https://launchpad.net/ubuntu/+source/stacks/2.60+dfsg-1/+build/22362569 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-004 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:40:22 UTC 2021 ppc64le 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 23:32:59 ntpdate[2041]: adjust time server 10.211.37.1 offset -0.000444 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22362569 --image-type chroot /home/buildd/filecache-default/104362a8a1d4d9793492e39ad0c0e733056a927b Creating target for build PACKAGEBUILD-22362569 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22362569 Starting target for build PACKAGEBUILD-22362569 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22362569 '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-22362569 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=ppc64el PACKAGEBUILD-22362569 Updating target for build PACKAGEBUILD-22362569 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 ppc64el Packages [1357 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe ppc64el Packages [12.9 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5509 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el Packages [371 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [128 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el Packages [1867 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [891 kB] Fetched 24.1 MB in 6s (4225 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 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libquadmath0 libseccomp2 libselinux1 libsmartcols1 libsqlite3-0 libstdc++-11-dev libstdc++6 libtasn1-6 libtinfo6 libtsan0 libubsan1 libuuid1 libzstd1 lockfile-progs make mount ncurses-base ncurses-bin sensible-utils tzdata usrmerge util-linux 68 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 174 MB of archives. After this operation, 368 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el bsdutils ppc64el 1:2.37.2-4ubuntu1 [86.7 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el debianutils ppc64el 5.5-1 [78.2 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el debconf all 1.5.79 [126 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el dash ppc64el 0.5.11+git20210903+057cd650a4ed-1 [112 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el grep ppc64el 3.7-1 [167 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libncursesw6 ppc64el 6.2+20210905-1 [183 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libncurses6 ppc64el 6.2+20210905-1 [144 kB] Get:8 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libtinfo6 ppc64el 6.2+20210905-1 [129 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el ncurses-bin ppc64el 6.2+20210905-1 [193 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libblkid1 ppc64el 2.37.2-4ubuntu1 [132 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libselinux1 ppc64el 3.1-3build3 [93.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libmount1 ppc64el 2.37.2-4ubuntu1 [148 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el util-linux ppc64el 2.37.2-4ubuntu1 [1134 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el ncurses-base all 6.2+20210905-1 [19.9 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libcc1-0 ppc64el 11.2.0-10ubuntu1 [48.1 kB] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el gcc-11-base ppc64el 11.2.0-10ubuntu1 [21.0 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgcc-s1 ppc64el 11.2.0-10ubuntu1 [34.7 kB] Get:18 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgomp1 ppc64el 11.2.0-10ubuntu1 [129 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libitm1 ppc64el 11.2.0-10ubuntu1 [33.1 kB] Get:20 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libatomic1 ppc64el 11.2.0-10ubuntu1 [10.7 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libasan6 ppc64el 11.2.0-10ubuntu1 [2303 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el liblsan0 ppc64el 11.2.0-10ubuntu1 [997 kB] Get:23 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libtsan0 ppc64el 11.2.0-10ubuntu1 [2284 kB] Get:24 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libubsan1 ppc64el 11.2.0-10ubuntu1 [947 kB] Get:25 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libquadmath0 ppc64el 11.2.0-10ubuntu1 [166 kB] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el g++-11 ppc64el 11.2.0-10ubuntu1 [50.9 MB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libstdc++-11-dev ppc64el 11.2.0-10ubuntu1 [2180 kB] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgcc-11-dev ppc64el 11.2.0-10ubuntu1 [1490 kB] Get:29 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el gcc-11 ppc64el 11.2.0-10ubuntu1 [53.8 MB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el cpp-11 ppc64el 11.2.0-10ubuntu1 [46.2 MB] Get:31 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libstdc++6 ppc64el 11.2.0-10ubuntu1 [759 kB] Get:32 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libisl23 ppc64el 0.24-2 [835 kB] Get:33 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libmpc3 ppc64el 1.2.1-1 [52.9 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libzstd1 ppc64el 1.4.8+dfsg-3 [364 