https://launchpad.net/ubuntu/+source/art-nextgen-simulation-tools/20160605+dfsg-4build2/+build/22599297 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-023 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:52 UTC 2021 aarch64 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 17:34:53 ntpdate[1657]: adjust time server 10.211.37.1 offset 0.217539 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599297 --image-type chroot /home/buildd/filecache-default/c698bf6badd89264039f6cdfcd7c983f87611a3e Creating target for build PACKAGEBUILD-22599297 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599297 Starting target for build PACKAGEBUILD-22599297 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599297 '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-22599297 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599297 Updating target for build PACKAGEBUILD-22599297 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 armhf Packages [1351 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe armhf Packages [12.8 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5567 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf Packages [141 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [51.2 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf Packages [585 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [312 kB] Fetched 21.9 MB in 8s (2866 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-arm-linux-gnueabihf binutils-common 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 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 sensible-utils systemd systemd-sysv systemd-timesyncd tzdata usrmerge util-linux 101 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 69.3 MB of archives. After this operation, 337 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main armhf debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf libpam0g armhf 1.4.0-10ubuntu2 [56.0 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt-dev armhf 1:4.4.26-1 [122 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt1 armhf 1:4.4.26-1 [94.1 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf base-files armhf 12ubuntu2 [63.0 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf debianutils armhf 5.5-1ubuntu1 [106 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf bash armhf 5.1-5ubuntu1 [655 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf bsdutils armhf 1:2.37.2-4ubuntu1 [86.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf libgpg-error0 armhf 1.42-3 [60.1 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main armhf libgcrypt20 armhf 1.9.4-3ubuntu2 [438 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf bzip2 armhf 1.0.8-5 [34.2 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libbz2-1.0 armhf 1.0.8-5 [31.7 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf libcc1-0 armhf 11.2.0-12ubuntu1 [45.8 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11-base armhf 11.2.0-12ubuntu1 [20.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf libgcc-s1 armhf 11.2.0-12ubuntu1 [42.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main armhf libgomp1 armhf 11.2.0-12ubuntu1 [101 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main armhf libatomic1 armhf 11.2.0-12ubuntu1 [7624 B] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf libasan6 armhf 11.2.0-12ubuntu1 [2242 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf libubsan1 armhf 11.2.0-12ubuntu1 [894 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf g++-11 armhf 11.2.0-12ubuntu1 [9005 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main armhf libstdc++-11-dev armhf 11.2.0-12ubuntu1 [2180 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main armhf libgcc-11-dev armhf 11.2.0-12ubuntu1 [839 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11 armhf 11.2.0-12ubuntu1 [15.8 MB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf cpp-11 armhf 11.2.0-12ubuntu1 [7833 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf libstdc++6 armhf 11.2.0-12ubuntu1 [573 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf libisl23 armhf 0.24-2 [581 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf libmpc3 armhf 1.2.1-1 [39.5 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf libzstd1 armhf 1.4.8+dfsg-3 [285 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf libctf0 armhf 2.37-10ubuntu1 [93.7 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf libctf-nobfd0 armhf 2.37-10ubuntu1 [93.8 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf libbinutils armhf 2.37-10ubuntu1 [492 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main armhf binutils-common armhf 2.37-10ubuntu1 [213 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main armhf binutils armhf 2.37-10ubuntu1 [3174 B] Get:34 http://ftpmaster.internal/ubuntu jammy/main armhf binutils-arm-linux-gnueabihf armhf 2.37-10ubuntu1 [3057 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main armhf libssl3 armhf 3.0.0-1ubuntu1 [1575 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main armhf libblkid1 armhf 2.37.2-4ubuntu1 [136 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main armhf libuuid1 armhf 2.37.2-4ubuntu1 [23.3 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libcryptsetup12 armhf 2:2.4.2-1ubuntu3 [186 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main armhf libidn2-0 armhf 2.3.2-2 [67.8 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main