https://launchpad.net/ubuntu/+source/art-nextgen-simulation-tools/20160605+dfsg-4build2/+build/22599295 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-019 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 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 17:25:36 ntpdate[1707]: adjust time server 10.211.37.1 offset 0.000418 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22599295 --image-type chroot /home/buildd/filecache-default/b0c128df17a460089eca69348f06144377489985 Creating target for build PACKAGEBUILD-22599295 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22599295 Starting target for build PACKAGEBUILD-22599295 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22599295 '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-22599295 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22599295 Updating target for build PACKAGEBUILD-22599295 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 amd64 Packages [1399 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe amd64 Packages [13.3 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5567 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 Packages [150 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [51.2 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 Packages [653 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [312 kB] Fetched 22.5 MB in 3s (7390 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-x86-64-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 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 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 106 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 84.2 MB of archives. After this operation, 354 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main amd64 debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam0g amd64 1.4.0-10ubuntu2 [61.5 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main amd64 libcrypt-dev amd64 1:4.4.26-1 [112 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main amd64 libcrypt1 amd64 1:4.4.26-1 [82.1 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 base-files amd64 12ubuntu2 [63.3 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main amd64 debianutils amd64 5.5-1ubuntu1 [107 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 bash amd64 5.1-5ubuntu1 [771 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdutils amd64 1:2.37.2-4ubuntu1 [80.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main amd64 libgpg-error0 amd64 1.42-3 [68.1 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcrypt20 amd64 1.9.4-3ubuntu2 [515 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 bzip2 amd64 1.0.8-5 [34.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libbz2-1.0 amd64 1.0.8-5 [34.5 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main amd64 libcc1-0 amd64 11.2.0-12ubuntu1 [53.8 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main amd64 gcc-11-base amd64 11.2.0-12ubuntu1 [20.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcc-s1 amd64 11.2.0-12ubuntu1 [45.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main amd64 libgomp1 amd64 11.2.0-12ubuntu1 [117 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main amd64 libitm1 amd64 11.2.0-12ubuntu1 [30.0 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main amd64 libatomic1 amd64 11.2.0-12ubuntu1 [9998 B] Get:19 http://ftpmaster.internal/ubuntu jammy/main amd64 libasan6 amd64 11.2.0-12ubuntu1 [2282 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main amd64 liblsan0 amd64 11.2.0-12ubuntu1 [976 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main amd64 libtsan0 amd64 11.2.0-12ubuntu1 [2259 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main amd64 libubsan1 amd64 11.2.0-12ubuntu1 [922 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main amd64 libquadmath0 amd64 11.2.0-12ubuntu1 [154 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main amd64 g++-11 amd64 11.2.0-12ubuntu1 [11.4 MB] Get:25 http://ftpmaster.internal/ubuntu jammy/main amd64 libstdc++-11-dev amd64 11.2.0-12ubuntu1 [2098 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcc-11-dev amd64 11.2.0-12ubuntu1 [2532 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main amd64 gcc-11 amd64 11.2.0-12ubuntu1 [20.1 MB] Get:28 http://ftpmaster.internal/ubuntu jammy/main amd64 cpp-11 amd64 11.2.0-12ubuntu1 [9962 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main amd64 libstdc++6 amd64 11.2.0-12ubuntu1 [656 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main amd64 libisl23 amd64 0.24-2 [728 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main amd64 libmpc3 amd64 1.2.1-1 [46.9 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main amd64 libzstd1 amd64 1.4.8+dfsg-3 [324 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main amd64 libctf0 amd64 2.37-10ubuntu1 [103 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main amd64 libctf-nobfd0 amd64 2.37-10ubuntu1 [106 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main amd64 libbinutils amd64 2.37-10ubuntu1 [653 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils-common amd64 2.37-10ubuntu1 [213 