https://launchpad.net/ubuntu/+source/stacks/2.60+dfsg-1/+build/22362571 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-014 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:39:40 UTC 2021 s390x Buildd toolchain package versions: launchpad-buildd_203~505~ubuntu18.04.1 python3-lpbuildd_203~505~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 1 Nov 23:31:33 ntpdate[1726]: adjust time server 10.211.37.1 offset -0.000016 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22362571 --image-type chroot /home/buildd/filecache-default/63391afefe2c3c1f68eb13dcf1e745f5d0398db6 Creating target for build PACKAGEBUILD-22362571 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22362571 Starting target for build PACKAGEBUILD-22362571 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22362571 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22362571 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22362571 Updating target for build PACKAGEBUILD-22362571 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [254 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [105 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main s390x Packages [1335 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe s390x Packages [12.5 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5509 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x Packages [372 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [128 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x Packages [1818 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [891 kB] Fetched 23.6 MB in 5s (4463 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bsdutils ca-certificates cpp-11 dash debconf debianutils g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libblkid1 libcc1-0 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libisl23 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libseccomp2 libselinux1 libsmartcols1 libsqlite3-0 libstdc++-11-dev libstdc++6 libtasn1-6 libtinfo6 libubsan1 libuuid1 libzstd1 lockfile-progs make mount ncurses-base ncurses-bin sensible-utils tzdata usrmerge util-linux 65 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 158 MB of archives. After this operation, 388 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x bsdutils s390x 1:2.37.2-4ubuntu1 [81.0 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x debianutils s390x 5.5-1 [77.5 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x debconf all 1.5.79 [126 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x dash s390x 0.5.11+git20210903+057cd650a4ed-1 [92.6 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x grep s390x 3.7-1 [156 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libncursesw6 s390x 6.2+20210905-1 [142 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libncurses6 s390x 6.2+20210905-1 [109 kB] Get:8 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libtinfo6 s390x 6.2+20210905-1 [105 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x ncurses-bin s390x 6.2+20210905-1 [182 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libblkid1 s390x 2.37.2-4ubuntu1 [100 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libselinux1 s390x 3.1-3build3 [74.2 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libmount1 s390x 2.37.2-4ubuntu1 [119 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x util-linux s390x 2.37.2-4ubuntu1 [1055 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x ncurses-base all 6.2+20210905-1 [19.9 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libcc1-0 s390x 11.2.0-10ubuntu1 [52.8 kB] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gcc-11-base s390x 11.2.0-10ubuntu1 [21.0 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgcc-s1 s390x 11.2.0-10ubuntu1 [28.4 kB] Get:18 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgomp1 s390x 11.2.0-10ubuntu1 [113 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libitm1 s390x 11.2.0-10ubuntu1 [29.7 kB] Get:20 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libatomic1 s390x 11.2.0-10ubuntu1 [9018 B] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libasan6 s390x 11.2.0-10ubuntu1 [2247 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libubsan1 s390x 11.2.0-10ubuntu1 [911 kB] Get:23 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x g++-11 s390x 11.2.0-10ubuntu1 [47.7 MB] Get:24 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libstdc++-11-dev s390x 11.2.0-10ubuntu1 [2078 kB] Get:25 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgcc-11-dev s390x 11.2.0-10ubuntu1 [829 kB] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gcc-11 s390x 11.2.0-10ubuntu1 [49.8 MB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x cpp-11 s390x 11.2.0-10ubuntu1 [43.2 MB] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libstdc++6 s390x 11.2.0-10ubuntu1 [689 kB] Get:29 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libisl23 s390x 0.24-2 [699 kB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libmpc3 s390x 1.2.1-1 [47.6 kB] Get:31 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libzstd1 s390x 1.4.8+dfsg-3 [317 kB] Get:32 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgpg-error0 s390x 1.42-3 [67.6 kB] Get:33 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgcrypt20 s390x 1.9.4-3ubuntu2 [457 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libapt-pkg6.0 s390x 2.3.11 [869 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gpgv s390x 2.2.27-2ubuntu1 [133 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libseccomp2 s390x 2.5.1-1ubuntu2 [47.9 kB] Get:37 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x apt s390x 2.3.11 [1366 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libpam0g s390x 1.4.0-10ubuntu1 [60.2 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libpam-modules-bin s390x 1.4.0-10ubuntu1 [40.2 kB] Get:40 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libpam-modules s390x 1.4.0-10ubuntu1 [279 kB] Get:41 