https://launchpad.net/ubuntu/+source/art-nextgen-simulation-tools/20160605+dfsg-4build2/+build/22599300 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-010 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:52:46 UTC 2021 s390x Buildd toolchain package versions: launchpad-buildd_204~508~ubuntu18.04.1 python3-lpbuildd_204~508~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... 7 Dec 17:32:16 ntpdate[1713]: adjust time server 10.211.37.1 offset -0.000105 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22599300 --image-type chroot /home/buildd/filecache-default/63391afefe2c3c1f68eb13dcf1e745f5d0398db6 Creating target for build PACKAGEBUILD-22599300 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22599300 Starting target for build PACKAGEBUILD-22599300 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22599300 '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-22599300 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22599300 Updating target for build PACKAGEBUILD-22599300 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main s390x Packages [1334 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe s390x Packages [12.7 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5567 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x Packages [139 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [51.2 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x Packages [581 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [312 kB] Fetched 21.8 MB in 4s (5072 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: libsemanage2 libsepol2 libssl3 The following packages will be upgraded: apt base-files bash binutils binutils-common binutils-s390x-linux-gnu bsdutils bzip2 ca-certificates cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libbz2-1.0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdpkg-perl libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mount ncurses-base ncurses-bin openssl passwd pkgbinarymangler sed sensible-utils systemd systemd-sysv systemd-timesyncd tzdata usrmerge util-linux 103 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 69.1 MB of archives. After this operation, 311 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main s390x debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main s390x libpam0g s390x 1.4.0-10ubuntu2 [60.3 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main s390x libcrypt-dev s390x 1:4.4.26-1 [114 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main s390x libcrypt1 s390x 1:4.4.26-1 [85.3 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main s390x base-files s390x 12ubuntu2 [63.3 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main s390x debianutils s390x 5.5-1ubuntu1 [107 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main s390x bash s390x 5.1-5ubuntu1 [759 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main s390x bsdutils s390x 1:2.37.2-4ubuntu1 [81.0 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main s390x libgpg-error0 s390x 1.42-3 [67.6 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main s390x libgcrypt20 s390x 1.9.4-3ubuntu2 [457 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x bzip2 s390x 1.0.8-5 [34.4 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libbz2-1.0 s390x 1.0.8-5 [35.9 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main s390x libcc1-0 s390x 11.2.0-12ubuntu1 [52.8 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main s390x gcc-11-base s390x 11.2.0-12ubuntu1 [20.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main s390x libgcc-s1 s390x 11.2.0-12ubuntu1 [28.4 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main s390x libgomp1 s390x 11.2.0-12ubuntu1 [113 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main s390x libitm1 s390x 11.2.0-12ubuntu1 [29.7 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main s390x libatomic1 s390x 11.2.0-12ubuntu1 [9008 B] Get:19 http://ftpmaster.internal/ubuntu jammy/main s390x libasan6 s390x 11.2.0-12ubuntu1 [2246 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main s390x libubsan1 s390x 11.2.0-12ubuntu1 [911 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main s390x g++-11 s390x 11.2.0-12ubuntu1 [9156 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main s390x libstdc++-11-dev s390x 11.2.0-12ubuntu1 [2115 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main s390x libgcc-11-dev s390x 11.2.0-12ubuntu1 [829 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main s390x gcc-11 s390x 11.2.0-12ubuntu1 [15.7 MB] Get:25 http://ftpmaster.internal/ubuntu jammy/main s390x cpp-11 s390x 11.2.0-12ubuntu1 [7835 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main s390x libstdc++6 s390x 11.2.0-12ubuntu1 [689 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main s390x libisl23 s390x 0.24-2 [699 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main s390x libmpc3 s390x 1.2.1-1 [47.6 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main s390x libzstd1 s390x 1.4.8+dfsg-3 [317 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main s390x libctf0 s390x 2.37-10ubuntu1 [99.4 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main s390x libctf-nobfd0 s390x 2.37-10ubuntu1 [101 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main s390x libbinutils s390x 2.37-10ubuntu1 [456 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main s390x binutils-common s390x 2.37-10ubuntu1 [213 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main s390x binutils s390x 2.37-10ubuntu1 [3160 B] Get:35 http://ftpmaster.internal/ubuntu jammy/main s390x binutils-s390x-linux-gnu s390x 2.37-10ubuntu1 [2198 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main s390x libssl3 s390x 3.0.0-1ubuntu1 [1566 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main s390x libblkid1 s390x 2.37.2-4ubuntu1 [100 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main s390x libuuid1 s390x 2.37.2-4ubuntu1 [23.9 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libcryptsetup12 s390x 2:2.4.2-1ubuntu3 [197 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main s390x libidn2-0 s390x 2.3.2-2 [66.3 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main s390x libp11-kit0 s390x 0.24.0-6 [258 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main s390x libtasn1-6 s390x 4.18.0-4 [43.3 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main s390x libgnutls30 s390x 3.7.2-2ubuntu1 [867 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x systemd-timesyncd s390x 249.5-2ubuntu1 [29.3 kB] Get:45 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x systemd-sysv s390x 249.5-2ubuntu1 [10.5 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main s390x libapparmor1 s390x 3.0.3-0ubuntu4 [37.3 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main s390x libip4tc2 s390x 1.8.7-1ubuntu4 [19.5 