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils amd64 2.37-10ubuntu1 [3192 B] Get:38 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils-x86-64-linux-gnu amd64 2.37-10ubuntu1 [2314 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main amd64 libssl3 amd64 3.0.0-1ubuntu1 [1896 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main amd64 libblkid1 amd64 2.37.2-4ubuntu1 [103 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main amd64 libuuid1 amd64 2.37.2-4ubuntu1 [23.8 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcryptsetup12 amd64 2:2.4.2-1ubuntu3 [208 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main amd64 libidn2-0 amd64 2.3.2-2 [66.5 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main amd64 libp11-kit0 amd64 0.24.0-6 [252 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main amd64 libtasn1-6 amd64 4.18.0-4 [42.9 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main amd64 libgnutls30 amd64 3.7.2-2ubuntu1 [957 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd-timesyncd amd64 249.5-2ubuntu1 [31.0 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd-sysv amd64 249.5-2ubuntu1 [10.5 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main amd64 libapparmor1 amd64 3.0.3-0ubuntu4 [37.9 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main amd64 libip4tc2 amd64 1.8.7-1ubuntu4 [19.8 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main amd64 libkmod2 amd64 28-1ubuntu5 [48.0 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main amd64 libpcre2-8-0 amd64 10.39-3 [220 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libselinux1 amd64 3.3-1build1 [74.5 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main amd64 libmount1 amd64 2.37.2-4ubuntu1 [122 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main amd64 libseccomp2 amd64 2.5.2-2ubuntu2 [48.3 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main amd64 login amd64 1:4.8.1-2ubuntu1 [188 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main amd64 util-linux amd64 2.37.2-4ubuntu1 [1063 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main amd64 mount amd64 2.37.2-4ubuntu1 [114 kB] Get:59 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd amd64 249.5-2ubuntu1 [4542 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsystemd0 amd64 249.5-2ubuntu1 [319 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libudev1 amd64 249.5-2ubuntu1 [78.0 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main amd64 libapt-pkg6.0 amd64 2.3.13 [904 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main amd64 dpkg amd64 1.20.9ubuntu3 [1266 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-3 [91.8 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main amd64 grep amd64 3.7-1 [156 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main amd64 libncurses6 amd64 6.3-1 [111 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main amd64 libncursesw6 amd64 6.3-1 [147 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main amd64 libtinfo6 amd64 6.3-1 [104 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-bin amd64 6.3-1 [184 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 sed amd64 4.8-1 [188 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-base all 6.3-1 [19.9 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgv amd64 2.2.27-2ubuntu1 [137 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main amd64 apt amd64 2.3.13 [1387 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main amd64 libsepol2 amd64 3.3-1 [281 kB] Get:75 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsemanage-common all 3.3-1build1 [10.0 kB] Get:76 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsemanage2 amd64 3.3-1build1 [92.4 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main amd64 passwd amd64 1:4.8.1-2ubuntu1 [765 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam-modules-bin amd64 1.4.0-10ubuntu2 [37.6 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam-modules amd64 1.4.0-10ubuntu2 [280 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main amd64 logsave amd64 1.46.4-1ubuntu1 [10.9 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main amd64 libext2fs2 amd64 1.46.4-1ubuntu1 [209 kB] Get:82 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amd64 1.46.4-1ubuntu1 [12.3 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main amd64 sensible-utils all 0.0.17 [20.1 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main amd64 usrmerge all 25ubuntu2 [54.7 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main amd64 openssl amd64 3.0.0-1ubuntu1 [1180 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/main amd64 ca-certificates all 20211016 [148 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main amd64 libsqlite3-0 amd64 3.36.0-2 [641 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main amd64 tzdata all 2021e-1ubuntu1 [343 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main amd64 libgdbm6 amd64 1.22-1 [35.2 kB] Get:99 http://ftpmaster.internal/ubuntu jammy/main amd64 dpkg-dev all 1.20.9ubuntu3 [933 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main amd64 libdpkg-perl all 