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgpg-error0 ppc64el 1.42-3 [84.4 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgcrypt20 ppc64el 1.9.4-3ubuntu2 [697 kB] Get:37 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libapt-pkg6.0 ppc64el 2.3.11 [1030 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el gpgv ppc64el 2.2.27-2ubuntu1 [176 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libseccomp2 ppc64el 2.5.1-1ubuntu2 [59.8 kB] Get:40 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el apt ppc64el 2.3.11 [1438 kB] Get:41 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpam0g ppc64el 1.4.0-10ubuntu1 [69.3 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpam-modules-bin ppc64el 1.4.0-10ubuntu1 [45.0 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpam-modules ppc64el 1.4.0-10ubuntu1 [326 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el mount ppc64el 2.37.2-4ubuntu1 [121 kB] Get:45 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libattr1 ppc64el 1:2.5.1-1 [14.3 kB] Get:46 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libk5crypto3 ppc64el 1.18.3-7 [117 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libkrb5support0 ppc64el 1.18.3-7 [37.6 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libkrb5-3 ppc64el 1.18.3-7 [436 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgssapi-krb5-2 ppc64el 1.18.3-7 [183 kB] Get:50 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libpam-runtime all 1.4.0-10ubuntu1 [40.2 kB] Get:51 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libsmartcols1 ppc64el 2.37.2-4ubuntu1 [63.0 kB] Get:52 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libuuid1 ppc64el 2.37.2-4ubuntu1 [27.1 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main ppc64el libidn2-0 ppc64el 2.3.2-2 [70.4 kB] Get:54 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libp11-kit0 ppc64el 0.24.0-5 [264 kB] Get:55 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libtasn1-6 ppc64el 4.17.0-2 [56.1 kB] Get:56 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el sensible-utils all 0.0.17 [20.1 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main ppc64el usrmerge all 25ubuntu2 [54.7 kB] Get:58 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el ca-certificates all 20211016 [148 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main ppc64el libapparmor1 ppc64el 3.0.3-0ubuntu2 [43.8 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libsqlite3-0 ppc64el 3.36.0-2 [744 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el tzdata all 2021e-1ubuntu1 [343 kB] Get:62 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgdbm6 ppc64el 1.22-1 [43.1 kB] Get:63 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el gpg ppc64el 2.2.27-2ubuntu1 [661 kB] Get:64 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el gpgconf ppc64el 2.2.27-2ubuntu1 [104 kB] Get:65 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el gpg-agent ppc64el 2.2.27-2ubuntu1 [247 kB] Get:66 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libgdbm-compat4 ppc64el 1.22-1 [6864 B] Get:67 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el lockfile-progs ppc64el 0.1.19 [10.2 kB] Get:68 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el make ppc64el 4.3-4ubuntu2 [211 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 174 MB in 5s (34.3 MB/s) (Reading database ... 13185 files and directories currently installed.) 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(Reading database ... 13172 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.4.0-10ubuntu1_ppc64el.deb ... Unpacking libpam-modules:ppc64el (1.4.0-10ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam-modules:ppc64el (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 ... 13173 files and directories currently installed.) Preparing to unpack .../mount_2.37.2-4ubuntu1_ppc64el.deb ... Unpacking mount (2.37.2-4ubuntu1) over (2.36.1-8ubuntu1) ... Preparing to unpack .../libattr1_1%3a2.5.1-1_ppc64el.deb ... Unpacking libattr1:ppc64el (1:2.5.1-1) over (1:2.4.48-6build2) ... Setting up libattr1:ppc64el (1:2.5.1-1) ... Installing new version of config file /etc/xattr.conf ... (Reading database ... 13174 files and directories currently installed.) Preparing to unpack .../libk5crypto3_1.18.3-7_ppc64el.deb ... Unpacking libk5crypto3:ppc64el (1.18.3-7) over (1.18.3-6) ... Setting up libk5crypto3:ppc64el (1.18.3-7) ... (Reading database ... 13174 files and directories currently installed.) Preparing to unpack .../libkrb5support0_1.18.3-7_ppc64el.deb ... Unpacking libkrb5support0:ppc64el (1.18.3-7) over (1.18.3-6) ... Setting up libkrb5support0:ppc64el (1.18.3-7) ... (Reading database ... 13174 files and directories currently installed.) Preparing to unpack .../libkrb5-3_1.18.3-7_ppc64el.deb ... Unpacking libkrb5-3:ppc64el (1.18.3-7) over (1.18.3-6) ... Setting up libkrb5-3:ppc64el (1.18.3-7) ... (Reading database ... 13174 files and directories currently installed.) Preparing to unpack .../libgssapi-krb5-2_1.18.3-7_ppc64el.deb ... Unpacking libgssapi-krb5-2:ppc64el (1.18.3-7) over (1.18.3-6) ... Setting up libgssapi-krb5-2:ppc64el (1.18.3-7) ... (Reading database ... 