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main s390x libkmod2 s390x 28-1ubuntu5 [46.8 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main s390x libpcre2-8-0 s390x 10.39-3 [198 kB] Get:50 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libselinux1 s390x 3.3-1build1 [74.6 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main s390x libmount1 s390x 2.37.2-4ubuntu1 [119 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main s390x libseccomp2 s390x 2.5.2-2ubuntu2 [48.1 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main s390x login s390x 1:4.8.1-2ubuntu1 [187 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main s390x util-linux s390x 2.37.2-4ubuntu1 [1055 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main s390x mount s390x 2.37.2-4ubuntu1 [113 kB] Get:56 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x systemd s390x 249.5-2ubuntu1 [4302 kB] Get:57 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsystemd0 s390x 249.5-2ubuntu1 [311 kB] Get:58 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libudev1 s390x 249.5-2ubuntu1 [76.6 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main s390x libapt-pkg6.0 s390x 2.3.13 [869 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main s390x dpkg s390x 1.20.9ubuntu3 [1241 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main s390x dash s390x 0.5.11+git20210903+057cd650a4ed-3 [92.2 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main s390x grep s390x 3.7-1 [156 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main s390x libncurses6 s390x 6.3-1 [109 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main s390x libncursesw6 s390x 6.3-1 [142 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main s390x libtinfo6 s390x 6.3-1 [105 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main s390x ncurses-bin s390x 6.3-1 [185 kB] Get:67 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x sed s390x 4.8-1 [188 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main s390x ncurses-base all 6.3-1 [19.9 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main s390x gpgv s390x 2.2.27-2ubuntu1 [133 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main s390x apt s390x 2.3.13 [1362 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main s390x libsepol2 s390x 3.3-1 [267 kB] Get:72 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsemanage-common all 3.3-1build1 [10.0 kB] Get:73 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsemanage2 s390x 3.3-1build1 [88.7 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main s390x passwd s390x 1:4.8.1-2ubuntu1 [764 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main s390x libpam-modules-bin s390x 1.4.0-10ubuntu2 [40.1 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main s390x libpam-modules s390x 1.4.0-10ubuntu2 [279 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main s390x logsave s390x 1.46.4-1ubuntu1 [10.8 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main s390x libext2fs2 s390x 1.46.4-1ubuntu1 [210 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main s390x e2fsprogs s390x 1.46.4-1ubuntu1 [582 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main s390x libattr1 s390x 1:2.5.1-1 [13.3 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main s390x libcom-err2 s390x 1.46.4-1ubuntu1 [9948 B] Get:82 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libk5crypto3 s390x 1.19.2-0ubuntu1 [88.3 kB] Get:83 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libkrb5support0 s390x 1.19.2-0ubuntu1 [32.4 kB] Get:84 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libkrb5-3 s390x 1.19.2-0ubuntu1 [348 kB] Get:85 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgssapi-krb5-2 s390x 1.19.2-0ubuntu1 [138 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main s390x libpam-runtime all 1.4.0-10ubuntu2 [40.2 kB] Get:87 http://ftpmaster.internal/ubuntu jammy/main s390x libsmartcols1 s390x 2.37.2-4ubuntu1 [50.0 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main s390x libss2 s390x 1.46.4-1ubuntu1 [12.1 kB] Get:89 http://ftpmaster.internal/ubuntu jammy/main s390x sensible-utils all 0.0.17 [20.1 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/main s390x usrmerge all 25ubuntu2 [54.7 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main s390x openssl s390x 3.0.0-1ubuntu1 [1169 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main s390x ca-certificates all 20211016 [148 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main s390x libsqlite3-0 s390x 3.36.0-2 [630 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main s390x tzdata all 2021e-1ubuntu1 [343 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/main s390x libgdbm6 s390x 1.22-1 [35.3 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main s390x dpkg-dev all 1.20.9ubuntu3 [933 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main s390x libdpkg-perl all 1.20.9ubuntu3 [235 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main s390x make s390x 4.3-4ubuntu2 [181 kB] Get:99 http://ftpmaster.internal/ubuntu jammy/main s390x lto-disabled-list all 17 [12.1 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main s390x gpg s390x 2.2.27-2ubuntu1 [505 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/main s390x gpgconf s390x 2.2.27-2ubuntu1 [94.0 kB] Get:102 http://ftpmaster.internal/ubuntu jammy/main s390x gpg-agent s390x 2.2.27-2ubuntu1 [206 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main s390x libgdbm-compat4 s390x 1.22-1 [6554 B] Get:104 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x linux-libc-dev s390x 5.15.0-13.13 [1269 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main s390x lockfile-progs s390x 0.1.19 [9654 B] Get:106 http://ftpmaster.internal/ubuntu jammy/main s390x pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 69.1 MB in 6s (11.7 MB/s) (Reading database ... 13030 files and directories currently installed.) Preparing to unpack .../debconf_1.5.79_all.deb ... Unpacking debconf (1.5.79) over (1.5.77) ... Setting up debconf (1.5.79) ... (Reading database ... 13029 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-10ubuntu2_s390x.deb ... Unpacking libpam0g:s390x (1.4.0-10ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam0g:s390x (1.4.0-10ubuntu2) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 13029 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.26-1_s390x.deb ... Unpacking libcrypt-dev:s390x (1:4.4.26-1) over (1:4.4.18-4ubuntu2) ... Preparing to unpack .../libcrypt1_1%3a4.4.26-1_s390x.deb ... Unpacking libcrypt1:s390x (1:4.4.26-1) over (1:4.4.18-4ubuntu2) ... Setting up libcrypt1:s390x (1:4.4.26-1) ... (Reading database ... 13029 files and directories currently installed.) Preparing to unpack .../base-files_12ubuntu2_s390x.deb ... 