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x mount s390x 2.37.2-4ubuntu1 [113 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libattr1 s390x 1:2.5.1-1 [13.3 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libk5crypto3 s390x 1.18.3-7 [88.3 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libkrb5support0 s390x 1.18.3-7 [32.2 kB] Get:45 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libkrb5-3 s390x 1.18.3-7 [347 kB] Get:46 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgssapi-krb5-2 s390x 1.18.3-7 [138 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libpam-runtime all 1.4.0-10ubuntu1 [40.2 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsmartcols1 s390x 2.37.2-4ubuntu1 [50.0 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libuuid1 s390x 2.37.2-4ubuntu1 [23.9 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main s390x libidn2-0 s390x 2.3.2-2 [66.3 kB] Get:51 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libp11-kit0 s390x 0.24.0-5 [258 kB] Get:52 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libtasn1-6 s390x 4.17.0-2 [43.9 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x sensible-utils all 0.0.17 [20.1 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main s390x usrmerge all 25ubuntu2 [54.7 kB] Get:55 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x ca-certificates all 20211016 [148 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main s390x libapparmor1 s390x 3.0.3-0ubuntu2 [37.3 kB] Get:57 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsqlite3-0 s390x 3.36.0-2 [630 kB] Get:58 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x tzdata all 2021e-1ubuntu1 [343 kB] Get:59 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgdbm6 s390x 1.22-1 [35.3 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gpg s390x 2.2.27-2ubuntu1 [505 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gpgconf s390x 2.2.27-2ubuntu1 [94.0 kB] Get:62 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gpg-agent s390x 2.2.27-2ubuntu1 [206 kB] Get:63 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgdbm-compat4 s390x 1.22-1 [6554 B] Get:64 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x lockfile-progs s390x 0.1.19 [9654 B] Get:65 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x make s390x 4.3-4ubuntu2 [181 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 158 MB in 18s (8794 kB/s) (Reading database ... 13030 files and directories currently 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Preparing to unpack .../bsdutils_1%3a2.37.2-4ubuntu1_s390x.deb ... Unpacking bsdutils (1:2.37.2-4ubuntu1) over (1:2.36.1-8ubuntu1) ... Setting up bsdutils (1:2.37.2-4ubuntu1) ... (Reading database ... 13030 files and directories currently installed.) Preparing to unpack .../debianutils_5.5-1_s390x.deb ... Unpacking debianutils (5.5-1) over (4.11.2build1) ... Setting up debianutils (5.5-1) ... update-alternatives: using /usr/bin/which.debianutils to provide /usr/bin/which (which) in auto mode (Reading database ... 13025 files and directories currently installed.) Preparing to unpack .../debconf_1.5.79_all.deb ... Unpacking debconf (1.5.79) over (1.5.77) ... Setting up debconf (1.5.79) ... (Reading database ... 13024 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20210903+057cd650a4ed-1_s390x.deb ... Unpacking dash (0.5.11+git20210903+057cd650a4ed-1) over (0.5.11+git20210120+802ebd4-1build1) ... Setting up dash (0.5.11+git20210903+057cd650a4ed-1) ... 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Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 13019 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.4.0-10ubuntu1_s390x.deb ... Unpacking libpam-modules-bin (1.4.0-10ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam-modules-bin (1.4.0-10ubuntu1) ... (Reading database ... 13017 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.4.0-10ubuntu1_s390x.deb ... Unpacking libpam-modules:s390x (1.4.0-10ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam-modules:s390x (1.4.0-10ubuntu1) ... Installing new version of config file /etc/security/namespace.conf ... Installing new version of config file /etc/security/pam_env.conf ... (Reading database ... 13018 files and directories currently installed.) Preparing to unpack .../mount_2.37.2-4ubuntu1_s390x.deb ... Unpacking mount (2.37.2-4ubuntu1) over (2.36.1-8ubuntu1) ... 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Unpacking gpg-agent (2.2.27-2ubuntu1) over (2.2.20-1ubuntu4) ... Preparing to unpack .../10-libgdbm-compat4_1.22-1_s390x.deb ... Unpacking libgdbm-compat4:s390x (1.22-1) over (1.19-2build1) ... Preparing to unpack .../11-lockfile-progs_0.1.19_s390x.deb ... Unpacking lockfile-progs (0.1.19) over (0.1.18build1) ... Preparing to unpack .../12-make_4.3-4ubuntu2_s390x.deb ... Unpacking make (4.3-4ubuntu2) over (4.3-4ubuntu1) ... Setting up libapparmor1:s390x (3.0.3-0ubuntu2) ... Setting up libsqlite3-0:s390x (3.36.0-2) ... Setting up libgomp1:s390x (11.2.0-10ubuntu1) ... Setting up libasan6:s390x (11.2.0-10ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 1 23:32:11 UTC 2021. Universal Time is now: Mon Nov 1 23:32:11 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:s390x (6.2+20210905-1) ... Setting up libmpc3:s390x (1.2.1-1) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:s390x (11.2.0-10ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libncursesw6:s390x (6.2+20210905-1) ... Setting up libubsan1:s390x (11.2.0-10ubuntu1) ... Setting up mount (2.37.2-4ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up gpgconf (2.2.27-2ubuntu1) ... Setting up libisl23:s390x (0.24-2) ... Setting up libcc1-0:s390x (11.2.0-10ubuntu1) ... Setting up gpg (2.2.27-2ubuntu1) ... Setting up libitm1:s390x (11.2.0-10ubuntu1) ... Setting up libgdbm6:s390x (1.22-1) ... Setting up cpp-11 (11.2.0-10ubuntu1) ... Setting up gpg-agent (2.2.27-2ubuntu1) ... Setting up libgdbm-compat4:s390x (1.22-1) ... Setting up libgcc-11-dev:s390x (11.2.0-10ubuntu1) ... Setting