1.20.9ubuntu3 [235 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/main amd64 make amd64 4.3-4ubuntu2 [179 kB] Get:102 http://ftpmaster.internal/ubuntu jammy/main amd64 lto-disabled-list all 17 [12.1 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg amd64 2.2.27-2ubuntu1 [518 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgconf amd64 2.2.27-2ubuntu1 [93.9 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg-agent amd64 2.2.27-2ubuntu1 [209 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main amd64 libgdbm-compat4 amd64 1.22-1 [6450 B] Get:107 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 linux-libc-dev amd64 5.15.0-13.13 [1273 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main amd64 lockfile-progs amd64 0.1.19 [10.0 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/main amd64 pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.2 MB in 3s (31.1 MB/s) (Reading database ... 13258 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 ... 13257 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-10ubuntu2_amd64.deb ... Unpacking libpam0g:amd64 (1.4.0-10ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam0g:amd64 (1.4.0-10ubuntu2) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 13257 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.26-1_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.26-1) over (1:4.4.18-4ubuntu2) ... Preparing to unpack .../libcrypt1_1%3a4.4.26-1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.26-1) over (1:4.4.18-4ubuntu2) ... Setting up libcrypt1:amd64 (1:4.4.26-1) ... (Reading database ... 13257 files and directories currently installed.) Preparing to unpack .../base-files_12ubuntu2_amd64.deb ... 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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 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:amd64 (1.22-1) ... Setting up libgcc-11-dev:amd64 (11.2.0-12ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.37-10ubuntu1) ... Setting up systemd-sysv (249.5-2ubuntu1) ... Setting up binutils (2.37-10ubuntu1) ... Setting up dpkg-dev (1.20.9ubuntu3) ... Setting up libstdc++-11-dev:amd64 (11.2.0-12ubuntu1) ... Setting up gcc-11 (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-22599295 amd64 jammy-proposed -c chroot:build-PACKAGEBUILD-22599295 --arch=amd64 --dist=jammy-proposed --nolog -A art-nextgen-simulation-tools_20160605+dfsg-4build2.dsc Initiating build PACKAGEBUILD-22599295 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lgw01-amd64-019.buildd +============================================================================================+ | art-nextgen-simulation-tools 20160605+dfsg-4build2 (amd64) Tue, 07 Dec 2021 17:26:14 +0000 | +============================================================================================+ Package: art-nextgen-simulation-tools Version: 20160605+dfsg-4build2 Source Version: 20160605+dfsg-4build2 Distribution: jammy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22599295/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-6iK6Li/art-nextgen-simulation-tools-20160605+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/art-nextgen-simulation-tools-6iK6Li' 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-3fPJmh/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-3fPJmh/apt_archive ./ InRelease Get:2 copy:/<>/resolver-3fPJmh/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-3fPJmh/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-3fPJmh/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-3fPJmh/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (149 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-3fPJmh/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 ... 13453 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.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 (amd64 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-3fPJmh/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-3fPJmh/apt_archive ./ InRelease Get:2 copy:/<>/resolver-3fPJmh/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-3fPJmh/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-3fPJmh/apt_archive ./ Sources [515 B] Get:5 copy:/<>/resolver-3fPJmh/apt_archive ./ Packages [593 B] Fetched 2071 B in 0s (190 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 20.3 MB of archives. After this operation, 74.9 MB of additional disk space will be used. Get:1 copy:/<>/resolver-3fPJmh/apt_archive ./ sbuild-build-depends-art-nextgen-simulation-tools-dummy 0.invalid.0 [682 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdextrautils amd64 2.37.2-4ubuntu1 [71.1 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main amd64 libuchardet0 amd64 0.0.7-1build1 [76.