armhf libp11-kit0 armhf 0.24.0-6 [219 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main armhf libtasn1-6 armhf 4.18.0-4 [36.3 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main armhf libgnutls30 armhf 3.7.2-2ubuntu1 [923 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd-timesyncd armhf 249.5-2ubuntu1 [30.8 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd-sysv armhf 249.5-2ubuntu1 [10.5 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main armhf libapparmor1 armhf 3.0.3-0ubuntu4 [32.3 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main armhf libip4tc2 armhf 1.8.7-1ubuntu4 [17.7 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main armhf libkmod2 armhf 28-1ubuntu5 [40.9 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main armhf libpcre2-8-0 armhf 10.39-3 [190 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libselinux1 armhf 3.3-1build1 [66.7 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main armhf libmount1 armhf 2.37.2-4ubuntu1 [151 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main armhf libseccomp2 armhf 2.5.2-2ubuntu2 [47.7 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main armhf login armhf 1:4.8.1-2ubuntu1 [186 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main armhf util-linux armhf 2.37.2-4ubuntu1 [1130 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main armhf mount armhf 2.37.2-4ubuntu1 [125 kB] Get:55 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd armhf 249.5-2ubuntu1 [4440 kB] Get:56 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsystemd0 armhf 249.5-2ubuntu1 [296 kB] Get:57 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libudev1 armhf 249.5-2ubuntu1 [70.7 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main armhf libapt-pkg6.0 armhf 2.3.13 [899 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main armhf dpkg armhf 1.20.9ubuntu3 [1215 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main armhf dash armhf 0.5.11+git20210903+057cd650a4ed-3 [83.8 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main armhf grep armhf 3.7-1 [150 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main armhf libncurses6 armhf 6.3-1 [87.5 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main armhf libncursesw6 armhf 6.3-1 [118 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main armhf libtinfo6 armhf 6.3-1 [88.2 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-bin armhf 6.3-1 [175 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-base all 6.3-1 [19.9 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main armhf gpgv armhf 2.2.27-2ubuntu1 [185 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main armhf apt armhf 2.3.13 [1378 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main armhf libsepol2 armhf 3.3-1 [263 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsemanage-common all 3.3-1build1 [10.0 kB] Get:71 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsemanage2 armhf 3.3-1build1 [84.1 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main armhf passwd armhf 1:4.8.1-2ubuntu1 [740 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules-bin armhf 1.4.0-10ubuntu2 [35.6 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules armhf 1.4.0-10ubuntu2 [263 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main armhf logsave armhf 1.46.4-1ubuntu1 [10.3 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main armhf libext2fs2 armhf 1.46.4-1ubuntu1 [192 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main armhf e2fsprogs armhf 1.46.4-1ubuntu1 [565 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main armhf libattr1 armhf 1:2.5.1-1 [12.2 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main armhf libcom-err2 armhf 1.46.4-1ubuntu1 [9224 B] Get:80 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libk5crypto3 armhf 1.19.2-0ubuntu1 [83.6 kB] Get:81 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libkrb5support0 armhf 1.19.2-0ubuntu1 [30.5 kB] Get:82 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libkrb5-3 armhf 1.19.2-0ubuntu1 [330 kB] Get:83 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libgssapi-krb5-2 armhf 1.19.2-0ubuntu1 [120 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-runtime all 1.4.0-10ubuntu2 [40.2 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main armhf libsmartcols1 armhf 2.37.2-4ubuntu1 [93.7 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main armhf libss2 armhf 1.46.4-1ubuntu1 [10.1 kB] Get:87 http://ftpmaster.internal/ubuntu jammy/main armhf sensible-utils all 0.0.17 [20.1 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main armhf usrmerge all 25ubuntu2 [54.7 kB] Get:89 http://ftpmaster.internal/ubuntu jammy/main armhf openssl armhf 3.0.0-1ubuntu1 [1148 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/main armhf ca-certificates all 20211016 [148 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main armhf libsqlite3-0 armhf 3.36.0-2 [571 kB] 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armhf linux-libc-dev armhf 5.15.0-13.13 [1235 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main armhf lockfile-progs armhf 0.1.19 [9508 B] Get:104 http://ftpmaster.internal/ubuntu jammy/main armhf pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 69.3 MB in 8s (8736 kB/s) (Reading database ... 12985 files and directories currently installed.) 