up gcc-11 (11.2.0-10ubuntu1) ... Setting up libstdc++-11-dev:s390x (11.2.0-10ubuntu1) ... Setting up g++-11 (11.2.0-10ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22362571 s390x jammy-proposed -c chroot:build-PACKAGEBUILD-22362571 --arch=s390x --dist=jammy-proposed --nolog stacks_2.60+dfsg-1.dsc Initiating build PACKAGEBUILD-22362571 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:39:40 UTC 2021 s390x sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-s390x-014.buildd +==============================================================================+ | stacks 2.60+dfsg-1 (s390x) Mon, 01 Nov 2021 23:32:13 +0000 | +==============================================================================+ Package: stacks Version: 2.60+dfsg-1 Source Version: 2.60+dfsg-1 Distribution: jammy-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22362571/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- stacks_2.60+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/stacks-LR2TQs/stacks-2.60+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-LR2TQs' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-2rGQU6/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-2rGQU6/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2rGQU6/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-2rGQU6/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2rGQU6/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-2rGQU6/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 654 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-2rGQU6/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [654 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 654 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13029 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev dpkg-deb: building package 'sbuild-build-depends-stacks-dummy' in '/<>/resolver-2rGQU6/apt_archive/sbuild-build-depends-stacks-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-stacks-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-2rGQU6/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2rGQU6/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-2rGQU6/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2rGQU6/apt_archive ./ Sources [524 B] Get:5 copy:/<>/resolver-2rGQU6/apt_archive ./ Packages [602 B] Fetched 2089 B in 0s (208 kB/s) Reading package lists... Reading package lists... Install stacks build dependencies (apt-based resolver) ------------------------------------------------------ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbam-dev libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu67 libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbam-dev libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu67 libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf samtools sbuild-build-depends-stacks-dummy zlib1g-dev 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 26.5 MB of archives. After this operation, 85.3 MB of additional disk space will be used. Get:1 copy:/<>/resolver-2rGQU6/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [694 B] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x bsdextrautils s390x 2.37.2-4ubuntu1 [72.2 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main s390x libuchardet0 s390x 0.0.7-1build1 [76.1 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main s390x groff-base s390x 1.22.4-7 [926 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main s390x libpipeline1 s390x 1.5.3-1build1 [23.0 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main s390x man-db s390x 2.9.4-2build1 [1177 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libelf1 s390x 0.185-2 [55.1 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main s390x libicu67 s390x 67.1-7ubuntu1 [10.0 MB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libxml2 s390x 2.9.12+dfsg-5 [711 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main s390x libmagic-mgc s390x 1:5.39-3build1 [237 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main s390x libmagic1 s390x 1:5.39-3build1 [87.7 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main s390x file s390x 1:5.39-3build1 [24.5 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main s390x gettext-base s390x 0.21-4ubuntu3 [38.4 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main s390x libpsl5 s390x 0.21.0-1.2build1 [57.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main s390x libsigsegv2 s390x 2.13-1ubuntu2 [14.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main s390x m4 s390x 1.4.18-5ubuntu1 [197 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x autoconf all 2.71-2 [338 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main s390x autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x automake all 1:1.16.5-1 [558 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main s390x autopoint all 0.21-4ubuntu3 [422 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libdebhelper-perl all 13.3.4ubuntu3 [62.4 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main s390x libtool all 2.4.6-15build1 [164 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main s390x dh-autoreconf all 20 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libfile-stripnondeterminism-perl all 1.12.0-2 [18.0 kB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x dh-strip-nondeterminism all 1.12.0-2 [5208 B] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libdw1 s390x 0.185-2 [247 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main s390x debugedit s390x 1:5.0-0ubuntu2 [48.9 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main s390x dwz s390x 0.14-1build1 [104 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main s390x gettext s390x 0.21-4ubuntu3 [848 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x debhelper all 13.3.4ubuntu3 [921 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-2ubuntu7 [170 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x libbam-dev s390x 0.1.19+dfsg-4 [114 