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Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:s390x (6.3-1) ... Setting up libmpc3:s390x (1.2.1-1) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:s390x (11.2.0-12ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:s390x (1.46.4-1ubuntu1) ... Setting up libncursesw6:s390x (6.3-1) ... Setting up libdpkg-perl (1.20.9ubuntu3) ... Setting up logsave (1.46.4-1ubuntu1) ... Setting up libubsan1:s390x (11.2.0-12ubuntu1) ... Setting up mount (2.37.2-4ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:s390x (1:4.4.26-1) ... Setting up gpgconf (2.2.27-2ubuntu1) ... Setting up libcryptsetup12:s390x (2:2.4.2-1ubuntu3) ... Setting up libbinutils:s390x (2.37-10ubuntu1) ... Setting up libisl23:s390x (0.24-2) ... Setting up openssl (3.0.0-1ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libcc1-0:s390x (11.2.0-12ubuntu1) ... Setting up gpg (2.2.27-2ubuntu1) ... Setting up libitm1:s390x (11.2.0-12ubuntu1) ... Setting up libkmod2:s390x (28-1ubuntu5) ... Setting up libgdbm6:s390x (1.22-1) ... Setting up libctf0:s390x (2.37-10ubuntu1) ... Setting up cpp-11 (11.2.0-12ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.37-10ubuntu1) ... Setting up gpg-agent (2.2.27-2ubuntu1) ... Setting up pkgbinarymangler (149) ... Setting up e2fsprogs (1.46.4-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up systemd (249.5-2ubuntu1) ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Initializing machine ID from random generator. Setting up binutils (2.37-10ubuntu1) ... Setting up dpkg-dev (1.20.9ubuntu3) ... 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 systemd-timesyncd (249.5-2ubuntu1) ... Setting up libgdbm-compat4:s390x (1.22-1) ... Setting up libgcc-11-dev:s390x (11.2.0-12ubuntu1) ... Setting up gcc-11 (11.2.0-12ubuntu1) ... Setting up systemd-sysv (249.5-2ubuntu1) ... Setting up libstdc++-11-dev:s390x (11.2.0-12ubuntu1) ... Setting up g++-11 (11.2.0-12ubuntu1) ... 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-22599300 s390x jammy-proposed -c chroot:build-PACKAGEBUILD-22599300 --arch=s390x --dist=jammy-proposed --nolog art-nextgen-simulation-tools_20160605+dfsg-4build2.dsc Initiating build PACKAGEBUILD-22599300 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:52:46 UTC 2021 s390x sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-s390x-010.buildd +============================================================================================+ | art-nextgen-simulation-tools 20160605+dfsg-4build2 (s390x) Tue, 07 Dec 2021 17:32:48 +0000 | +============================================================================================+ Package: art-nextgen-simulation-tools Version: 20160605+dfsg-4build2 Source Version: 20160605+dfsg-4build2 Distribution: jammy-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22599300/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- art-nextgen-simulation-tools_20160605+dfsg-4build2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/art-nextgen-simulation-tools-6icrIm/art-nextgen-simulation-tools-20160605+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/art-nextgen-simulation-tools-6icrIm' 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-56WGX8/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-56WGX8/apt_archive ./ InRelease Get:2 copy:/<>/resolver-56WGX8/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-56WGX8/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-56WGX8/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-56WGX8/apt_archive ./ Packages [435 B] Fetched 1741 B in 0s (154 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 package was automatically installed and is no longer required: systemd-timesyncd Use 'apt autoremove' to remove it. 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 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-56WGX8/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13224 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libgsl-dev Filtered Build-Depends: debhelper-compat (= 12), libgsl-dev dpkg-deb: building package 'sbuild-build-depends-art-nextgen-simulation-tools-dummy' in '/<>/resolver-56WGX8/apt_archive/sbuild-build-depends-art-nextgen-simulation-tools-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-art-nextgen-simulation-tools-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-56WGX8/apt_archive ./ InRelease Get:2 copy:/<>/resolver-56WGX8/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-56WGX8/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-56WGX8/apt_archive ./ Sources [515 B] Get:5 copy:/<>/resolver-56WGX8/apt_archive ./ Packages [590 B] Fetched 2068 B in 0s (163 kB/s) Reading package lists... Reading package lists... Install art-nextgen-simulation-tools build dependencies (apt-based resolver) ---------------------------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: systemd-timesyncd Use 'apt autoremove' to remove it. 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 libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libgsl-dev libgsl27 libgslcblas0 libicu67 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl 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 libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libgsl-dev libgsl27 libgslcblas0 libicu67 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-art-nextgen-simulation-tools-dummy 0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 20.0 MB of archives. After this operation, 75.0 MB of additional disk space will be used. Get:1 copy:/<>/resolver-56WGX8/apt_archive ./ sbuild-build-depends-art-nextgen-simulation-tools-dummy 0.invalid.0 [682 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main s390x bsdextrautils s390x 2.37.2-4ubuntu1 [72.2 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main s390x libuchardet0 s390x 0.0.7-1build1 [76.1 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main s390x groff-base s390x 1.22.4-7 [926 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main s390x libpipeline1 s390x 1.5.4-1 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main s390x man-db s390x 2.9.4-2build1 [1177 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main s390x libelf1 s390x 0.186-1 [55.2 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main s390x libicu67 s390x 67.1-7ubuntu1 [10.0 MB] Get:9 http://ftpmaster.internal/ubuntu jammy/main s390x libxml2 s390x 2.9.12+dfsg-5 [711 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main s390x libmagic-mgc s390x 1:5.41-2 [259 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main s390x libmagic1 s390x 1:5.41-2 [84.