_2.68+dfsg-1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 30736540 bytes: control archive=1100 bytes. 786 bytes, 12 lines control 1249 bytes, 12 lines md5sums Package: stacks-dbgsym Source: stacks Version: 2.68+dfsg-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 32146 Depends: stacks (= 2.68+dfsg-1) Section: debug Priority: optional Description: debug symbols for stacks Build-Ids: 04b2d7810843ebbf3b08995312f50e9a4d96f065 294c01b1bcf8faebce89e34ce4c4903aba7d7b38 2daeea8c39261189e080a962b351b7c95ed596ac 3b084710d4123b7840822fb3863526581c97f26d 3f6d1a52e68df037094ee2acb2860d8474302458 522e966e821396220e1f078561bd69757f8fc087 604ab67f29351236c471ae3ea259758b88bf6cbd 657b6994946c06e90b25e00d8b7a2deea207a339 81d43ed8ad2f4ea3b1de6049ef2abd804dd4e2ad b4815e401bb83fa60ce472e8ca8c0d1dbfb7e9c4 fe73f747c67db16a7ca4d7b12b8d81cfaf404833 drwxr-xr-x root/root 0 2024-08-31 09:24 ./ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/04/ -rw-r--r-- root/root 3146768 2024-08-31 09:24 ./usr/lib/debug/.build-id/04/b2d7810843ebbf3b08995312f50e9a4d96f065.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/29/ -rw-r--r-- root/root 2139552 2024-08-31 09:24 ./usr/lib/debug/.build-id/29/4c01b1bcf8faebce89e34ce4c4903aba7d7b38.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/2d/ -rw-r--r-- root/root 2727456 2024-08-31 09:24 ./usr/lib/debug/.build-id/2d/aeea8c39261189e080a962b351b7c95ed596ac.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/3b/ -rw-r--r-- root/root 2444792 2024-08-31 09:24 ./usr/lib/debug/.build-id/3b/084710d4123b7840822fb3863526581c97f26d.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/3f/ -rw-r--r-- root/root 6006488 2024-08-31 09:24 ./usr/lib/debug/.build-id/3f/6d1a52e68df037094ee2acb2860d8474302458.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/52/ -rw-r--r-- root/root 2789008 2024-08-31 09:24 ./usr/lib/debug/.build-id/52/2e966e821396220e1f078561bd69757f8fc087.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/60/ -rw-r--r-- root/root 2233288 2024-08-31 09:24 ./usr/lib/debug/.build-id/60/4ab67f29351236c471ae3ea259758b88bf6cbd.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/65/ -rw-r--r-- root/root 5242368 2024-08-31 09:24 ./usr/lib/debug/.build-id/65/7b6994946c06e90b25e00d8b7a2deea207a339.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/81/ -rw-r--r-- root/root 2057632 2024-08-31 09:24 ./usr/lib/debug/.build-id/81/d43ed8ad2f4ea3b1de6049ef2abd804dd4e2ad.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/b4/ -rw-r--r-- root/root 1631712 2024-08-31 09:24 ./usr/lib/debug/.build-id/b4/815e401bb83fa60ce472e8ca8c0d1dbfb7e9c4.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.build-id/fe/ -rw-r--r-- root/root 1040360 2024-08-31 09:24 ./usr/lib/debug/.build-id/fe/73f747c67db16a7ca4d7b12b8d81cfaf404833.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 1429520 2024-08-31 09:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/stacks.debug drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/share/doc/stacks-dbgsym -> stacks stacks_2.68+dfsg-1_amd64.deb ---------------------------- new Debian package, version 2.0. size 1261044 bytes: control archive=1608 bytes. 992 bytes, 20 lines control 1796 bytes, 25 lines md5sums Package: stacks Version: 2.68+dfsg-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 6161 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 14), zlib1g (>= 1:1.2.6), samtools, libdbi-perl, bsdextrautils, python3 Recommends: libspreadsheet-writeexcel-perl, littler Suggests: gdb Provides: stacks-web Section: science Priority: optional Homepage: https://creskolab.uoregon.edu/stacks/ Description: pipeline for building loci from short-read DNA sequences Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. . Note that this package installs Stacks such that all commands must be run as: $ stacks drwxr-xr-x root/root 0 2024-08-31 09:24 ./ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/bin/ -rwxr-xr-x root/root 775 2024-08-31 09:15 ./usr/bin/stacks drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/ lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/cstacks -> ../../stacks/bin/cstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/gstacks -> ../../stacks/bin/gstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/populations -> ../../stacks/bin/populations lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/ref_map -> ../../stacks/bin/ref_map lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/sstacks -> ../../stacks/bin/sstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-count-reads-per-sample-per-locus -> ../../stacks/bin/stacks-count-reads-per-sample-per-locus lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-private-alleles -> ../../stacks/bin/stacks-private-alleles lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/debian-med/bin/ustacks -> ../../stacks/bin/ustacks drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/stacks/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/libexec/stacks/bin/ -rwxr-xr-x root/root 418424 2024-08-31 09:24 ./usr/libexec/stacks/bin/clone_filter -rwxr-xr-x root/root 503800 2024-08-31 09:24 ./usr/libexec/stacks/bin/cstacks lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/stacks/bin/denovo_map -> denovo_map.pl -rwxr-xr-x root/root 32933 2024-08-31 09:24 ./usr/libexec/stacks/bin/denovo_map.pl -rwxr-xr-x root/root 863880 2024-08-31 09:24 ./usr/libexec/stacks/bin/gstacks -rwxr-xr-x root/root 287256 2024-08-31 09:24 ./usr/libexec/stacks/bin/kmer_filter -rwxr-xr-x root/root 381208 2024-08-31 09:24 ./usr/libexec/stacks/bin/phasedstacks -rwxr-xr-x root/root 1187288 2024-08-31 09:24 ./usr/libexec/stacks/bin/populations -rwxr-xr-x root/root 589336 2024-08-31 09:24 ./usr/libexec/stacks/bin/process_radtags -rwxr-xr-x root/root 423384 2024-08-31 09:24 ./usr/libexec/stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2024-08-31 09:24 ./usr/libexec/stacks/bin/ref_map -> ref_map.pl -rwxr-xr-x root/root 15395 2024-08-31 09:24 ./usr/libexec/stacks/bin/ref_map.pl -rwxr-xr-x root/root 458648 2024-08-31 09:24 ./usr/libexec/stacks/bin/sstacks -rwxr-xr-x root/root 1040 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-count-reads-per-sample-per-locus -rwxr-xr-x root/root 7331 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-dist-extract -rwxr-xr-x root/root 1244 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-gdb -rwxr-xr-x root/root 1773 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-hist2d-loci-samples-coverage -rwxr-xr-x root/root 22320 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-integrate-alignments -rwxr-xr-x root/root 40422 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-private-alleles -rwxr-xr-x root/root 3037 2024-08-31 09:24 ./usr/libexec/stacks/bin/stacks-samtools-tview -rwxr-xr-x root/root 482728 2024-08-31 09:24 ./usr/libexec/stacks/bin/tsv2bam -rwxr-xr-x root/root 500504 2024-08-31 09:24 ./usr/libexec/stacks/bin/ustacks drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-08-31 09:24 ./usr/share/doc/stacks/ -rw-r--r-- root/root 1451 2024-08-31 09:15 ./usr/share/doc/stacks/README.Debian -rw-r--r-- root/root 1430 2024-08-31 09:24 ./usr/share/doc/stacks/changelog.Debian.gz -rw-r--r-- root/root 32538 2024-08-23 15:56 ./usr/share/doc/stacks/changelog.gz -rw-r--r-- root/root 1730 2024-08-31 09:15 ./usr/share/doc/stacks/copyright +------------------------------------------------------------------------------+ | Post Build Wed, 22 Jan 2025 15:12:22 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Wed, 22 Jan 2025 15:12:22 +0000 | +------------------------------------------------------------------------------+ Purging /build/stacks-R4bWFK Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 22 Jan 2025 15:12:23 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 395912 Build-Time: 258 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 10 Job: /srv/debomatic/incoming/stacks_2.68+dfsg-1.dsc Machine Architecture: amd64 Package: stacks Package-Time: 283 Source-Version: 2.68+dfsg-1 Space: 395912 Status: successful Version: 2.68+dfsg-1 -------------------------------------------------------------------------------- Finished at 2025-01-22T15:12:20Z Build needed 00:04:43, 395912k disk space