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main s390x libbrotli1 s390x 1.0.9-2build4 [318 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsasl2-modules-db s390x 2.1.27+dfsg-2.2 [15.4 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsasl2-2 s390x 2.1.27+dfsg-2.2 [50.6 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main s390x libldap-2.5-0 s390x 2.5.6+dfsg-1~exp1ubuntu1 [181 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main s390x libnghttp2-14 s390x 1.43.0-1build1 [73.5 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build3 [56.4 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main s390x libssh-4 s390x 0.9.6-1 [175 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main s390x libcurl3-gnutls s390x 7.74.0-1.3ubuntu2 [260 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main s390x libcurl4-gnutls-dev s390x 7.74.0-1.3ubuntu2 [359 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main s390x libdeflate0 s390x 1.7-2ubuntu2 [55.4 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main s390x libdeflate-dev s390x 1.7-2ubuntu2 [48.7 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x libhtscodecs2 s390x 1.1.1-3 [61.0 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/universe s390x libhts3 s390x 1.13+ds-2 [374 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main s390x liblzma-dev s390x 5.2.5-2build1 [158 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/universe s390x libhts-dev s390x 1.13+ds-2 [5557 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/universe s390x libsparsehash-dev all 2.0.3-2 [71.7 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x samtools s390x 1.13-4 [517 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 26.5 MB in 2s (17.3 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 13029 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-4ubuntu1_s390x.deb ... Unpacking bsdextrautils (2.37.2-4ubuntu1) ... Selecting previously unselected package libuchardet0:s390x. Preparing to unpack .../01-libuchardet0_0.0.7-1build1_s390x.deb ... Unpacking libuchardet0:s390x (0.0.7-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_s390x.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../03-libpipeline1_1.5.3-1build1_s390x.deb ... Unpacking libpipeline1:s390x (1.5.3-1build1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2build1_s390x.deb ... Unpacking man-db (2.9.4-2build1) ... Selecting previously unselected package libelf1:s390x. Preparing to unpack .../05-libelf1_0.185-2_s390x.deb ... Unpacking libelf1:s390x (0.185-2) ... 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Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build3) ... Setting up libsigsegv2:s390x (2.13-1ubuntu2) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up libsasl2-2:s390x (2.1.27+dfsg-2.2) ... Setting up libssh-4:s390x (0.9.6-1) ... Setting up liblzma-dev:s390x (5.2.5-2build1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-2ubuntu7) ... Setting up libuchardet0:s390x (0.0.7-1build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:s390x (1.7-2ubuntu2) ... Setting up libelf1:s390x (0.185-2) ... Setting up libxml2:s390x (2.9.12+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up libdw1:s390x (0.185-2) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libtool (2.4.6-15build1) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libldap-2.5-0:s390x (2.5.6+dfsg-1~exp1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libbam-dev (0.1.19+dfsg-4) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-7) ... Setting up debugedit (1:5.0-0ubuntu2) ... Setting up automake (1:1.16.5-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:s390x (7.74.0-1.3ubuntu2) ... Setting up libcurl4-gnutls-dev:s390x (7.74.0-1.3ubuntu2) ... Setting up man-db (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up dh-autoreconf (20) ... Setting up libhts3:s390x (1.13+ds-2) ... Setting up libhts-dev:s390x (1.13+ds-2) ... Setting up debhelper (13.3.4ubuntu3) ... Setting up samtools (1.13-4) ... Setting up sbuild-build-depends-stacks-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-161-generic s390x (s390x) Toolchain package versions: binutils_2.37-7ubuntu1 dpkg-dev_1.20.9ubuntu2 g++-11_11.2.0-10ubuntu1 gcc-11_11.2.0-10ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-10ubuntu1 libstdc++6_11.2.0-10ubuntu1 linux-libc-dev_5.13.0-19.19 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu1 base-passwd_3.5.52 bash_5.1-3ubuntu2 binutils_2.37-7ubuntu1 binutils-common_2.37-7ubuntu1 binutils-s390x-linux-gnu_2.37-7ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-4ubuntu4 ca-certificates_20211016 coreutils_8.32-4ubuntu3 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-10ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-1 debconf_1.5.79 debhelper_13.3.4ubuntu3 debianutils_5.5-1 debugedit_1:5.0-0ubuntu2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.8-0ubuntu1 dpkg_1.20.9ubuntu2 dpkg-dev_1.20.9ubuntu2 dwz_0.14-1build1 e2fsprogs_1.46.3-1ubuntu3 fakeroot_1.25.3-1.1ubuntu3 file_1:5.39-3build1 findutils_4.8.0-1ubuntu2 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-10ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-10ubuntu1 gcc-11-base_11.2.0-10ubuntu1 gettext_0.21-4ubuntu3 gettext-base_0.21-4ubuntu3 gpg_2.2.27-2ubuntu1 gpg-agent_2.2.27-2ubuntu1 gpgconf_2.2.27-2ubuntu1 gpgv_2.2.27-2ubuntu1 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4ubuntu2 hostname_3.23ubuntu1 init_1.60build1 init-system-helpers_1.60build1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10ubuntu2 libapparmor1_3.0.3-0ubuntu2 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build22 libasan6_11.2.0-10ubuntu1 libassuan0_2.5.5-1 libatomic1_11.2.0-10ubuntu1 libattr1_1:2.5.1-1 libaudit-common_1:3.0-2ubuntu3 libaudit1_1:3.0-2ubuntu3 libbam-dev_0.1.19+dfsg-4 libbinutils_2.37-7ubuntu1 libblkid1_2.37.2-4ubuntu1 libbrotli1_1.0.9-2build4 libbz2-1.0_1.0.8-4ubuntu4 libc-bin_2.34-0ubuntu3 libc-dev-bin_2.34-0ubuntu3 libc6_2.34-0ubuntu3 