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main s390x file s390x 1:5.41-2 [21.3 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main s390x gettext-base s390x 0.21-4ubuntu3 [38.4 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main s390x libsigsegv2 s390x 2.13-1ubuntu2 [14.6 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main s390x m4 s390x 1.4.18-5ubuntu1 [197 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main s390x autoconf all 2.71-2 [338 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main s390x autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main s390x automake all 1:1.16.5-1.1 [558 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main s390x autopoint all 0.21-4ubuntu3 [422 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main s390x libdebhelper-perl all 13.5.2ubuntu1 [66.0 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main s390x libtool all 2.4.6-15build1 [164 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main s390x dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:25 http://ftpmaster.internal/ubuntu jammy/main s390x libfile-stripnondeterminism-perl all 1.12.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main s390x dh-strip-nondeterminism all 1.12.1-1 [5200 B] Get:27 http://ftpmaster.internal/ubuntu jammy/main s390x libdw1 s390x 0.186-1 [248 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main s390x debugedit s390x 1:5.0-3 [48.2 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main s390x dwz s390x 0.14-1build1 [104 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main s390x gettext s390x 0.21-4ubuntu3 [848 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main s390x debhelper all 13.5.2ubuntu1 [926 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x libgslcblas0 s390x 2.7.1+dfsg-3 [94.3 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x libgsl27 s390x 2.7.1+dfsg-3 [949 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x libgsl-dev s390x 2.7.1+dfsg-3 [1167 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.0 MB in 1s (15.8 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 13224 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-4ubuntu1_s390x.deb ... Unpacking bsdextrautils (2.37.2-4ubuntu1) ... Selecting previously unselected package libuchardet0:s390x. Preparing to unpack .../01-libuchardet0_0.0.7-1build1_s390x.deb ... Unpacking libuchardet0:s390x (0.0.7-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_s390x.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../03-libpipeline1_1.5.4-1_s390x.deb ... Unpacking libpipeline1:s390x (1.5.4-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2build1_s390x.deb ... Unpacking man-db (2.9.4-2build1) ... Selecting previously unselected package libelf1:s390x. Preparing to unpack .../05-libelf1_0.186-1_s390x.deb ... Unpacking libelf1:s390x (0.186-1) ... 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Unpacking sbuild-build-depends-art-nextgen-simulation-tools-dummy (0.invalid.0) ... Setting up libpipeline1:s390x (1.5.4-1) ... Setting up bsdextrautils (2.37.2-4ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:s390x (67.1-7ubuntu1) ... Setting up libgslcblas0:s390x (2.7.1+dfsg-3) ... Setting up libmagic-mgc (1:5.41-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.5.2ubuntu1) ... Setting up libmagic1:s390x (1:5.41-2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up libgsl27:s390x (2.7.1+dfsg-3) ... Setting up file (1:5.41-2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:s390x (2.13-1ubuntu2) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up libuchardet0:s390x (0.0.7-1build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:s390x (0.186-1) ... Setting up libxml2:s390x (2.9.12+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.12.1-1) ... Setting up libdw1:s390x (0.186-1) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libgsl-dev (2.7.1+dfsg-3) ... Setting up libtool (2.4.6-15build1) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.1-1) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-7) ... Setting up debugedit (1:5.0-3) ... Setting up automake (1:1.16.5-1.1) ... 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 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 debhelper (13.5.2ubuntu1) ... 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Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-163-generic s390x (s390x) Toolchain package versions: binutils_2.37-10ubuntu1 dpkg-dev_1.20.9ubuntu3 g++-11_11.2.0-12ubuntu1 gcc-11_11.2.0-12ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-12ubuntu1 libstdc++6_11.2.0-12ubuntu1 linux-libc-dev_5.15.0-13.13 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-5ubuntu1 binutils_2.37-10ubuntu1 binutils-common_2.37-10ubuntu1 binutils-s390x-linux-gnu_2.37-10ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 coreutils_8.32-4ubuntu3 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-12ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2ubuntu1 debianutils_5.5-1ubuntu1 debugedit_1:5.0-3 dh-autoreconf_20 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.8-0ubuntu1 dpkg_1.20.9ubuntu3 dpkg-dev_1.20.9ubuntu3 dwz_0.14-1build1 e2fsprogs_1.46.4-1ubuntu1 fakeroot_1.25.3-1.1ubuntu3 file_1:5.41-2 findutils_4.8.0-1ubuntu2 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-12ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-12ubuntu1 gcc-11-base_11.2.0-12ubuntu1 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_3.0.3-0ubuntu4 libapt-pkg6.0_2.3.13 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build22 libasan6_11.2.0-12ubuntu1 libassuan0_2.5.5-1 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Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Dec 7 17:23:04 2021 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./art-nextgen-simulation-tools_20160605+dfsg-4build2.dsc dpkg-source: info: extracting art-nextgen-simulation-tools in /<>/art-nextgen-simulation-tools-20160605+dfsg dpkg-source: info: unpacking art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz dpkg-source: info: unpacking art-nextgen-simulation-tools_20160605+dfsg-4build2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-test-comparison.patch dpkg-source: info: applying adapt_path_to_perl_scripts.patch dpkg-source: info: applying spellings.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-22599300 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22599300 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22599300 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-4build2 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:8: installing './compile' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' Makefile.am: installing './INSTALL' Makefile.am: installing './depcomp' dh_auto_configure -a ./configure --build=s390x-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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 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 stdlib.h... (cached) yes checking for main in -lm... yes checking for main in -lgslcblas... yes checking for main in -lgsl... yes checking whether make sets $(MAKE)... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for size_t... yes checking for floor... yes checking for pow... yes 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 dh_auto_build -a make -j4 make[1]: Entering directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' make all-am make[2]: Entering directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/art_illumina.o art_illumina_src/art_illumina.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/art_qual_scale.o art_illumina_src/art_qual_scale.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/empdist.o art_illumina_src/empdist.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/readSeqFile.o art_illumina_src/readSeqFile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/seqRead.o art_illumina_src/seqRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/samRead.o art_illumina_src/samRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/art_454.o art_454_src/art_454.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/art.o art_454_src/art.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/read_profile.o art_454_src/read_profile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/readSeqFile.o art_454_src/readSeqFile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/seqRead.o art_454_src/seqRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/samRead.o art_454_src/samRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/art_SOLiD.o art_SOLiD_src/art_SOLiD.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/art.o art_SOLiD_src/art.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/readSeqFile.o art_SOLiD_src/readSeqFile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/read_SOLiD.o art_SOLiD_src/read_SOLiD.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/samRead.o art_SOLiD_src/samRead.cpp g++ -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o art_illumina art_illumina_src/art_illumina.o art_illumina_src/art_qual_scale.o art_illumina_src/empdist.o art_illumina_src/readSeqFile.o art_illumina_src/seqRead.o art_illumina_src/samRead.o -lgsl -lgslcblas -lm g++ -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o art_454 art_454_src/art_454.o art_454_src/art.o art_454_src/read_profile.o art_454_src/readSeqFile.o art_454_src/seqRead.o art_454_src/samRead.o -lgsl -lgslcblas -lm g++ -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o art_SOLiD art_SOLiD_src/art_SOLiD.o art_SOLiD_src/art.o art_SOLiD_src/readSeqFile.o art_SOLiD_src/read_SOLiD.o art_SOLiD_src/samRead.o -lgsl -lgslcblas -lm make[2]: Leaving directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' set -e && \ cd examples && \ ./run_test_examples_454.sh && \ ./run_test_examples_SOLiD.sh && \ ./run_test_examples_illumina.sh =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Single-end simulation Total CPU time used: 0.062375 The random seed for the run: 1638898402 Parameters Settings number of flow cycles: 100 fold of read coverage: 10X 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence File: ./single_454_flx.fq ALN Alignment File: ./single_454_flx.aln SAM Alignment File: ./single_454_flx.sam Read Coverage File: ./single_454_flx.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Paired-end simulation Total CPU time used: 0.054864 The random seed for the run: 1638898402 Parameters Settings number of flow cycles: 100 fold of read coverage: 5X fragment length mean: 500 std: 20 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence Files: the 1st reads: ./paired_454_flx1.fq the 2nd reads: ./paired_454_flx2.fq ALN Alignment Files: the 1st reads: ./paired_454_flx1.aln the 2nd reads: ./paired_454_flx2.aln SAM Alignment File: ./paired_454_flx.sam Read Coverage File: ./paired_454_flx.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Paired-end simulation Total CPU time used: 0.052662 The random seed for the run: 1638898402 Parameters Settings number of flow cycles: 200 fold of read coverage: 6X fragment length mean: 500 std: 20 454 Profile for Simulation the built-in GS-FLX Titanium profile Output Files FASTQ Sequence Files: the 1st reads: ./paired_454_flxTitan1.fq the 2nd reads: ./paired_454_flxTitan2.fq ALN Alignment Files: the 1st reads: ./paired_454_flxTitan1.aln the 2nd reads: ./paired_454_flxTitan2.aln SAM Alignment File: ./paired_454_flxTitan.sam Read Coverage File: ./paired_454_flxTitan.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Amplicon 5'-end sequencing with single-end reads Total CPU time used: 10.4966 The random seed for the run: 1638898402 Parameters Settings number of flow cycles: 100 # reads per amplion: 10 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence File: ./amp_single_454.fq ALN Alignment File: ./amp_single_454.aln SAM Alignment File: ./amp_single_454.sam Read Coverage File: ./amp_single_454.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Amplicon two-end sequencing with paired-end reads Total CPU time used: 8.64325 The random seed for the run: 1638898413 Parameters Settings number of flow cycles: 100 # read pairs per amplion: 5 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence Files: the 1st reads: ./amp_paired_454.fq the 2nd reads: ./amp_paired_4542.fq ALN Alignment Files: the 1st reads: ./amp_paired_454.aln the 2nd reads: ./amp_paired_4542.aln SAM Alignment File: ./amp_paired_454.sam Read Coverage File: ./amp_paired_454.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Single-end simulation Total CPU time used: 0.061224 The random seed for the run: 777 Parameters Settings number of flow cycles: 100 fold of read coverage: 10X 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence File: ./single_454_t1.fq ALN Alignment File: ./single_454_t1.aln SAM Alignment File: ./single_454_t1.sam Read Coverage File: ./single_454_t1.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Single-end simulation Total CPU time used: 0.061668 The random seed for the run: 777 Parameters Settings number of flow cycles: 100 fold of read coverage: 10X 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence File: ./single_454_t2.fq ALN Alignment File: ./single_454_t2.aln SAM Alignment File: ./single_454_t2.sam Read Coverage File: ./single_454_t2.stat compare difference of two simulation datasets after normalising known difference ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Single-end simulation Total CPU time used: 0.096183 The random seed for the run: 1638898422 Parameters Settings fold of read coverage: 10X read length: 25 SOLiD Error Profile for Simulation the built-in 35bp error profile Output Files FASTQ Sequence File: ./single_dat.fq MAP Alignment File: ./single_dat.map SAM Alignment File: ./single_dat.sam convert a map file to a UCSC BED file ../map2bed.pl single_dat.bed single_dat.map ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Single-end simulation Total CPU time used: 0.120837 The random seed for the run: 1638898422 Parameters Settings fold of read coverage: 20X read length: 75 SOLiD Error Profile for Simulation the profile provided: ../SOLiD_profiles/profile_pseudo Output Files FASTQ Sequence File: ./dat_userProfile.fq MAP Alignment File: ./dat_userProfile.map SAM Alignment File: ./dat_userProfile.