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main amd64 groff-base amd64 1.22.4-7 [956 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 libpipeline1 amd64 1.5.4-1 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main amd64 man-db amd64 2.9.4-2build1 [1180 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 libelf1 amd64 0.186-1 [51.4 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 libicu67 amd64 67.1-7ubuntu1 [10.1 MB] Get:9 http://ftpmaster.internal/ubuntu jammy/main amd64 libxml2 amd64 2.9.12+dfsg-5 [761 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main amd64 libmagic-mgc amd64 1:5.41-2 [257 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main amd64 libmagic1 amd64 1:5.41-2 [87.3 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main amd64 file amd64 1:5.41-2 [21.5 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main amd64 gettext-base amd64 0.21-4ubuntu3 [36.6 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main amd64 libsigsegv2 amd64 2.13-1ubuntu2 [14.6 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main amd64 m4 amd64 1.4.18-5ubuntu1 [199 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main amd64 autoconf all 2.71-2 [338 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main amd64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main amd64 automake all 1:1.16.5-1.1 [558 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main amd64 autopoint all 0.21-4ubuntu3 [422 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main amd64 libdebhelper-perl all 13.5.2ubuntu1 [66.0 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main amd64 libtool all 2.4.6-15build1 [164 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:25 http://ftpmaster.internal/ubuntu jammy/main amd64 libfile-stripnondeterminism-perl all 1.12.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-strip-nondeterminism all 1.12.1-1 [5200 B] Get:27 http://ftpmaster.internal/ubuntu jammy/main amd64 libdw1 amd64 0.186-1 [251 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main amd64 debugedit amd64 1:5.0-3 [47.0 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main amd64 dwz amd64 0.14-1build1 [104 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main amd64 gettext amd64 0.21-4ubuntu3 [824 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main amd64 debhelper all 13.5.2ubuntu1 [926 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libgslcblas0 amd64 2.7.1+dfsg-3 [94.4 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libgsl27 amd64 2.7.1+dfsg-3 [1000 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libgsl-dev amd64 2.7.1+dfsg-3 [1257 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.3 MB in 1s (17.7 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 13453 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-4ubuntu1_amd64.deb ... Unpacking bsdextrautils (2.37.2-4ubuntu1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1build1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_amd64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.4-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.4-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2build1_amd64.deb ... Unpacking man-db (2.9.4-2build1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../05-libelf1_0.186-1_amd64.deb ... Unpacking libelf1:amd64 (0.186-1) ... 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Setting up sbuild-build-depends-art-nextgen-simulation-tools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-163-generic amd64 (x86_64) 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-x86-64-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 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zlib1g_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | 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-22599295 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22599295 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22599295 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 amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf 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 ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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 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: 0.05495 The random seed for the run: 1638898003 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: 0.041166 The random seed for the run: 1638898003 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: 0.048518 The random seed for the run: 1638898003 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: 9.0459 The random seed for the run: 1638898003 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: 6.95392 The random seed for the run: 1638898012 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: 0.055492 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: 0.054521 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: 0.085488 The random seed for the run: 1638898019 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: 0.11127 The random seed for the run: 1638898019 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: 0.140253 The random seed for the run: 1638898019 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: 0.072259 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: 0.064457 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: 0.225998 The random seed for the run: 1638898020 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: 213.53 The random seed for the run: 1638898020 