libc6-dev_2.34-0ubuntu3 libcap-ng0_0.7.9-2.2build2 libcap2_1:2.44-1build2 libcc1-0_11.2.0-10ubuntu1 libcom-err2_1.46.3-1ubuntu3 libcrypt-dev_1:4.4.18-4ubuntu2 libcrypt1_1:4.4.18-4ubuntu2 libcryptsetup12_2:2.3.6-0ubuntu1 libctf-nobfd0_2.37-7ubuntu1 libctf0_2.37-7ubuntu1 libcurl3-gnutls_7.74.0-1.3ubuntu2 libcurl4-gnutls-dev_7.74.0-1.3ubuntu2 libdb5.3_5.3.28+dfsg1-0.8ubuntu2 libdebconfclient0_0.256ubuntu4 libdebhelper-perl_13.3.4ubuntu3 libdeflate-dev_1.7-2ubuntu2 libdeflate0_1.7-2ubuntu2 libdevmapper1.02.1_2:1.02.175-2.1ubuntu3 libdpkg-perl_1.20.9ubuntu2 libdw1_0.185-2 libelf1_0.185-2 libext2fs2_1.46.3-1ubuntu3 libfakeroot_1.25.3-1.1ubuntu3 libffi8_3.4.2-1ubuntu5 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-11-dev_11.2.0-10ubuntu1 libgcc-s1_11.2.0-10ubuntu1 libgcrypt20_1.9.4-3ubuntu2 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-1ubuntu3 libgnutls30_3.7.1-5ubuntu1 libgomp1_11.2.0-10ubuntu1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1build1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7ubuntu1 libidn2-0_2.3.2-2 libip4tc2_1.8.7-1ubuntu3 libisl23_0.24-2 libitm1_11.2.0-10ubuntu1 libjson-c5_0.15-2build3 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2ubuntu2 libkmod2_28-1ubuntu4 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libldap-2.5-0_2.5.6+dfsg-1~exp1ubuntu1 liblockfile-bin_1.17-1build1 liblockfile1_1.17-1build1 liblz4-1_1.9.3-2build1 liblzma-dev_5.2.5-2build1 liblzma5_5.2.5-2build1 libmagic-mgc_1:5.39-3build1 libmagic1_1:5.39-3build1 libmount1_2.37.2-4ubuntu1 libmpc3_1.2.1-1 libmpfr6_4.1.0-3build2 libncurses6_6.2+20210905-1 libncursesw6_6.2+20210905-1 libnettle8_3.7.3-1build1 libnghttp2-14_1.43.0-1build1 libnpth0_1.6-3build1 libnsl-dev_1.3.0-2build1 libnsl2_1.3.0-2build1 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10ubuntu1 libpam-modules-bin_1.4.0-10ubuntu1 libpam-runtime_1.4.0-10ubuntu1 libpam0g_1.4.0-10ubuntu1 libpcre2-8-0_10.37-0ubuntu2 libpcre3_2:8.39-13build4 libperl5.32_5.32.1-3ubuntu3 libpipeline1_1.5.3-1build1 libpng16-16_1.6.37-3build4 libprocps8_2:3.3.17-5ubuntu3 libpsl5_0.21.0-1.2build1 libreadline8_8.1-2build1 librtmp1_2.4+20151223.gitfa8646d.1-2build3 libsasl2-2_2.1.27+dfsg-2.2 libsasl2-modules-db_2.1.27+dfsg-2.2 libseccomp2_2.5.1-1ubuntu2 libselinux1_3.1-3build3 libsemanage-common_3.1-1ubuntu3 libsemanage1_3.1-1ubuntu3 libsepol1_3.1-1ubuntu2 libsigsegv2_2.13-1ubuntu2 libsmartcols1_2.37.2-4ubuntu1 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.36.0-2 libss2_1.46.3-1ubuntu3 libssh-4_0.9.6-1 libssl1.1_1.1.1l-1ubuntu1 libstdc++-11-dev_11.2.0-10ubuntu1 libstdc++6_11.2.0-10ubuntu1 libsub-override-perl_0.09-2 libsystemd0_248.3-1ubuntu8 libtasn1-6_4.17.0-2 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15build1 libubsan1_11.2.0-10ubuntu1 libuchardet0_0.0.7-1build1 libudev1_248.3-1ubuntu8 libunistring2_0.9.10-6 libuuid1_2.37.2-4ubuntu1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2build1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.13.0-19.19 lockfile-progs_0.1.19 login_1:4.8.1-1ubuntu9 logsave_1.46.3-1ubuntu3 lsb-base_11.1.0ubuntu3 lto-disabled-list_16 m4_1.4.18-5ubuntu1 make_4.3-4ubuntu2 man-db_2.9.4-2build1 mawk_1.3.4.20200120-2build1 mount_2.37.2-4ubuntu1 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 openssl_1.1.1l-1ubuntu1 optipng_0.7.7-2 passwd_1:4.8.1-1ubuntu9 patch_2.7.6-7build1 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1build1 pkgbinarymangler_148 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 samtools_1.13-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-stacks-dummy_0.invalid.0 sed_4.7-1ubuntu2 sensible-utils_0.0.17 systemd_248.3-1ubuntu8 systemd-sysv_248.3-1ubuntu8 systemd-timesyncd_248.3-1ubuntu8 sysvinit-utils_2.96-7ubuntu2 tar_1.34+dfsg-1build2 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Nov 1 18:45:08 2021 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./stacks_2.60+dfsg-1.dsc dpkg-source: info: extracting stacks in /<>/stacks-2.60+dfsg dpkg-source: info: unpacking stacks_2.60+dfsg.orig.tar.xz dpkg-source: info: unpacking stacks_2.60+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 2to3.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-22362571 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22362571 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22362571 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package stacks dpkg-buildpackage: info: source version 2.60+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>/stacks-2.60+dfsg' dh_clean rm -f ./constants.php make[1]: Leaving directory '/<>/stacks-2.60+dfsg' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:28: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:28: You should run autoupdate. ./lib/autoconf/headers.m4:704: 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:42: installing 'config/config.guess' configure.ac:42: installing 'config/config.sub' 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 '/<>/stacks-2.60+dfsg' dh_auto_configure -- --enable-sparsehash --enable-bam \ --with-bam-include-path=/usr/include/samtools \ --with-bam-lib-path=/usr/lib ./configure --build=s390x-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/s390x-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... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking build system type... s390x-ibm-linux-gnu checking host system type... s390x-ibm-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 '/<>/stacks-2.60+dfsg' dh_auto_build -a make -j4 make[1]: Entering directory '/<>/stacks-2.60+dfsg' make all-recursive make[2]: Entering directory '/<>/stacks-2.60+dfsg' make[3]: Entering directory '/<>/stacks-2.60+dfsg' g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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/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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -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=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>/stacks-2.60+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -flto=auto -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 '/<>/stacks-2.60+dfsg' make[2]: Leaving directory '/<>/stacks-2.60+dfsg' make[1]: Leaving directory '/<>/stacks-2.60+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/stacks-2.60+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 '/<>/stacks-2.60+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>/stacks-2.60+dfsg' dh_auto_install --no-parallel make -j1 install DESTDIR=/<>/stacks-2.60\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>/stacks-2.60+dfsg' make[3]: Entering directory '/<>/stacks-2.60+dfsg' make[4]: Entering directory '/<>/stacks-2.60+dfsg' /usr/bin/mkdir -p '/<>/stacks-2.60+dfsg/debian/stacks/usr/bin' /usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/<>/stacks-2.60+dfsg/debian/stacks/usr/bin' /usr/bin/mkdir -p '/<>/stacks-2.60+dfsg/debian/stacks/usr/bin' /usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/<>/stacks-2.60+dfsg/debian/stacks/usr/bin' make install-data-hook make[5]: Entering directory '/<>/stacks-2.60+dfsg' sed -e 's,_VERSION_,2.60,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl > /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst mv /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl chmod +x /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl sed -e 's,_VERSION_,2.60,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl > /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl.subst mv /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl chmod +x /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.60,' /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.60,' /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-samtools-tview rm -f /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp rm -f /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp chmod +x /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments chmod +x /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-dist-extract chmod +x /<>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-gdb make[5]: Leaving directory '/<>/stacks-2.60+dfsg' make[4]: Leaving directory '/<>/stacks-2.60+dfsg' make[3]: Leaving directory '/<>/stacks-2.60+dfsg' make[2]: Leaving directory '/<>/stacks-2.60+dfsg' make[1]: Leaving directory '/<>/stacks-2.60+dfsg' debian/rules override_dh_install make[1]: Entering directory '/<>/stacks-2.60+dfsg' mkdir -p debian/stacks/usr/lib/stacks mv debian/stacks/usr/bin debian/stacks/usr/lib/stacks cd debian/stacks/usr/lib/stacks/bin && \ for f in *.pl ; do \ ln -s "$f" "`basename $f .pl`" ; \ sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $f ; \ done dh_install make[1]: Leaving directory '/<>/stacks-2.60+dfsg' dh_installdocs -a dh_installchangelogs -a dh_perl -a debian/rules override_dh_link make[1]: Entering directory '/<>/stacks-2.60+dfsg' dh_link mkdir -p debian/stacks/usr/lib/debian-med/bin cd debian/stacks/usr/lib/debian-med/bin && \ for f in `ls /<>/stacks-2.60+dfsg/debian/stacks/usr/lib/stacks/bin` ; do \ ln -s ../../stacks/bin/$f ; \ done make[1]: Leaving directory '/<>/stacks-2.60+dfsg' dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a debugedit: debian/stacks/usr/lib/stacks/bin/gstacks: Unknown DWARF DW_FORM_0x1f21 3358f506fe000535c4803fc79fb8585e540fa0c0 debugedit: debian/stacks/usr/lib/stacks/bin/phasedstacks: Unknown DWARF DW_FORM_0x1f20 113c05e1813b69fa312a617919304d962c068d37 debugedit: debian/stacks/usr/lib/stacks/bin/kmer_filter: Unknown DWARF DW_FORM_0x1f20 ce41f2c9669b8f94c2e203f016901dcc5ebf198d debugedit: debian/stacks/usr/lib/stacks/bin/sstacks: Unknown DWARF DW_FORM_0x1f20 f47f28d457e8ffbbc1f47afdc5f7d929c3d81fe9 debugedit: debian/stacks/usr/lib/stacks/bin/process_radtags: Unknown DWARF DW_FORM_0x1f20 1387f1fdfd2acd3525af1e7edbb88820b3fcc991 debugedit: debian/stacks/usr/lib/stacks/bin/tsv2bam: Unknown DWARF DW_FORM_0x1f20 4676433bff7bb6b82fe336a45d6f7deb87844e59 debugedit: debian/stacks/usr/lib/stacks/bin/populations: Unknown DWARF DW_FORM_0x1f20 db7125775fe89ccbb1ea7471a31187fe2c5ff3ab debugedit: debian/stacks/usr/lib/stacks/bin/clone_filter: Unknown DWARF DW_FORM_0x1f20 2fa25649eb1bcccaa2741b4d763b76f153fa8722 debugedit: debian/stacks/usr/lib/stacks/bin/cstacks: Unknown DWARF DW_FORM_0x1f21 e3e1ce2df64ca51c802dd30ea47e1e6f1a008afc debugedit: debian/stacks/usr/lib/stacks/bin/process_shortreads: Unknown DWARF DW_FORM_0x1f20 32bb62c2b3f2f746c307d35e133707545e53b7ac debugedit: debian/stacks/usr/lib/stacks/bin/ustacks: Unknown DWARF DW_FORM_0x1f20 b640ce471bddda1c772c7afac4e1ba2693464705 dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a 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 -a dh_builddeb -a /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. INFO: pkgstriptranslations version 148 INFO: pkgstriptranslations version 148 pkgstriptranslations: processing stacks (in debian/stacks); do_strip: , oemstrip: pkgstriptranslations: processing stacks-dbgsym (in debian/.debhelper/stacks/dbgsym-root); do_strip: , oemstrip: /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. pkgstripfiles: processing control file: debian/stacks/DEBIAN/control, package stacks, directory debian/stacks pkgstripfiles: Truncating usr/share/doc/stacks/changelog.Debian.gz to topmost ten records pkgstripfiles: processing control file: debian/.debhelper/stacks/dbgsym-root/DEBIAN/control, package stacks-dbgsym, directory debian/.debhelper/stacks/dbgsym-root dpkg-deb: building package 'stacks-dbgsym' in 'debian/.debhelper/scratch-space/build-stacks/stacks-dbgsym_2.60+dfsg-1_s390x.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package stacks ... pkgstripfiles: No PNG files. dpkg-deb: building package 'stacks' in '../stacks_2.60+dfsg-1_s390x.deb'. Renaming stacks-dbgsym_2.60+dfsg-1_s390x.deb to stacks-dbgsym_2.60+dfsg-1_s390x.