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Mate-Pair (F3-R3) simulation Total CPU time used: 0.159392 The random seed for the run: 1638898422 Parameters Settings fold of read coverage: 20X F3 read length: 35 R3 read length: 35 fragment length mean: 2000 std: 50 SOLiD Error Profile for Simulation the built-in 35bp error profile Output Files FASTQ Sequence Files: the 1st reads: ./matepair_dat_R3.fq the 2nd reads: ./matepair_dat_F3.fq MAP Alignment Files: the 1st reads: ./matepair_dat_R3.map the 2nd reads: ./matepair_dat_F3.map SAM Alignment File: ./matepair_dat.sam convert two map files to a UCSC BED file ../map2bed.pl maptepair.bed matepair_dat1.map matepair_dat2.map ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Mate-Pair (F3-R3) simulation Total CPU time used: 0.070724 The random seed for the run: 777 Parameters Settings fold of read coverage: 10X F3 read length: 50 R3 read length: 50 fragment length mean: 1500 std: 50 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./matepair_fs1_R3.fq the 2nd reads: ./matepair_fs1_F3.fq MAP Alignment Files: the 1st reads: ./matepair_fs1_R3.map the 2nd reads: ./matepair_fs1_F3.map SAM Alignment File: ./matepair_fs1.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Mate-Pair (F3-R3) simulation Total CPU time used: 0.070629 The random seed for the run: 777 Parameters Settings fold of read coverage: 10X F3 read length: 50 R3 read length: 50 fragment length mean: 1500 std: 50 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./matepair_fs2_R3.fq the 2nd reads: ./matepair_fs2_F3.fq MAP Alignment Files: the 1st reads: ./matepair_fs2_R3.map the 2nd reads: ./matepair_fs2_F3.map SAM Alignment File: ./matepair_fs2.sam compare two simulation datasets 4c4 < @PG ID:03 PN:ART_SOLiD CL:../art_SOLiD -r 777 -s testSeq.fa ./matepair_fs1 50 10 1500 50 --- > @PG ID:03 PN:ART_SOLiD CL:../art_SOLiD -r 777 -s testSeq.fa ./matepair_fs2 50 10 1500 50 ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Paired-end (F3-F5) simulation Total CPU time used: 0.253641 The random seed for the run: 1638898422 Parameters Settings fold of read coverage: 50X F3 read length: 75 F5 read length: 35 fragment length mean: 250 std: 10 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./paired_dat_F5.fq the 2nd reads: ./paired_dat_F3.fq MAP Alignment Files: the 1st reads: ./paired_dat_F5.map the 2nd reads: ./paired_dat_F3.map SAM Alignment File: ./paired_dat.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Amplicon single-end sequencing simulation Total CPU time used: 242.956 The random seed for the run: 1638898422 Parameters Settings # reads per amplion: 100 read length: 25 SOLiD Error Profile for Simulation the built-in 35bp error profile Output Files FASTQ Sequence File: ./amp_single.fq MAP Alignment File: ./amp_single.map SAM Alignment File: ./amp_single.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Amplicon matepair sequencing simulation Total CPU time used: 141.726 The random seed for the run: 1638898665 Parameters Settings # read pairs per amplion: 80 F3 read length: 50 R3 read length: 50 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./amp_matepair_R3.fq the 2nd reads: ./amp_matepair_F3.fq MAP Alignment Files: the 1st reads: ./amp_matepair_R3.map the 2nd reads: ./amp_matepair_F3.map SAM Alignment File: ./amp_matepair.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Amplicon paired-end sequencing simulation Total CPU time used: 107.33 The random seed for the run: 1638898807 Parameters Settings # read pairs per amplion: 50 F3 read length: 35 F5 read length: 25 SOLiD Error Profile for Simulation the built-in 35bp error profile Output Files FASTQ Sequence Files: the 1st reads: ./amp_paired_F5.fq the 2nd reads: ./amp_paired_F3.fq MAP Alignment Files: the 1st reads: ./amp_paired_F5.map the 2nd reads: ./amp_paired_F3.map SAM Alignment File: ./amp_paired.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Single-end Simulation Total CPU time used: 0.062998 The random seed for the run: 1638898915 Parameters used during run Read Length: 35 Genome masking 'N' cutoff frequency: 1 in 35 Fold Coverage: 10X Profile Type: Combined ID Tag: Quality Profile(s) First Read: Genome Analyzer I Length 36 R1 (built-in profile) Output files FASTQ Sequence File: ./single_end_com.fq ALN Alignment File: ./single_end_com.aln SAM Alignment File: ./single_end_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Single-end Simulation Total CPU time used: 0.043206 The random seed for the run: 1638898915 Parameters used during run Read Length: 50 Genome masking 'N' cutoff frequency: 1 in 50 Fold Coverage: 10X Profile Type: Separated ID Tag: Quality Profile(s) First Read: MiniSeq TruSeq Length 51 R1 (built-in profile) Output files FASTQ Sequence File: ./single_end_sep.fq ALN Alignment File: ./single_end_sep.aln SAM Alignment File: ./single_end_sep.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.025936 The random seed for the run: 1638898915 Parameters used during run Read Length: 150 Genome masking 'N' cutoff frequency: 1 in 150 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeq 2500 Length 150 R1 (built-in profile) First Read: HiSeq 2500 Length 150 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_com1.fq the 2nd reads: ./paired_end_com2.fq ALN Alignment Files: the 1st reads: ./paired_end_com1.aln the 2nd reads: ./paired_end_com2.aln SAM Alignment File: ./paired_end_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.04302 The random seed for the run: 1638898915 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Separated ID Tag: Quality Profile(s) First Read: HiSeq 2000 Length 100 R1 (built-in profile) First Read: HiSeq 2000 Length 100 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_sep1.fq the 2nd reads: ./paired_end_sep2.fq ALN Alignment Files: the 1st reads: ./paired_end_sep1.aln the 2nd reads: ./paired_end_sep2.aln SAM Alignment File: ./paired_end_sep.