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: 210.633 The random seed for the run: 1638898234 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: 104.543 The random seed for the run: 1638898444 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: 0.05606 The random seed for the run: 1638898549 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: 0.04551 The random seed for the run: 1638898549 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: 0.026887 The random seed for the run: 1638898549 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: 0.046904 The random seed for the run: 1638898549 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: 0.031958 The random seed for the run: 1638898549 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: 0.315568 The random seed for the run: 1638898549 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: 0.354211 The random seed for the run: 1638898550 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: 0.518116 The random seed for the run: 1638898550 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: 0.032342 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: 0.031187 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: 0.033919 The random seed for the run: 1638898551 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: 0.036841 The random seed for the run: 1638898551 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 dh_auto_install 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_install -Nart-nextgen-simulation-tools dh_installdocs 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_installexamples -Nart-nextgen-simulation-tools dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip debugedit: debian/art-nextgen-simulation-tools/usr/bin/art_SOLiD: Unknown DWARF DW_FORM_0x1f21 3ee33fccde1e930995669056665ee589f792916b debugedit: debian/art-nextgen-simulation-tools/usr/bin/art_illumina: Unknown DWARF DW_FORM_0x1f20 8b52490806346182a7885dfb3bf0fe9b66e16839 debugedit: debian/art-nextgen-simulation-tools/usr/bin/art_454: Unknown DWARF DW_FORM_0x1f21 2be5d861d6216ab7f7b9a096a2bf65b1601441b7 dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package art-nextgen-simulation-tools-profiles: substitution variable ${perl:Depends} unused, but is defined 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 dh_builddeb INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing art-nextgen-simulation-tools-dbgsym (in debian/.debhelper/art-nextgen-simulation-tools/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing art-nextgen-simulation-tools-profiles (in debian/art-nextgen-simulation-tools-profiles); do_strip: , oemstrip: pkgstriptranslations: processing art-nextgen-simulation-tools (in debian/art-nextgen-simulation-tools); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com 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-dbgsym' in 'debian/.debhelper/scratch-space/build-art-nextgen-simulation-tools/art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_amd64.deb'. pkgstripfiles: processing control file: debian/art-nextgen-simulation-tools-profiles/DEBIAN/control, package art-nextgen-simulation-tools-profiles, directory debian/art-nextgen-simulation-tools-profiles .. removing usr/share/doc/art-nextgen-simulation-tools-profiles/changelog.gz INFO: pkgstripfiles: waiting for lock (art-nextgen-simulation-tools-profiles) ... 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. dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.deb'. Renaming art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_amd64.deb to art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_amd64.ddeb pkgstripfiles: Running PNG optimization (using 4 cpus) for package art-nextgen-simulation-tools-profiles ... pkgstripfiles: No PNG files. dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-4build2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-12-07T17:36:07Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.changes: ----------------------------------------------------------------- Format: 1.8 Date: Tue, 07 Dec 2021 17:23:03 +0000 Source: art-nextgen-simulation-tools Binary: art-nextgen-simulation-tools art-nextgen-simulation-tools-profiles Built-For-Profiles: noudeb Architecture: amd64 all 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 art-nextgen-simulation-tools-profiles - profiles for art simulation tools Changes: art-nextgen-simulation-tools (20160605+dfsg-4build2) jammy; urgency=medium . * No-change rebuild against libgsl27 Checksums-Sha1: 393abd5b3487e5459678d3e8ea5758b7a57ddebd 1161184 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_amd64.ddeb 773e8b82f415135ee2f46880746903946b3a6c1b 1924596 art-nextgen-simulation-tools-profiles_20160605+dfsg-4build2_all.deb 41ba5d1c2cc53a744a4582cc83f4456c548f257e 6505 art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.buildinfo 338ae65228556c0ed21fd0a5d6e64634867f5cdd 1751024 art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.deb Checksums-Sha256: 007ab70cd6ca8d53e9e0ea38f9d13ebe60557c730b4f6bec12f415dadfbb1a93 1161184 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_amd64.ddeb 