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../stacks_2.60+dfsg-1_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-11-01T23:34:15Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ stacks_2.60+dfsg-1_s390x.changes: --------------------------------- Format: 1.8 Date: Tue, 02 Nov 2021 00:08:37 +0530 Source: stacks Binary: stacks Built-For-Profiles: noudeb Architecture: s390x Version: 2.60+dfsg-1 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nilesh Patra Description: stacks - pipeline for building loci from short-read DNA sequences Changes: stacks (2.60+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version 2.60+dfsg * Run cme Checksums-Sha1: 405d03ab461c0f45ea0a080df22437b01f40f246 13577668 stacks-dbgsym_2.60+dfsg-1_s390x.ddeb 6b486d287cdafa2bb620d46787ebfccef801e149 6555 stacks_2.60+dfsg-1_s390x.buildinfo d9175fd6fd70b3f83e4df76a5402d7e0dfb8007b 934614 stacks_2.60+dfsg-1_s390x.deb Checksums-Sha256: 16c3fdc29c75263d8b195c57017009676aff347f6d2e0cc790f4a018bde29d30 13577668 stacks-dbgsym_2.60+dfsg-1_s390x.ddeb 0ab71ce63a7cc0b7330518502603ebbf0907f87fe0c5a8752da5bda024c14e78 6555 stacks_2.60+dfsg-1_s390x.buildinfo 31a682f583ffd2d728e6517468164b2d4f6c37885d1607d9cef8150d5dc8b52b 934614 stacks_2.60+dfsg-1_s390x.deb Files: e017747eeefefb0c91e1309819946b8e 13577668 debug optional stacks-dbgsym_2.60+dfsg-1_s390x.ddeb 5f92f965946331d6da0ffe23e2ecb73d 6555 science optional stacks_2.60+dfsg-1_s390x.buildinfo fbd65efe36d52f5841c0ebd7d5127701 934614 science optional stacks_2.60+dfsg-1_s390x.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: stacks Binary: stacks stacks-dbgsym Architecture: s390x Version: 2.60+dfsg-1 Checksums-Md5: e017747eeefefb0c91e1309819946b8e 13577668 stacks-dbgsym_2.60+dfsg-1_s390x.ddeb fbd65efe36d52f5841c0ebd7d5127701 934614 stacks_2.60+dfsg-1_s390x.deb Checksums-Sha1: 405d03ab461c0f45ea0a080df22437b01f40f246 13577668 stacks-dbgsym_2.60+dfsg-1_s390x.ddeb d9175fd6fd70b3f83e4df76a5402d7e0dfb8007b 934614 stacks_2.60+dfsg-1_s390x.deb Checksums-Sha256: 16c3fdc29c75263d8b195c57017009676aff347f6d2e0cc790f4a018bde29d30 13577668 stacks-dbgsym_2.60+dfsg-1_s390x.ddeb 31a682f583ffd2d728e6517468164b2d4f6c37885d1607d9cef8150d5dc8b52b 934614 stacks_2.60+dfsg-1_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Mon, 01 Nov 2021 23:34:15 +0000 Build-Path: /<>/stacks-2.60+dfsg Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20180224.1+nmu1), base-files (= 12ubuntu1), base-passwd (= 3.5.52), bash (= 5.1-3ubuntu2), binutils (= 2.37-7ubuntu1), binutils-common (= 2.37-7ubuntu1), binutils-s390x-linux-gnu (= 2.37-7ubuntu1), bsdextrautils (= 2.37.2-4ubuntu1), bsdutils (= 1:2.37.2-4ubuntu1), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-4ubuntu4), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-10ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-1), debconf (= 1.5.79), debhelper (= 13.3.4ubuntu3), debianutils (= 5.5-1), debugedit (= 1:5.0-0ubuntu2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.12.0-2), diffutils (= 1:3.8-0ubuntu1), dpkg (= 1.20.9ubuntu2), dpkg-dev (= 1.20.9ubuntu2), dwz (= 0.14-1build1), file (= 1:5.39-3build1), findutils (= 4.8.0-1ubuntu2), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-10ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-10ubuntu1), gcc-11-base (= 11.2.0-10ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), hostname (= 3.23ubuntu1), init-system-helpers (= 1.60build1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10ubuntu2), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-10ubuntu1), libatomic1 (= 11.2.0-10ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbam-dev (= 0.1.19+dfsg-4), libbinutils (= 2.37-7ubuntu1), libblkid1 (= 2.37.2-4ubuntu1), libbrotli1 (= 1.0.9-2build4), libbz2-1.0 (= 1.0.8-4ubuntu4), libc-bin (= 2.34-0ubuntu3), libc-dev-bin (= 2.34-0ubuntu3), libc6 (= 2.34-0ubuntu3), libc6-dev (= 2.34-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build2), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-10ubuntu1), libcom-err2 (= 1.46.3-1ubuntu3), libcrypt-dev (= 1:4.4.18-4ubuntu2), libcrypt1 (= 1:4.4.18-4ubuntu2), libctf-nobfd0 (= 2.37-7ubuntu1), libctf0 (= 2.37-7ubuntu1), libcurl3-gnutls (= 7.74.0-1.3ubuntu2), libcurl4-gnutls-dev (= 7.74.0-1.3ubuntu2), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.256ubuntu4), libdebhelper-perl (= 13.3.4ubuntu3), libdeflate-dev (= 1.7-2ubuntu2), libdeflate0 (= 1.7-2ubuntu2), libdpkg-perl (= 1.20.9ubuntu2), libdw1 (= 0.185-2), libelf1 (= 0.185-2), libffi8 (= 3.4.2-1ubuntu5), libfile-stripnondeterminism-perl (= 1.12.0-2), libgcc-11-dev (= 11.2.0-10ubuntu1), libgcc-s1 (= 11.2.0-10ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu2), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgmp10 (= 2:6.2.1+dfsg-1ubuntu3), libgnutls30 (= 3.7.1-5ubuntu1), libgomp1 (= 11.2.0-10ubuntu1), libgpg-error0 (= 1.42-3), libgssapi-krb5-2 (= 1.18.3-7), libhogweed6 (= 3.7.3-1build1), libhts-dev (= 1.13+ds-2), libhts3 (= 1.13+ds-2), libhtscodecs2 (= 1.1.1-3), libicu67 (= 67.1-7ubuntu1), libidn2-0 (= 2.3.2-2), libisl23 (= 0.24-2), libitm1 (= 11.2.0-10ubuntu1), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), libldap-2.5-0 (= 2.5.6+dfsg-1~exp1ubuntu1), liblz4-1 (= 1.9.3-2build1), liblzma-dev (= 5.2.5-2build1), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.39-3build1), libmagic1 (= 1:5.39-3build1), libmount1 (= 2.37.2-4ubuntu1), libmpc3 (= 1.2.1-1), libmpfr6 (= 4.1.0-3build2), libncurses6 (= 6.2+20210905-1), libnettle8 (= 3.7.3-1build1), libnghttp2-14 (= 1.43.0-1build1), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libp11-kit0 (= 0.24.0-5), libpam-modules (= 1.4.0-10ubuntu1), libpam-modules-bin (= 1.4.0-10ubuntu1), libpam-runtime (= 1.4.0-10ubuntu1), libpam0g (= 1.4.0-10ubuntu1), libpcre2-8-0 (= 10.37-0ubuntu2), libpcre3 (= 2:8.39-13build4), libperl5.32 (= 5.32.1-3ubuntu3), libpipeline1 (= 1.5.3-1build1), libpsl5 (= 0.21.0-1.2build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build3), libsasl2-2 (= 2.1.27+dfsg-2.2), libsasl2-modules-db (= 2.1.27+dfsg-2.2), libseccomp2 (= 2.5.1-1ubuntu2), libselinux1 (= 3.1-3build3), libsigsegv2 (= 2.13-1ubuntu2), libsmartcols1 (= 