13174 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.4.0-10ubuntu1_all.deb ... 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Preparing to unpack .../libp11-kit0_0.24.0-5_ppc64el.deb ... Unpacking libp11-kit0:ppc64el (0.24.0-5) over (0.23.22-1build1) ... Setting up libp11-kit0:ppc64el (0.24.0-5) ... (Reading database ... 13174 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.17.0-2_ppc64el.deb ... Unpacking libtasn1-6:ppc64el (4.17.0-2) over (4.16.0-2build1) ... Setting up libtasn1-6:ppc64el (4.17.0-2) ... (Reading database ... 13174 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) over (0.0.14) ... Preparing to unpack .../01-usrmerge_25ubuntu2_all.deb ... Unpacking usrmerge (25ubuntu2) over (25ubuntu1) ... Preparing to unpack .../02-ca-certificates_20211016_all.deb ... Unpacking ca-certificates (20211016) over (20210119ubuntu1) ... Preparing to unpack .../03-libapparmor1_3.0.3-0ubuntu2_ppc64el.deb ... Unpacking libapparmor1:ppc64el (3.0.3-0ubuntu2) over (3.0.3-0ubuntu1) ... Preparing to unpack .../04-libsqlite3-0_3.36.0-2_ppc64el.deb ... Unpacking libsqlite3-0:ppc64el (3.36.0-2) over (3.35.5-1) ... Preparing to unpack .../05-tzdata_2021e-1ubuntu1_all.deb ... Unpacking tzdata (2021e-1ubuntu1) over (2021a-2ubuntu1) ... Preparing to unpack .../06-libgdbm6_1.22-1_ppc64el.deb ... Unpacking libgdbm6:ppc64el (1.22-1) over (1.19-2build1) ... Preparing to unpack .../07-gpg_2.2.27-2ubuntu1_ppc64el.deb ... Unpacking gpg (2.2.27-2ubuntu1) over (2.2.20-1ubuntu4) ... Preparing to unpack .../08-gpgconf_2.2.27-2ubuntu1_ppc64el.deb ... Unpacking gpgconf (2.2.27-2ubuntu1) over (2.2.20-1ubuntu4) ... Preparing to unpack .../09-gpg-agent_2.2.27-2ubuntu1_ppc64el.deb ... Unpacking gpg-agent (2.2.27-2ubuntu1) over (2.2.20-1ubuntu4) ... Preparing to unpack .../10-libgdbm-compat4_1.22-1_ppc64el.deb ... Unpacking libgdbm-compat4:ppc64el (1.22-1) over (1.19-2build1) ... Preparing to unpack .../11-lockfile-progs_0.1.19_ppc64el.deb ... Unpacking lockfile-progs (0.1.19) over (0.1.18build1) ... Preparing to unpack .../12-make_4.3-4ubuntu2_ppc64el.deb ... Unpacking make (4.3-4ubuntu2) over (4.3-4ubuntu1) ... Setting up libapparmor1:ppc64el (3.0.3-0ubuntu2) ... Setting up libsqlite3-0:ppc64el (3.36.0-2) ... Setting up libgomp1:ppc64el (11.2.0-10ubuntu1) ... Setting up libasan6:ppc64el (11.2.0-10ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 1 23:33:28 UTC 2021. Universal Time is now: Mon Nov 1 23:33:28 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:ppc64el (6.2+20210905-1) ... Setting up libquadmath0:ppc64el (11.2.0-10ubuntu1) ... Setting up libmpc3:ppc64el (1.2.1-1) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:ppc64el (11.2.0-10ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libncursesw6:ppc64el (6.2+20210905-1) ... Setting up libubsan1:ppc64el (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:ppc64el (0.24-2) ... Setting up libcc1-0:ppc64el (11.2.0-10ubuntu1) ... Setting up gpg (2.2.27-2ubuntu1) ... Setting up liblsan0:ppc64el (11.2.0-10ubuntu1) ... Setting up libitm1:ppc64el (11.2.0-10ubuntu1) ... Setting up libgdbm6:ppc64el (1.22-1) ... Setting up libtsan0:ppc64el (11.2.0-10ubuntu1) ... Setting up cpp-11 (11.2.0-10ubuntu1) ... Setting up gpg-agent (2.2.27-2ubuntu1) ... Setting up libgdbm-compat4:ppc64el (1.22-1) ... Setting up libgcc-11-dev:ppc64el (11.2.0-10ubuntu1) ... Setting up gcc-11 (11.2.0-10ubuntu1) ... Setting up libstdc++-11-dev:ppc64el (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-22362569 ppc64el jammy-proposed -c chroot:build-PACKAGEBUILD-22362569 --arch=ppc64el --dist=jammy-proposed --nolog stacks_2.60+dfsg-1.dsc Initiating build PACKAGEBUILD-22362569 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:40:22 UTC 2021 ppc64le sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-ppc64el-004.buildd +==============================================================================+ | stacks 2.60+dfsg-1 (ppc64el) Mon, 01 Nov 2021 23:33:33 +0000 | +==============================================================================+ Package: stacks Version: 2.60+dfsg-1 Source Version: 2.60+dfsg-1 Distribution: jammy-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22362569/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-mLw6XW/stacks-2.60+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-mLw6XW' 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-FccTHx/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-FccTHx/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FccTHx/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-FccTHx/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FccTHx/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-FccTHx/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (111 kB/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-FccTHx/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 ... 13184 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.