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Matepair-end sequencing simulation Total CPU time used: 0.030515 The random seed for the run: 1638898915 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 2500 Standard Deviation: 50 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeq 2500 Length 126 R1 (built-in profile) First Read: HiSeq 2500 Length 126 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./matepair_com1.fq the 2nd reads: ./matepair_com2.fq ALN Alignment Files: the 1st reads: ./matepair_com1.aln the 2nd reads: ./matepair_com2.aln SAM Alignment File: ./matepair_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon 5'-end sequencing simulation Total CPU time used: 0.318507 The random seed for the run: 1638898915 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 # Reads per Amplion: 2 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeqX v2.5 TruSeq Length 151 R1 (built-in profile) Output files FASTQ Sequence File: ./amp_5_end_com.fq ALN Alignment File: ./amp_5_end_com.aln SAM Alignment File: ./amp_5_end_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon paired-end sequencing simulation Total CPU time used: 0.362674 The random seed for the run: 1638898916 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 # Read Pairs per Amplion: 1 Profile Type: Combined ID Tag: Quality Profile(s) First Read: MiSeq v1 Length 250 R1 (built-in profile) First Read: MiSeq v1 Length 250 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./amp_pair1.fq the 2nd reads: ./amp_pair2.fq ALN Alignment Files: the 1st reads: ./amp_pair1.aln the 2nd reads: ./amp_pair2.aln SAM Alignment File: ./amp_pair.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon matepair sequencing simulation Total CPU time used: 0.544553 The random seed for the run: 1638898916 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 # Read Pairs per Amplion: 1 Profile Type: Combined ID Tag: Quality Profile(s) First Read: MiSeq v3 Length 251 R1 (built-in profile) First Read: MiSeq v3 Length 251 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./amp_matepair1.fq the 2nd reads: ./amp_matepair2.fq ALN Alignment Files: the 1st reads: ./amp_matepair1.aln the 2nd reads: ./amp_matepair2.aln SAM Alignment File: ./amp_matepair.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.030337 The random seed for the run: 777 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeqX v2.5 PCR free Length 151 R1 (built-in profile) First Read: HiSeqX v2.5 PCR free Length 151 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_com_f11.fq the 2nd reads: ./paired_end_com_f12.fq ALN Alignment Files: the 1st reads: ./paired_end_com_f11.aln the 2nd reads: ./paired_end_com_f12.aln SAM Alignment File: ./paired_end_com_f1.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.029787 The random seed for the run: 777 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeqX v2.5 PCR free Length 151 R1 (built-in profile) First Read: HiSeqX v2.5 PCR free Length 151 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_com_f21.fq the 2nd reads: ./paired_end_com_f22.fq ALN Alignment Files: the 1st reads: ./paired_end_com_f21.aln the 2nd reads: ./paired_end_com_f22.aln SAM Alignment File: ./paired_end_com_f2.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.033332 The random seed for the run: 1638898917 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 First quality shift: 10 Second quality shift: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeq 2000 Length 100 R1 (built-in profile) First Read: HiSeq 2000 Length 100 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_com_f11.fq the 2nd reads: ./paired_end_com_f12.fq ALN Alignment Files: the 1st reads: ./paired_end_com_f11.aln the 2nd reads: ./paired_end_com_f12.aln SAM Alignment File: ./paired_end_com_f1.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.034537 The random seed for the run: 1638898917 Parameters used during run Read Length: 75 'N' genomic regions masking turned off Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: NextSeq 500 v2 Length 76 R1 (built-in profile) First Read: NextSeq 500 v2 Length 76 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_nomask1.fq the 2nd reads: ./paired_nomask2.fq ALN Alignment Files: the 1st reads: ./paired_nomask1.aln the 2nd reads: ./paired_nomask2.aln SAM Alignment File: ./paired_nomask.sam rm -f *.aln *.fq *.bed *.map *.sam *.stat make[1]: Leaving directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a make -j4 install DESTDIR=/<>/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Entering directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/mkdir -p '/<>/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c art_illumina art_454 art_SOLiD '/<>/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c aln2bed.pl map2bed.pl ART_profiler_454/art_profiler_454 ART_profiler_illumina/combinedAvg.pl ART_profiler_illumina/fastqReadAvg.pl ART_profiler_illumina/art_profiler_illumina ART_profiler_illumina/empDist.pl ART_profiler_illumina/summation.pl '/<>/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' make[2]: Leaving directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_install-arch make[1]: Entering directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' dh_install -a # aln2bed.pl seems to be of general use - the other perl scripts are called by art_profiler_illumina # see patch for the latter regarding PATH to *.pl files mkdir -p debian/art-nextgen-simulation-tools/usr/lib/art-nextgen-simulation-tools for pl in debian/art-nextgen-simulation-tools/usr/bin/*.pl ; do \ if [ `basename ${pl}` = aln2bed.pl ] ; then \ mv ${pl} debian/art-nextgen-simulation-tools/usr/bin/`basename ${pl} .pl` ; \ else \ mv ${pl} debian/art-nextgen-simulation-tools/usr/lib/art-nextgen-simulation-tools ; \ fi ; \ done make[1]: Leaving directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' dh_installchangelogs ChangeLog make[1]: Leaving directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_installexamples-arch make[1]: Entering directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' dh_installexamples -a for ex in examples/run_test_examples_*.sh ; do \ sed -e 's?=\.\./?=/usr/bin/?' \ -e 's?^\.\./?/usr/bin/?' \ -e 's/aln2bed\.pl/aln2bed/' \ $ex > debian/art-nextgen-simulation-tools/usr/share/doc/art-nextgen-simulation-tools/examples/`basename $ex` ; \ done make[1]: Leaving directory '/<>/art-nextgen-simulation-tools-20160605+dfsg' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/art-nextgen-simulation-tools/usr/bin/art_454: Unknown DWARF DW_FORM_0x1f20 da60de76e27e98809b4dfe23c2ac195ba7307779 debugedit: debian/art-nextgen-simulation-tools/usr/bin/art_illumina: Unknown DWARF DW_FORM_0x1f20 55d618413c57e75a40a5d1cccbbccd0e7e25dc92 debugedit: debian/art-nextgen-simulation-tools/usr/bin/art_SOLiD: Unknown DWARF DW_FORM_0x1f21 7d0c8d68d91c2d08782631995d7a94cb242c00fe dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing art-nextgen-simulation-tools (in debian/art-nextgen-simulation-tools); do_strip: , oemstrip: pkgstriptranslations: processing art-nextgen-simulation-tools-dbgsym (in debian/.debhelper/art-nextgen-simulation-tools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/art-nextgen-simulation-tools/DEBIAN/control, package art-nextgen-simulation-tools, directory debian/art-nextgen-simulation-tools .. removing usr/share/doc/art-nextgen-simulation-tools/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package art-nextgen-simulation-tools ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/.debhelper/art-nextgen-simulation-tools/dbgsym-root/DEBIAN/control, package art-nextgen-simulation-tools-dbgsym, directory debian/.debhelper/art-nextgen-simulation-tools/dbgsym-root dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-4build2_s390x.