2.37.2-4ubuntu1), libsparsehash-dev (= 2.0.3-2), libssh-4 (= 0.9.6-1), libssl1.1 (= 1.1.1l-1ubuntu1), libstdc++-11-dev (= 11.2.0-10ubuntu1), libstdc++6 (= 11.2.0-10ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 248.3-1ubuntu8), libtasn1-6 (= 4.17.0-2), libtinfo6 (= 6.2+20210905-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libubsan1 (= 11.2.0-10ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 248.3-1ubuntu8), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4ubuntu1), libxml2 (= 2.9.12+dfsg-5), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.13.0-19.19), login (= 1:4.8.1-1ubuntu9), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 16), m4 (= 1.4.18-5ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), ncurses-base (= 6.2+20210905-1), ncurses-bin (= 6.2+20210905-1), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu5), samtools (= 1.13-4), sed (= 4.7-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 2.96-7ubuntu2), tar (= 1.34+dfsg-1build2), util-linux (= 2.37.2-4ubuntu1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1635791917" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ stacks_2.60+dfsg-1_s390x.deb ---------------------------- new Debian package, version 2.0. size 934614 bytes: control archive=1584 bytes. 1084 bytes, 22 lines control 1800 bytes, 26 lines md5sums Package: stacks Version: 2.60+dfsg-1 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3432 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 11), zlib1g (>= 1:1.2.6), samtools, libdbi-perl Recommends: libspreadsheet-writeexcel-perl, python3, littler Conflicts: stacks-web Replaces: stacks-web 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 2021-11-01 18:38 ./ drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/ drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/bin/ -rwxr-xr-x root/root 771 2021-11-01 18:35 ./usr/bin/stacks drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/ drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/ lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/count_fixed_catalog_snps.py -> ../../stacks/bin/count_fixed_catalog_snps.py lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/cstacks -> ../../stacks/bin/cstacks lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/gstacks -> ../../stacks/bin/gstacks lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/integrate_alignments.py -> ../../stacks/bin/integrate_alignments.py lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/populations -> ../../stacks/bin/populations lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/ref_map -> ../../stacks/bin/ref_map lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/sstacks -> ../../stacks/bin/sstacks lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-count-reads-per-sample-per-locus -> ../../stacks/bin/stacks-count-reads-per-sample-per-locus lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/ustacks -> ../../stacks/bin/ustacks drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/stacks/ drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/stacks/bin/ -rwxr-xr-x root/root 134600 2021-11-01 18:38 ./usr/lib/stacks/bin/clone_filter -rwxr-xr-x root/root 8652 2021-11-01 18:38 ./usr/lib/stacks/bin/count_fixed_catalog_snps.py -rwxr-xr-x root/root 179280 2021-11-01 18:38 ./usr/lib/stacks/bin/cstacks lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/stacks/bin/denovo_map -> denovo_map.pl -rwxr-xr-x root/root 30920 2021-11-01 18:38 ./usr/lib/stacks/bin/denovo_map.pl -rwxr-xr-x root/root 576912 2021-11-01 18:38 ./usr/lib/stacks/bin/gstacks -rwxr-xr-x root/root 10879 2021-11-01 18:38 ./usr/lib/stacks/bin/integrate_alignments.py -rwxr-xr-x root/root 126304 2021-11-01 18:38 ./usr/lib/stacks/bin/kmer_filter -rwxr-xr-x root/root 192624 2021-11-01 18:38 ./usr/lib/stacks/bin/phasedstacks -rwxr-xr-x root/root 855024 2021-11-01 18:38 ./usr/lib/stacks/bin/populations -rwxr-xr-x root/root 351248 2021-11-01 18:38 ./usr/lib/stacks/bin/process_radtags -rwxr-xr-x root/root 196880 2021-11-01 18:38 ./usr/lib/stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/stacks/bin/ref_map -> ref_map.pl -rwxr-xr-x root/root 15360 2021-11-01 18:38 ./usr/lib/stacks/bin/ref_map.pl -rwxr-xr-x root/root 154488 2021-11-01 18:38 ./usr/lib/stacks/bin/sstacks -rwxr-xr-x root/root 1040 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-count-reads-per-sample-per-locus -rwxr-xr-x root/root 773 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-dist-extract -rwxr-xr-x root/root 1207 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-gdb -rwxr-xr-x root/root 1773 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-hist2d-loci-samples-coverage -rwxr-xr-x root/root 22248 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-integrate-alignments -rwxr-xr-x root/root 3037 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-samtools-tview -rwxr-xr-x root/root 265488 2021-11-01 18:38 ./usr/lib/stacks/bin/tsv2bam -rwxr-xr-x root/root 328552 2021-11-01 18:38 ./usr/lib/stacks/bin/ustacks drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/share/ drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/share/doc/stacks/ -rw-r--r-- root/root 229 2021-11-01 18:35 ./usr/share/doc/stacks/NEWS.Debian.gz -rw-r--r-- root/root 1451 2021-11-01 18:35 ./usr/share/doc/stacks/README.Debian -rw-r--r-- root/root 1001 2021-11-01 18:38 ./usr/share/doc/stacks/changelog.Debian.gz -rw-r--r-- root/root 1684 2021-11-01 18:35 ./usr/share/doc/stacks/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: n/a Build-Time: 114 Distribution: jammy-proposed Host Architecture: s390x Install-Time: 7 Job: stacks_2.60+dfsg-1.dsc Machine Architecture: s390x Package: stacks Package-Time: 122 Source-Version: 2.60+dfsg-1 Space: n/a Status: successful Version: 2.60+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-11-01T23:34:15Z Build needed 00:02:02, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22362571 Scanning for processes to kill in build PACKAGEBUILD-22362571