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 (ppc64el 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-FccTHx/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-FccTHx/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FccTHx/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-FccTHx/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FccTHx/apt_archive ./ Sources [524 B] Get:5 copy:/<>/resolver-FccTHx/apt_archive ./ Packages [603 B] Fetched 2090 B in 0s (133 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 28.5 MB of archives. After this operation, 95.3 MB of additional disk space will be used. Get:1 copy:/<>/resolver-FccTHx/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [698 B] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el bsdextrautils ppc64el 2.37.2-4ubuntu1 [77.8 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main ppc64el libuchardet0 ppc64el 0.0.7-1build1 [80.3 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main ppc64el groff-base ppc64el 1.22.4-7 [1033 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpipeline1 ppc64el 1.5.3-1build1 [27.0 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main ppc64el man-db ppc64el 2.9.4-2build1 [1231 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libelf1 ppc64el 0.185-2 [62.6 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main ppc64el libicu67 ppc64el 67.1-7ubuntu1 [10.4 MB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libxml2 ppc64el 2.9.12+dfsg-5 [838 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main ppc64el libmagic-mgc ppc64el 1:5.39-3build1 [236 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main ppc64el libmagic1 ppc64el 1:5.39-3build1 [105 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main ppc64el file ppc64el 1:5.39-3build1 [25.6 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main ppc64el gettext-base ppc64el 0.21-4ubuntu3 [40.5 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main ppc64el libpsl5 ppc64el 0.21.0-1.2build1 [59.6 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main ppc64el libsigsegv2 ppc64el 2.13-1ubuntu2 [15.3 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main ppc64el m4 ppc64el 1.4.18-5ubuntu1 [213 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el autoconf all 2.71-2 [338 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main ppc64el autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el automake all 1:1.16.5-1 [558 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main ppc64el autopoint all 0.21-4ubuntu3 [422 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libdebhelper-perl all 13.3.4ubuntu3 [62.4 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main ppc64el libtool all 2.4.6-15build1 [164 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main ppc64el libsub-override-perl all 0.09-2 [9532 B] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libfile-stripnondeterminism-perl all 1.12.0-2 [18.0 kB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el dh-strip-nondeterminism all 1.12.0-2 [5208 B] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libdw1 ppc64el 0.185-2 [289 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main ppc64el debugedit ppc64el 1:5.0-0ubuntu2 [52.4 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main ppc64el dwz ppc64el 0.14-1build1 [125 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main ppc64el gettext ppc64el 0.21-4ubuntu3 [895 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el debhelper all 13.3.4ubuntu3 [921 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-2ubuntu7 [177 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el libbam-dev ppc64el 0.1.19+dfsg-4 [151 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main ppc64el libbrotli1 ppc64el 1.0.9-2build4 [372 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libsasl2-modules-db ppc64el 2.1.27+dfsg-2.2 [18.0 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main ppc64el libsasl2-2 ppc64el 2.1.27+dfsg-2.2 [65.3 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main ppc64el libldap-2.5-0 ppc64el 2.5.6+dfsg-1~exp1ubuntu1 [222 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main ppc64el libnghttp2-14 ppc64el 1.43.0-1build1 [89.0 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build3 [65.8 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main ppc64el libssh-4 ppc64el 0.9.6-1 [237 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main ppc64el libcurl3-gnutls ppc64el 7.74.0-1.3ubuntu2 [347 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main ppc64el libcurl4-gnutls-dev ppc64el 7.74.0-1.3ubuntu2 [429 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main ppc64el libdeflate0 ppc64el 1.7-2ubuntu2 [49.7 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main ppc64el libdeflate-dev ppc64el 1.7-2ubuntu2 [43.3 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el libhtscodecs2 ppc64el 1.1.1-3 [80.0 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libhts3 ppc64el 1.13+ds-2 [507 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main ppc64el liblzma-dev ppc64el 5.2.5-2build1 [181 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libhts-dev ppc64el 1.13+ds-2 [6009 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/universe ppc64el libsparsehash-dev all 2.0.3-2 [71.7 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/universe ppc64el samtools ppc64el 1.13-4 [586 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.5 MB in 1s (27.2 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 13184 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-4ubuntu1_ppc64el.deb ... Unpacking bsdextrautils (2.37.2-4ubuntu1) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../01-libuchardet0_0.0.7-1build1_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.7-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_ppc64el.