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in 'debian/.debhelper/scratch-space/build-art-nextgen-simulation-tools/art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_s390x.deb'. Renaming art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_s390x.deb to art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_s390x.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../art-nextgen-simulation-tools_20160605+dfsg-4build2_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-12-07T17:42:08Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ art-nextgen-simulation-tools_20160605+dfsg-4build2_s390x.changes: ----------------------------------------------------------------- Format: 1.8 Date: Tue, 07 Dec 2021 17:23:03 +0000 Source: art-nextgen-simulation-tools Binary: art-nextgen-simulation-tools Built-For-Profiles: noudeb Architecture: s390x Version: 20160605+dfsg-4build2 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: art-nextgen-simulation-tools - simulation tools to generate synthetic next-generation sequencing Changes: art-nextgen-simulation-tools (20160605+dfsg-4build2) jammy; urgency=medium . * No-change rebuild against libgsl27 Checksums-Sha1: 682699c335245f2472c22047f12662a0adc86eeb 1138110 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_s390x.ddeb 2df8ca871da065a062e1d4fc28cc43ec0f8dd08f 5992 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Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: art-nextgen-simulation-tools Binary: art-nextgen-simulation-tools art-nextgen-simulation-tools-dbgsym Architecture: s390x Version: 20160605+dfsg-4build2 Checksums-Md5: 1f02e9e18561961ec65b0a87db60c850 1138110 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_s390x.ddeb 13432733025fa42e70b136fb3af5d1d3 1754746 art-nextgen-simulation-tools_20160605+dfsg-4build2_s390x.deb Checksums-Sha1: 682699c335245f2472c22047f12662a0adc86eeb 1138110 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_s390x.ddeb d9c4b680b5eb9bf5bcc7eb093102567c964147af 1754746 art-nextgen-simulation-tools_20160605+dfsg-4build2_s390x.deb Checksums-Sha256: e7d448953fc961aeaa11659f70b2119a801fea073605d224849d7b1cc58c19a8 1138110 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_s390x.ddeb 38765e0d2683665936cdf829c87ee9abab66424e5feeabf1fac6d556df471465 1754746 art-nextgen-simulation-tools_20160605+dfsg-4build2_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Tue, 07 Dec 2021 17:42:07 +0000 Build-Path: /<>/art-nextgen-simulation-tools-20160605+dfsg Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.1), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20180224.1+nmu1), base-files (= 12ubuntu2), base-passwd (= 3.5.52), bash (= 5.1-5ubuntu1), binutils (= 2.37-10ubuntu1), binutils-common (= 2.37-10ubuntu1), binutils-s390x-linux-gnu (= 2.37-10ubuntu1), bsdextrautils (= 2.37.2-4ubuntu1), bsdutils (= 1:2.37.2-4ubuntu1), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-5), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-12ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 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LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1638897783" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ art-nextgen-simulation-tools_20160605+dfsg-4build2_s390x.deb ------------------------------------------------------------ new Debian package, version 2.0. size 1754746 bytes: control archive=2081 bytes. 1810 bytes, 30 lines control 2723 bytes, 33 lines md5sums Package: art-nextgen-simulation-tools Version: 20160605+dfsg-4build2 Architecture: s390x Maintainer: Ubuntu Developers Installed-Size: 8980 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libgsl27 (>= 2.7.1), libstdc++6 (>= 9) Suggests: art-nextgen-simulation-tools-profiles Section: science Priority: optional Homepage: https://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Description: simulation tools to generate synthetic next-generation sequencing reads ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. VarSim) for evaluating variant calling tools or methods. 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./usr/share/doc/art-nextgen-simulation-tools/art_454_README.gz -rw-r--r-- root/root 3431 2016-06-06 02:33 ./usr/share/doc/art-nextgen-simulation-tools/art_SOLiD_README.gz -rw-r--r-- root/root 5458 2016-06-06 02:33 ./usr/share/doc/art-nextgen-simulation-tools/art_illumina_README.gz -rw-r--r-- root/root 711 2021-12-07 17:23 ./usr/share/doc/art-nextgen-simulation-tools/changelog.Debian.gz -rw-r--r-- root/root 1951 2020-02-23 05:21 ./usr/share/doc/art-nextgen-simulation-tools/copyright drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/doc/art-nextgen-simulation-tools/examples/ -rw-r--r-- root/root 3497445 2016-04-17 16:54 ./usr/share/doc/art-nextgen-simulation-tools/examples/amplicon_reference.fa -rw-r--r-- root/root 1790 2021-12-07 17:23 ./usr/share/doc/art-nextgen-simulation-tools/examples/run_test_examples_454.sh -rw-r--r-- root/root 1749 2021-12-07 17:23 ./usr/share/doc/art-nextgen-simulation-tools/examples/run_test_examples_SOLiD.sh -rw-r--r-- root/root 3289 2021-12-07 17:23 ./usr/share/doc/art-nextgen-simulation-tools/examples/run_test_examples_illumina.sh -rw-r--r-- root/root 10482 2016-04-17 16:54 ./usr/share/doc/art-nextgen-simulation-tools/examples/testSeq.fa -rw-r--r-- root/root 409 2020-02-23 05:21 ./usr/share/doc/art-nextgen-simulation-tools/run-unit-test drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/man/ drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/man/man1/ -rw-r--r-- root/root 312 2021-12-07 17:23 ./usr/share/man/man1/aln2bed.1.gz -rw-r--r-- root/root 1451 2021-12-07 17:23 ./usr/share/man/man1/art_454.1.gz -rw-r--r-- root/root 1459 2021-12-07 17:23 ./usr/share/man/man1/art_SOLiD.1.gz -rw-r--r-- root/root 2319 2021-12-07 17:23 ./usr/share/man/man1/art_illumina.1.gz -rw-r--r-- root/root 500 2021-12-07 17:23 ./usr/share/man/man1/art_profiler_454.1.gz -rw-r--r-- root/root 673 2021-12-07 17:23 ./usr/share/man/man1/art_profiler_illumina.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: n/a Build-Time: 544 Distribution: jammy-proposed Host Architecture: s390x Install-Time: 14 Job: art-nextgen-simulation-tools_20160605+dfsg-4build2.dsc Machine Architecture: s390x Package: art-nextgen-simulation-tools Package-Time: 560 Source-Version: 20160605+dfsg-4build2 Space: n/a Status: successful Version: 20160605+dfsg-4build2 -------------------------------------------------------------------------------- Finished at 2021-12-07T17:42:08Z Build needed 00:09:20, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22599300 Scanning for processes to kill in build PACKAGEBUILD-22599300