5673aedec4346856b5b5abfd057b1f6d8f656ded190ae697cbbf6d94aae8341c 1924596 art-nextgen-simulation-tools-profiles_20160605+dfsg-4build2_all.deb 2318290f40e3e98194ae48a3effc08c164e1d3f51c7fb377f6be6bb96a8583d3 6505 art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.buildinfo 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art-nextgen-simulation-tools-profiles Architecture: all amd64 Version: 20160605+dfsg-4build2 Checksums-Md5: 2206a7f1870491fbbd172cb4425fa63b 1161184 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_amd64.ddeb c95e77337664465f0c915227c03556bf 1924596 art-nextgen-simulation-tools-profiles_20160605+dfsg-4build2_all.deb 9a95b0999838805b87912d5dbafd35b2 1751024 art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.deb Checksums-Sha1: 393abd5b3487e5459678d3e8ea5758b7a57ddebd 1161184 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_amd64.ddeb 773e8b82f415135ee2f46880746903946b3a6c1b 1924596 art-nextgen-simulation-tools-profiles_20160605+dfsg-4build2_all.deb 338ae65228556c0ed21fd0a5d6e64634867f5cdd 1751024 art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.deb Checksums-Sha256: 007ab70cd6ca8d53e9e0ea38f9d13ebe60557c730b4f6bec12f415dadfbb1a93 1161184 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_amd64.ddeb 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https://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Description: profiles for art simulation tools 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. . This package contains profile data for art-nextgen-simulation-tools. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2021-12-07 17:23 ./ drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/ drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/ drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/art-nextgen-simulation-tools/ drwxr-xr-x root/root 0 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/454_profiles/ drwxr-xr-x root/root 0 2016-04-16 20:38 ./usr/share/art-nextgen-simulation-tools/454_profiles/GS_FLX_Titanium_profile/ -rw-r--r-- root/root 456 2016-04-16 20:38 ./usr/share/art-nextgen-simulation-tools/454_profiles/GS_FLX_Titanium_profile/indel_error_profile -rw-r--r-- root/root 6920 2016-04-16 20:38 ./usr/share/art-nextgen-simulation-tools/454_profiles/GS_FLX_Titanium_profile/length_dist -rw-r--r-- root/root 7970 2016-04-16 20:38 ./usr/share/art-nextgen-simulation-tools/454_profiles/GS_FLX_Titanium_profile/qual_1st_profile -rw-r--r-- root/root 603284 2016-04-16 20:38 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20:37 ./usr/share/art-nextgen-simulation-tools/Illumina_profiles/MiSeqv3L250R1.txt -rw-r--r-- root/root 376629 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/Illumina_profiles/MiSeqv3L250R2.txt -rw-r--r-- root/root 16458 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/Illumina_profiles/MiniSeqTruSeqL50.txt -rw-r--r-- root/root 27147 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/Illumina_profiles/NextSeq500v2L75R1.txt -rw-r--r-- root/root 27767 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/Illumina_profiles/NextSeq500v2L75R2.txt drwxr-xr-x root/root 0 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/SOLiD_profiles/ -rw-r--r-- root/root 291 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/SOLiD_profiles/getPsuedoProfile.pl -rw-r--r-- root/root 13275 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/SOLiD_profiles/profile_default -rw-r--r-- root/root 27339 2016-04-16 20:37 ./usr/share/art-nextgen-simulation-tools/SOLiD_profiles/profile_pseudo drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/doc/art-nextgen-simulation-tools-profiles/ -rw-r--r-- root/root 711 2021-12-07 17:23 ./usr/share/doc/art-nextgen-simulation-tools-profiles/changelog.Debian.gz -rw-r--r-- root/root 1951 2020-02-23 05:21 ./usr/share/doc/art-nextgen-simulation-tools-profiles/copyright drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/lintian/ drwxr-xr-x root/root 0 2021-12-07 17:23 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 129 2020-02-23 05:21 ./usr/share/lintian/overrides/art-nextgen-simulation-tools-profiles art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64.deb ------------------------------------------------------------ new Debian package, version 2.0. size 1751024 bytes: control archive=2075 bytes. 1810 bytes, 30 lines control 2723 bytes, 33 lines md5sums Package: art-nextgen-simulation-tools Version: 20160605+dfsg-4build2 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 9004 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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+------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 584 Distribution: jammy-proposed Host Architecture: amd64 Install-Time: 8 Job: art-nextgen-simulation-tools_20160605+dfsg-4build2.dsc Machine Architecture: amd64 Package: art-nextgen-simulation-tools Package-Time: 593 Source-Version: 20160605+dfsg-4build2 Space: n/a Status: successful Version: 20160605+dfsg-4build2 -------------------------------------------------------------------------------- Finished at 2021-12-07T17:36:07Z Build needed 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