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../03-libpipeline1_1.5.3-1build1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.3-1build1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2build1_ppc64el.deb ... Unpacking man-db (2.9.4-2build1) ... Selecting previously unselected package libelf1:ppc64el. Preparing to unpack .../05-libelf1_0.185-2_ppc64el.deb ... 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Setting up libdeflate0:ppc64el (1.7-2ubuntu2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up file (1:5.39-3build1) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libsasl2-modules-db:ppc64el (2.1.27+dfsg-2.2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build3) ... Setting up libsigsegv2:ppc64el (2.13-1ubuntu2) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up libsasl2-2:ppc64el (2.1.27+dfsg-2.2) ... Setting up libssh-4:ppc64el (0.9.6-1) ... Setting up liblzma-dev:ppc64el (5.2.5-2build1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-2ubuntu7) ... Setting up libuchardet0:ppc64el (0.0.7-1build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:ppc64el (1.7-2ubuntu2) ... Setting up libelf1:ppc64el (0.185-2) ... Setting up libxml2:ppc64el (2.9.12+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up libdw1:ppc64el (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:ppc64el (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:ppc64el (7.74.0-1.3ubuntu2) ... Setting up libcurl4-gnutls-dev:ppc64el (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:ppc64el (1.13+ds-2) ... Setting up libhts-dev:ppc64el (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 ppc64el (ppc64le) 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-powerpc64le-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 liblsan0_11.2.0-10ubuntu1 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 libquadmath0_11.2.0-10ubuntu1 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 libtsan0_11.2.0-10ubuntu1 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-22362569 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22362569 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22362569 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 ppc64el 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=powerpc64le-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/powerpc64le-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... powerpc64le-unknown-linux-gnu checking host system type... powerpc64le-unknown-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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 In file included from src/ustacks.h:65, from src/ustacks.cc:25: src/GappedAln.h: In member function ‘GappedAln::init(int, int, bool) [clone .constprop.1]’: src/GappedAln.h:208:23: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 208 | this->_m_size = new_size; | ~~~~~~~~~~~~~~^~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 In file included from /usr/include/c++/11/bits/regex_scanner.h:272, from /usr/include/c++/11/regex:61, from src/catalog_utils.cc:28: /usr/include/c++/11/bits/regex_scanner.tcc: In member function ‘std::__detail::_Scanner::_Scanner(char const*, char const*, std::regex_constants::syntax_option_type, std::locale)’: /usr/include/c++/11/bits/regex_scanner.tcc:56:5: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 56 | _Scanner<_CharT>:: | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/regex_scanner.h:272, from /usr/include/c++/11/regex:61, from src/constants.cc:1: /usr/include/c++/11/bits/regex_scanner.tcc: In member function ‘std::__detail::_Scanner::_Scanner(char const*, char const*, std::regex_constants::syntax_option_type, std::locale)’: /usr/include/c++/11/bits/regex_scanner.tcc:56:5: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 56 | _Scanner<_CharT>:: | ^~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from src/constants.h:53, from src/models.h:24, from src/models.cc:30: /usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = std::pair*; _Distance = long int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ src/locus.cc: In member function ‘Locus::Locus(Locus const&)’: src/locus.cc:28:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 28 | Locus::Locus(const Locus &templ) | ^~~~~ src/mstack.cc: In member function ‘MergedStack::MergedStack()’: src/mstack.cc:28:1: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 28 | MergedStack::MergedStack() { | ^~~~~~~~~~~ src/models.cc: In function ‘record_dummy_snp(SNP&, unsigned int)’: src/models.cc:159:6: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 159 | void record_dummy_snp(SNP& snp, uint