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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 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:armhf (1.22-1) ... Setting up libstdc++-11-dev:armhf (11.2.0-12ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (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 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-22599297 armhf jammy-proposed -c chroot:build-PACKAGEBUILD-22599297 --arch=armhf --dist=jammy-proposed --nolog art-nextgen-simulation-tools_20160605+dfsg-4build2.dsc Initiating build PACKAGEBUILD-22599297 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:52 UTC 2021 armv7l sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-023.buildd +============================================================================================+ | art-nextgen-simulation-tools 20160605+dfsg-4build2 (armhf) Tue, 07 Dec 2021 17:36:08 +0000 | +============================================================================================+ Package: art-nextgen-simulation-tools Version: 20160605+dfsg-4build2 Source Version: 20160605+dfsg-4build2 Distribution: jammy-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22599297/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-Gz3WIb/art-nextgen-simulation-tools-20160605+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/art-nextgen-simulation-tools-Gz3WIb' 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-c6nMEo/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-c6nMEo/apt_archive ./ InRelease Get:2 copy:/<>/resolver-c6nMEo/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-c6nMEo/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-c6nMEo/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-c6nMEo/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (53.1 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-c6nMEo/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 (52.7 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13179 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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 (armhf 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-c6nMEo/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-c6nMEo/apt_archive ./ InRelease Get:2 copy:/<>/resolver-c6nMEo/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-c6nMEo/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-c6nMEo/apt_archive ./ Sources [515 B] Get:5 copy:/<>/resolver-c6nMEo/apt_archive ./ Packages [593 B] Fetched 2071 B in 0s (57.2 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 19.3 MB of archives. After this operation, 66.3 MB of additional disk space will be used. Get:1 copy:/<>/resolver-c6nMEo/apt_archive ./ sbuild-build-depends-art-nextgen-simulation-tools-dummy 0.invalid.0 [678 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf bsdextrautils armhf 2.37.2-4ubuntu1 [77.1 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main armhf libuchardet0 armhf 0.0.7-1build1 [75.6 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main armhf groff-base armhf 1.22.4-7 [870 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf libpipeline1 armhf 1.5.4-1 [25.2 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf man-db armhf 2.9.4-2build1 [1143 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf libelf1 armhf 0.186-1 [43.2 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf libicu67 armhf 67.1-7ubuntu1 [9788 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf libxml2 armhf 2.9.12+dfsg-5 [598 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main armhf libmagic-mgc armhf 1:5.41-2 [257 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main armhf libmagic1 armhf 1:5.41-2 [80.2 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main armhf file armhf 1:5.41-2 [20.6 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf gettext-base armhf 0.21-4ubuntu3 [36.0 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main armhf libsigsegv2 armhf 2.13-1ubuntu2 [13.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf m4 armhf 1.4.18-5ubuntu1 [192 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main armhf autoconf all 2.71-2 [338 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main armhf autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf automake all 1:1.16.5-1.1 [558 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf autopoint all 0.21-4ubuntu3 [422 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf libdebhelper-perl all 13.5.2ubuntu1 [66.0 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main armhf libtool all 2.4.6-15build1 [164 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main armhf dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf libfile-stripnondeterminism-perl all 1.12.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf dh-strip-nondeterminism all 1.12.1-1 [5200 B] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf libdw1 armhf 0.186-1 [228 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf debugedit armhf 1:5.0-3 [43.2 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf dwz armhf 0.14-1build1 [99.2 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf gettext armhf 0.21-4ubuntu3 [755 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main armhf debhelper all 13.5.2ubuntu1 [926 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf libgslcblas0 armhf 2.7.1+dfsg-3 [73.7 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf libgsl27 armhf 2.7.1+dfsg-3 [842 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf libgsl-dev armhf 2.7.1+dfsg-3 [1080 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.3 MB in 1s (17.9 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 13179 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-4ubuntu1_armhf.deb ... Unpacking bsdextrautils (2.37.2-4ubuntu1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1build1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_armhf.