col) { | ^~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 src/Seq.cc: In member function ‘Seq::Seq(Seq const&)’: src/Seq.cc:52:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 52 | Seq::Seq(const Seq& other) | ^~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 -O3 -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 In file included from src/stacks.h:37, from src/stacks.cc:33: src/Seq.h: In member function ‘PStack::extend(PhyLoc const&, int)’: src/Seq.h:43:32: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 43 | : chr_(NULL), bp(other.bp), strand(other.strand) { | ~~~~~~^~ src/sql_utilities.cc: In function ‘load_snp_calls(std::__cxx11::basic_string, std::allocator >, std::map, std::allocator > >&)’: src/sql_utilities.cc:209:5: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 209 | int load_snp_calls(string sample, map &snpres) { | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 -O3 -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 -O3 -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 In file included from /usr/include/c++/11/bits/regex_scanner.h:272, from /usr/include/c++/11/regex:61, from src/utils.cc:29: /usr/include/c++/11/bits/regex_scanner.tcc: In member function ‘std::__detail::_Scanner::_Scanner(char const*, char const*, std::regex_constants::syntax_option_type, std::locale)’: /usr/include/c++/11/bits/regex_scanner.tcc:56:5: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 56 | _Scanner<_CharT>:: | ^~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 In file included from src/cstacks.h:53, from src/cstacks.cc:26: src/GappedAln.h: In member function ‘GappedAln::init(int, int, bool) [clone .constprop.0]’: src/GappedAln.h:208:23: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 208 | this->_m_size = new_size; | ~~~~~~~~~~~~~~^~~~~~~~~~ In file included from src/sstacks.h:53, from src/sstacks.cc:34: src/GappedAln.h: In member function ‘GappedAln::init(int, int, bool) [clone .constprop.0]’: src/GappedAln.h:208:23: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 208 | this->_m_size = new_size; | ~~~~~~~~~~~~~~^~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 In file included from src/populations.h:49, from src/populations.cc:29: src/PopMap.h: In function ‘PopMap::populate_external(CSLocus*, Datum**, int, VcfRecord const&, VcfHeader const&, MetaPopInfo const*, std::vector > const&)’: src/PopMap.h:389:1: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 389 | PopMap::populate_external( | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 -O3 -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 In file included from src/phasedstacks.h:48, from src/phasedstacks.cc:25: src/sql_utilities.h: In function ‘load_loci(std::__cxx11::basic_string, std::allocator > const&, std::map, std::allocator > >&, int, bool, bool&, bool)int’: src/sql_utilities.h:52:1: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 52 | load_loci(const string& sample, map &loci, int store_reads, bool load_all_model_calls, bool &compressed, bool verbose=true) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -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 -O3 -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 In file included from src/tsv2bam.cc:10: src/sql_utilities.h: In function ‘load_loci(std::__cxx11::basic_string, std::allocator > const&, std::map, std::allocator > >&, int, bool, bool&, bool)int’: src/sql_utilities.h:52:1: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 52 | load_loci(const string& sample, map &loci, int store_reads, bool load_all_model_calls, bool &compressed, bool verbose=true) | ^~~~~~~~~ g++ -g -O3 -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 src/GappedAln.h: In member function ‘init.constprop.isra’: src/GappedAln.h:208:23: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 208 | this->_m_size = new_size; | ^ src/ustacks.cc: In function ‘_Z14call_consensusRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEERS_IiP5StackS3_SaIS4_IS5_SB_EEERS_IiP3RemS3_SaIS4_IS5_SH_EEEb._omp_fn.0’: src/ustacks.cc:1177:13: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 1177 | #pragma omp parallel private(i) | ^ src/GappedAln.h: In member function ‘trace_global_alignment’: src/GappedAln.h:674:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 674 | GappedAln::trace_global_alignment(const string& tag_1, const string& tag_2) | ^ src/sql_utilities.h: In function ‘load_loci.constprop’: src/sql_utilities.h:52:1: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 52 | load_loci(const string& sample, map &loci, int store_reads, bool load_all_model_calls, bool &compressed, bool verbose=true) | ^ /usr/include/c++/11/bits/stl_algo.h: In function ‘__introsort_loop.constprop’: /usr/include/c++/11/bits/stl_algo.h:1925:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1925 | __introsort_loop(_RandomAccessIterator __first, | ^ In file included from /usr/include/c++/11/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/include/c++/11/bits/stl_algo.h: In function ‘std::__unguarded_linear_insert<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__ops::_Val_comp_iter >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__ops::_Val_comp_iter)void [clone .constprop.0]’: /usr/include/c++/11/bits/stl_algo.h:1799:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O3 -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 /usr/include/c++/11/bits/stl_algo.h: In function ‘__unguarded_linear_insert.constprop’: /usr/include/c++/11/bits/stl_algo.h:1799:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^ src/GappedAln.h: In member function ‘trace_global_alignment’: src/GappedAln.h:674:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 674 | GappedAln::trace_global_alignment(const string& tag_1, const string& tag_2) | ^ src/locus.cc: In member function ‘__ct_base ’: src/locus.cc:28:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 28 | Locus::Locus(const Locus &templ) | ^ g++ -g -O3 -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 /usr/include/c++/11/bits/stl_algo.h: In function ‘__unguarded_linear_insert.constprop’: /usr/include/c++/11/bits/stl_algo.h:1799:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^ g++ -g -O3 -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 /usr/include/c++/11/bits/move.h: In function ‘swap’: /usr/include/c++/11/bits/move.h:196:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 196 | swap(_Tp& __a, _Tp& __b) | ^ g++ -g -O3 -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 src/BamUnalignedI.h: In member function ‘next_seq’: src/BamUnalignedI.h:93:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 93 | BamUnAln::next_seq(Seq& s) | ^ src/BamUnalignedI.h: In member function ‘next_seq’: src/BamUnalignedI.h:93:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 93 | BamUnAln::next_seq(Seq& s) | ^ g++ -g -O3 -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 -O3 -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 src/BamUnalignedI.h: In member function ‘next_seq’: src/BamUnalignedI.h:93:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 93 | BamUnAln::next_seq(Seq& s) | ^ g++ -g -O3 -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 src/populations.cc: In member function ‘next_batch_external_loci’: g++ -g -O3 -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 src/populations.cc:877:1: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 877 | BatchLocusProcessor::next_batch_external_loci(ostream &log_fh) | ^ src/PopMap.h: In function ‘populate_internal’: src/PopMap.h:168:6: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 168 | void PopMap::populate_internal( | ^ src/BamI.cc: In member function ‘next_seq’: src/BamI.cc:196:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 196 | Bam::next_seq(Seq& s) | ^ /usr/include/c++/11/bits/regex_compiler.tcc: In member function ‘__ct_base ’: /usr/include/c++/11/bits/regex_compiler.tcc:65:5: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 65 | _Compiler<_TraitsT>:: | ^ g++ -g -O3 -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 src/GappedAln.h: In member function ‘trace_local_alignment’: src/GappedAln.h:790:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 790 | GappedAln::trace_local_alignment(const string& query, const string& subj) | ^ src/BamI.cc: In member function ‘next_seq’: src/BamI.cc:196:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 196 | Bam::next_seq(Seq& s) | ^ /usr/include/c++/11/bits/stl_heap.h: In function ‘__adjust_heap’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^ /usr/include/c++/11/bits/stl_algo.h: In function ‘__introsort_loop.constprop’: /usr/include/c++/11/bits/stl_algo.h:1925:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1925 | __introsort_loop(_RandomAccessIterator __first, | ^ /usr/include/c++/11/bits/stl_heap.h: In function ‘__adjust_heap.constprop’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^ src/gstacks.cc: In member function ‘process’: src/gstacks.cc:1166:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1166 | LocusProcessor::process(CLocAlnSet& aln_loc) | ^ /usr/include/c++/11/bits/stl_algo.h: In function ‘__insertion_sort.constprop’: /usr/include/c++/11/bits/stl_algo.h:1819:5: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1819 | __insertion_sort(_RandomAccessIterator __first, | ^ src/gstacks.cc: In function ‘align_reads_to_contig.isra’: src/gstacks.cc:1309:1: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 1309 | LocusProcessor::align_reads_to_contig(SuffixTree *st, GappedAln *g_aln, DNASeq4 &enc_query, AlignRes &aln_res) const | ^ 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 d0c7f8d290d66714fb1ac384001842322a57816b debugedit: debian/stacks/usr/lib/stacks/bin/kmer_filter: Unknown DWARF DW_FORM_0x1f20 f014a2447d0f0be71ba2d1c6c147e5855b66600b debugedit: debian/stacks/usr/lib/stacks/bin/clone_filter: Unknown DWARF DW_FORM_0x1f21 d5eac077e8bbea74f583fe20309c0699edfd4e6d debugedit: debian/stacks/usr/lib/stacks/bin/cstacks: Unknown DWARF DW_FORM_0x1f20 cc84504385159e966f8fd45f53f9ccebf51be137 debugedit: debian/stacks/usr/lib/stacks/bin/tsv2bam: Unknown DWARF DW_FORM_0x1f21 307550229efc46b9e28852da0779a3983752c95e debugedit: debian/stacks/usr/lib/stacks/bin/process_radtags: Unknown DWARF DW_FORM_0x1f21 