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.4-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.4-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2build1_armhf.deb ... Unpacking man-db (2.9.4-2build1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../05-libelf1_0.186-1_armhf.deb ... Unpacking libelf1:armhf (0.186-1) ... 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Unpacking sbuild-build-depends-art-nextgen-simulation-tools-dummy (0.invalid.0) ... Setting up libpipeline1:armhf (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:armhf (67.1-7ubuntu1) ... Setting up libgslcblas0:armhf (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:armhf (1:5.41-2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up libgsl27:armhf (2.7.1+dfsg-3) ... Setting up file (1:5.41-2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:armhf (2.13-1ubuntu2) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up libuchardet0:armhf (0.0.7-1build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:armhf (0.186-1) ... Setting up libxml2:armhf (2.9.12+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.12.1-1) ... Setting up libdw1:armhf (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 arm64 (armv7l) 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-arm-linux-gnueabihf_2.37-10ubuntu1 binutils-common_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 libatomic1_11.2.0-12ubuntu1 libattr1_1:2.5.1-1 libaudit-common_1:3.0-2ubuntu3 libaudit1_1:3.0-2ubuntu3 libbinutils_2.37-10ubuntu1 libblkid1_2.37.2-4ubuntu1 libbz2-1.0_1.0.8-5 libc-bin_2.34-0ubuntu3 libc-dev-bin_2.34-0ubuntu3 libc6_2.34-0ubuntu3 libc6-dev_2.34-0ubuntu3 libcap-ng0_0.7.9-2.2build2 libcap2_1:2.44-1build2 libcc1-0_11.2.0-12ubuntu1 libcom-err2_1.46.4-1ubuntu1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libcryptsetup12_2:2.4.2-1ubuntu3 libctf-nobfd0_2.37-10ubuntu1 libctf0_2.37-10ubuntu1 libdb5.3_5.3.28+dfsg1-0.8ubuntu2 libdebconfclient0_0.256ubuntu4 libdebhelper-perl_13.5.2ubuntu1 libdevmapper1.02.1_2:1.02.175-2.1ubuntu3 libdpkg-perl_1.20.9ubuntu3 libdw1_0.186-1 libelf1_0.186-1 libext2fs2_1.46.4-1ubuntu1 libfakeroot_1.25.3-1.1ubuntu3 libffi8_3.4.2-1ubuntu5 libfile-stripnondeterminism-perl_1.12.1-1 libgcc-11-dev_11.2.0-12ubuntu1 libgcc-s1_11.2.0-12ubuntu1 libgcrypt20_1.9.4-3ubuntu2 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-1ubuntu3 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+------------------------------------------------------------------------------+ 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-22599297 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22599297 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22599297 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 armhf 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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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=. -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=. -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=. -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=. -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=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/seqRead.o art_illumina_src/seqRead.cpp In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from art_illumina_src/art_illumina.cpp:29: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from art_illumina_src/art_illumina.cpp:29: /usr/include/c++/11/bits/stl_vector.h: In function ‘void seqRead::set_rate(int, double, std::vector&, int, double)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -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=. -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=. -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=. -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=. -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=. -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=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/samRead.o art_454_src/samRead.cpp In file included from /usr/include/c++/11/vector:72, from art_454_src/read_profile.h:25, from art_454_src/read_profile.cpp:26: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from art_454_src/read_profile.h:25, from art_454_src/read_profile.cpp:26: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void read_profile::read_indel_error(std::string)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -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=. -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=. -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=. -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=. -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=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 In file included from /usr/include/c++/11/map:60, from art_SOLiD_src/read_SOLiD.h:33, from art_SOLiD_src/read_SOLiD.cpp:24: /usr/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:61, from art_SOLiD_src/read_SOLiD.h:33, from art_SOLiD_src/read_SOLiD.cpp:24: /usr/include/c++/11/bits/stl_map.h: In member function ‘bool SOLiDread::read_error_profile(std::istream&)’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h: In member function ‘void SOLiDread::convert_seq2cs(std::string&, std::vector&, std::map >&, bool)’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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: 0.316156 The random seed for the run: 1638898641 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: 0.249305 The random seed for the run: 1638898642 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: 0.26512 The random seed for the run: 1638898642 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: 56.1326 The random seed for the run: 1638898643 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: 47.2191 The random seed for the run: 1638898699 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: 0.297954 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: 0.306308 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: 0.432733 The random seed for the run: 1638898747 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: 0.447623 The random seed for the run: 1638898748 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: 0.698731 The random seed for the run: 1638898748 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: 0.296648 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: 0.281366 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: 1.03275 The random seed for the run: 1638898750 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: 1150.19 The random seed for the run: 1638898751 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: 583.845 The random seed for the run: 1638899902 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: 420.177 The random seed for the run: 1638900486 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: 0.367151 The random seed for the run: 1638900907 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: 0.273415 The random seed for the run: 1638900908 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: 0.137536 The random seed for the run: 1638900908 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: 0.216077 The random seed for the run: 1638900908 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: 0.167971 The random seed for the run: 1638900908 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: 2.02012 The random seed for the run: 1638900908 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: 1.95795 The random seed for the run: 1638900911 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: 2.35414 The random seed for the run: 1638900913 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: 0.189403 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: 0.161405 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: 0.180633 The random seed for the run: 1638900916 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: 0.191715 The random seed for the run: 1638900916 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_SOLiD: Unknown DWARF DW_FORM_0x1f20 384deb3be14fe123e3fb7d93f122f96c193f00c1 debugedit: debian/art-nextgen-simulation-tools/usr/bin/art_454: Unknown DWARF DW_FORM_0x1f21 f2b6bdeaa287cdbcc7978520ad7f5cc5b5972b32 debugedit: debian/art-nextgen-simulation-tools/usr/bin/art_illumina: Unknown DWARF DW_FORM_0x1f20 139da24d6791a6a9e5a2a03ef4b110414d203ae4 dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/art-nextgen-simulation-tools/usr/bin/art_454 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/art-nextgen-simulation-tools/usr/bin/art_illumina contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/art-nextgen-simulation-tools/usr/bin/art_SOLiD contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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. dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.deb'. 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_armhf.deb'. Renaming art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_armhf.deb to art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.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 2021-12-07T18:15:58Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.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: armhf 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: e52054130a165cea2c8ef20817302380314a1da7 1713676 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_armhf.ddeb 68f83b6647533315e226d92e152558a58709468b 5972 art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.buildinfo a161b806a514120db33ce0ace60862b3a1c24db9 1806522 art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.deb Checksums-Sha256: 326aee69b5d0488e241e70a23453ba7a6c29cf4ba8218e1fed4c28a204252979 1713676 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_armhf.ddeb 341e0497506cb8174c5de46fabca6ac071b79b3f303cb65252b498de362fa4ee 5972 art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.buildinfo 5acf65846472790f57dc4c423a017ff6140dfcc13a1e784398ae61de247489ae 1806522 art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.deb Files: e5f45d9e1838faae51fbc14c6b43e430 1713676 debug optional art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_armhf.ddeb 3786331ab3b1985ade2d8f3918bfba19 5972 science optional art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.buildinfo 2032cb2f6369ae68882879e91c8f8cb1 1806522 science optional art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.deb 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: armhf Version: 20160605+dfsg-4build2 Checksums-Md5: e5f45d9e1838faae51fbc14c6b43e430 1713676 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_armhf.ddeb 2032cb2f6369ae68882879e91c8f8cb1 1806522 art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.deb Checksums-Sha1: e52054130a165cea2c8ef20817302380314a1da7 1713676 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_armhf.ddeb a161b806a514120db33ce0ace60862b3a1c24db9 1806522 art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.deb Checksums-Sha256: 326aee69b5d0488e241e70a23453ba7a6c29cf4ba8218e1fed4c28a204252979 1713676 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4build2_armhf.ddeb 5acf65846472790f57dc4c423a017ff6140dfcc13a1e784398ae61de247489ae 1806522 art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Tue, 07 Dec 2021 18:15:57 +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-arm-linux-gnueabihf (= 2.37-10ubuntu1), binutils-common (= 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 (= 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), 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), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), hostname (= 3.23ubuntu1), init-system-helpers (= 1.60build1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10ubuntu2), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-12ubuntu1), libatomic1 (= 11.2.0-12ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbinutils (= 2.37-10ubuntu1), libblkid1 (= 2.37.2-4ubuntu1), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.34-0ubuntu3), libc-dev-bin (= 2.34-0ubuntu3), libc6 (= 2.34-0ubuntu3), libc6-dev (= 2.34-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build2), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-12ubuntu1), libcom-err2 (= 1.46.4-1ubuntu1), libcrypt-dev (= 1:4.4.26-1), libcrypt1 (= 1:4.4.26-1), libctf-nobfd0 (= 2.37-10ubuntu1), libctf0 (= 2.37-10ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.256ubuntu4), libdebhelper-perl (= 13.5.2ubuntu1), libdpkg-perl (= 1.20.9ubuntu3), libdw1 (= 0.186-1), libelf1 (= 0.186-1), libfile-stripnondeterminism-perl (= 1.12.1-1), libgcc-11-dev (= 11.2.0-12ubuntu1), libgcc-s1 (= 11.2.0-12ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu2), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgmp10 (= 2:6.2.1+dfsg-1ubuntu3), libgomp1 (= 11.2.0-12ubuntu1), libgpg-error0 (= 1.42-3), libgsl-dev (= 2.7.1+dfsg-3), libgsl27 (= 2.7.1+dfsg-3), libgslcblas0 (= 2.7.1+dfsg-3), libgssapi-krb5-2 (= 1.19.2-0ubuntu1), libicu67 (= 67.1-7ubuntu1), libisl23 (= 0.24-2), libk5crypto3 (= 1.19.2-0ubuntu1), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.19.2-0ubuntu1), libkrb5support0 (= 1.19.2-0ubuntu1), liblz4-1 (= 1.9.3-2build1), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmount1 (= 2.37.2-4ubuntu1), libmpc3 (= 1.2.1-1), libmpfr6 (= 4.1.0-3build2), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libpam-modules (= 1.4.0-10ubuntu2), libpam-modules-bin (= 1.4.0-10ubuntu2), libpam-runtime (= 1.4.0-10ubuntu2), libpam0g (= 1.4.0-10ubuntu2), libpcre2-8-0 (= 10.39-3), libpcre3 (= 2:8.39-13build4), libperl5.32 (= 5.32.1-3ubuntu3), libpipeline1 (= 1.5.4-1), libseccomp2 (= 2.5.2-2ubuntu2), libselinux1 (= 3.3-1build1), libsigsegv2 (= 2.13-1ubuntu2), libsmartcols1 (= 2.37.2-4ubuntu1), libssl3 (= 3.0.0-1ubuntu1), libstdc++-11-dev (= 11.2.0-12ubuntu1), libstdc++6 (= 11.2.0-12ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.5-2ubuntu1), libtinfo6 (= 6.3-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libubsan1 (= 11.2.0-12ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 249.5-2ubuntu1), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4ubuntu1), libxml2 (= 2.9.12+dfsg-5), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.15.0-13.13), login (= 1:4.8.1-2ubuntu1), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 17), m4 (= 1.4.18-5ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), ncurses-base (= 6.3-1), ncurses-bin (= 6.3-1), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu5), sed (= 4.7-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 2.96-7ubuntu2), tar (= 1.34+dfsg-1build2), util-linux (= 2.37.2-4ubuntu1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1638897783" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ art-nextgen-simulation-tools_20160605+dfsg-4build2_armhf.deb ------------------------------------------------------------ new Debian package, version 2.0. size 1806522 bytes: control archive=2082 bytes. 1810 bytes, 30 lines control 2723 bytes, 33 lines md5sums Package: art-nextgen-simulation-tools Version: 20160605+dfsg-4build2 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 8949 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libstdc++6 (>= 5.2) 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: armhf Build Type: any Build-Space: n/a Build-Time: 2367 Distribution: jammy-proposed Host Architecture: armhf Install-Time: 19 Job: art-nextgen-simulation-tools_20160605+dfsg-4build2.dsc Machine Architecture: arm64 Package: art-nextgen-simulation-tools Package-Time: 2390 Source-Version: 20160605+dfsg-4build2 Space: n/a Status: successful Version: 20160605+dfsg-4build2 -------------------------------------------------------------------------------- Finished at 2021-12-07T18:15:58Z Build needed 00:39:50, 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=armhf PACKAGEBUILD-22599297 Scanning for processes to kill in build PACKAGEBUILD-22599297