bb64d434b8b9b81a24206bda8c383e65fd607600 debugedit: debian/stacks/usr/lib/stacks/bin/populations: Unknown DWARF DW_FORM_0x1f21 75036c0e7aa5fde4cdc397f9f3b31a212911df31 debugedit: debian/stacks/usr/lib/stacks/bin/phasedstacks: Unknown DWARF DW_FORM_0x1f20 01360e7dc3b5aada2f15292a3bcdb2f1d2d0888e debugedit: debian/stacks/usr/lib/stacks/bin/ustacks: Unknown DWARF DW_FORM_0x1f21 70835716a68dde0fac731a22aceabee37ba022eb debugedit: debian/stacks/usr/lib/stacks/bin/sstacks: Unknown DWARF DW_FORM_0x1f20 115d18783504c9e545b224ddbafd837207b731ed debugedit: debian/stacks/usr/lib/stacks/bin/process_shortreads: Unknown DWARF DW_FORM_0x1f20 cdb4f6880fc4da6066882d1b1b7b260debaf74e6 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: 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_ppc64el.deb'. pkgstripfiles: Truncating usr/share/doc/stacks/changelog.Debian.gz to topmost ten records 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_ppc64el.deb'. Renaming stacks-dbgsym_2.60+dfsg-1_ppc64el.deb to stacks-dbgsym_2.60+dfsg-1_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../stacks_2.60+dfsg-1_ppc64el.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 2021-11-01T23:36:33Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ stacks_2.60+dfsg-1_ppc64el.changes: ----------------------------------- Format: 1.8 Date: Tue, 02 Nov 2021 00:08:37 +0530 Source: stacks Binary: stacks Built-For-Profiles: noudeb Architecture: ppc64el 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: 8f74d09c9eafde19eb82a4d11b50bbb2896e47c7 15114512 stacks-dbgsym_2.60+dfsg-1_ppc64el.ddeb 0c4cb994d3d094e2b0f207d4fb7a8875bc58c365 6680 stacks_2.60+dfsg-1_ppc64el.buildinfo f89906c945cff492ce96367f0d732aebcdf7d793 1121232 stacks_2.60+dfsg-1_ppc64el.deb Checksums-Sha256: c7d1366c1bc4c7e46925278e6a5dc1bb5eea5c77ef728f2640aebae70ed28a60 15114512 stacks-dbgsym_2.60+dfsg-1_ppc64el.ddeb 46909fb3f7590bdb84bc1ff467632f594e9dc102a85253bae6a82460f38fec96 6680 stacks_2.60+dfsg-1_ppc64el.buildinfo 027519aeefba9e82d4c90a07143ed196047797e43f8390bf8db06b24f9142a97 1121232 stacks_2.60+dfsg-1_ppc64el.deb Files: 64a80cff38f38b05a189fa2061a182fb 15114512 debug optional stacks-dbgsym_2.60+dfsg-1_ppc64el.ddeb 4a4a3c59472c928e5a274dcae17cc073 6680 science optional stacks_2.60+dfsg-1_ppc64el.buildinfo db19ac4a9e722feeb1dc2db6945b68e4 1121232 science optional stacks_2.60+dfsg-1_ppc64el.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: stacks Binary: stacks stacks-dbgsym Architecture: ppc64el Version: 2.60+dfsg-1 Checksums-Md5: 64a80cff38f38b05a189fa2061a182fb 15114512 stacks-dbgsym_2.60+dfsg-1_ppc64el.ddeb db19ac4a9e722feeb1dc2db6945b68e4 1121232 stacks_2.60+dfsg-1_ppc64el.deb Checksums-Sha1: 8f74d09c9eafde19eb82a4d11b50bbb2896e47c7 15114512 stacks-dbgsym_2.60+dfsg-1_ppc64el.ddeb f89906c945cff492ce96367f0d732aebcdf7d793 1121232 stacks_2.60+dfsg-1_ppc64el.deb Checksums-Sha256: c7d1366c1bc4c7e46925278e6a5dc1bb5eea5c77ef728f2640aebae70ed28a60 15114512 stacks-dbgsym_2.60+dfsg-1_ppc64el.ddeb 027519aeefba9e82d4c90a07143ed196047797e43f8390bf8db06b24f9142a97 1121232 stacks_2.60+dfsg-1_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Mon, 01 Nov 2021 23:36:33 +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-powerpc64le-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), liblsan0 (= 11.2.0-10ubuntu1), 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), libquadmath0 (= 11.2.0-10ubuntu1), 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), libtsan0 (= 11.2.0-10ubuntu1), 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_ppc64el.deb ------------------------------ new Debian package, version 2.0. size 1121232 bytes: control archive=1588 bytes. 1086 bytes, 22 lines control 1800 bytes, 26 lines md5sums Package: stacks Version: 2.60+dfsg-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4485 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 200240 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 265400 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 724472 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 200136 2021-11-01 18:38 ./usr/lib/stacks/bin/kmer_filter -rwxr-xr-x root/root 266456 2021-11-01 18:38 ./usr/lib/stacks/bin/phasedstacks -rwxr-xr-x root/root 1121360 2021-11-01 18:38 ./usr/lib/stacks/bin/populations -rwxr-xr-x root/root 466048 2021-11-01 18:38 ./usr/lib/stacks/bin/process_radtags -rwxr-xr-x root/root 266616 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 199648 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 331128 2021-11-01 18:38 ./usr/lib/stacks/bin/tsv2bam -rwxr-xr-x root/root 398288 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: ppc64el Build Type: any Build-Space: n/a Build-Time: 171 Distribution: jammy-proposed Host Architecture: ppc64el Install-Time: 9 Job: stacks_2.60+dfsg-1.dsc Machine Architecture: ppc64el Package: stacks Package-Time: 180 Source-Version: 2.60+dfsg-1 Space: n/a Status: successful Version: 2.60+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-11-01T23:36:33Z Build needed 00:03:00, 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=ppc64el PACKAGEBUILD-22362569 Scanning for processes to kill in build PACKAGEBUILD-22362569