Fri Feb 28 15:53:28 UTC 2025 I: starting to build art-nextgen-simulation-tools/trixie/amd64 on jenkins on '2025-02-28 15:53' Fri Feb 28 15:53:28 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/50198/console.log Fri Feb 28 15:53:28 UTC 2025 I: Downloading source for trixie/art-nextgen-simulation-tools=20160605+dfsg-5 --2025-02-28 15:53:29-- http://deb.debian.org/debian/pool/main/a/art-nextgen-simulation-tools/art-nextgen-simulation-tools_20160605%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2400 (2.3K) [text/prs.lines.tag] Saving to: ‘art-nextgen-simulation-tools_20160605+dfsg-5.dsc’ 0K .. 100% 341M=0s 2025-02-28 15:53:29 (341 MB/s) - ‘art-nextgen-simulation-tools_20160605+dfsg-5.dsc’ saved [2400/2400] Fri Feb 28 15:53:29 UTC 2025 I: art-nextgen-simulation-tools_20160605+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: art-nextgen-simulation-tools Binary: art-nextgen-simulation-tools, art-nextgen-simulation-tools-profiles Architecture: any all Version: 20160605+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/art-nextgen-simulation-tools Vcs-Git: https://salsa.debian.org/med-team/art-nextgen-simulation-tools.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libgsl-dev Package-List: art-nextgen-simulation-tools deb science optional arch=any art-nextgen-simulation-tools-profiles deb science optional arch=all Checksums-Sha1: 73626f42dcb9acc1419b45d3749ff574050fd8d4 2229112 art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz f5dac1938b9a5acaeeff4b4d3a84de026ee6e652 9420 art-nextgen-simulation-tools_20160605+dfsg-5.debian.tar.xz Checksums-Sha256: d40569d3318f0714dc50ae58de72c915490968d3141d01a01b66093ea84c04cf 2229112 art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz cf05b945475b82cc1fe082c2750ee3fd88fa5827e6dde42987c94df79177d48a 9420 art-nextgen-simulation-tools_20160605+dfsg-5.debian.tar.xz Files: a36db8dfaa4e93ad6e68a73b6a690746 2229112 art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz 518444b26ac3f938b2bb46b03e4c74f6 9420 art-nextgen-simulation-tools_20160605+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWAkFYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHc0w//Wwxl27kUkAk+auMCvfS2NQfGdv5n87Y9 WNW2f/Y8HCjRhMzpEZYqZpxFV9pMNOYdAQCgoJ2H0hk+lKDero/w0oUA0Pso6+Vq r7/z3LURHFIDxeplqbgcd7Ztdtdqk/lJPU2WXvf4w+g+wUq7yHeJRxsqUpzZjZgq nbmy9hmea7MDGz/nr7qXKol+lUi06wzVtKMPzgRSI6u6k3LRqWiUyHlNKIiW6qtP pzH14PZyk92x+Sk4uYBSVNCCTjImDvoYVb/bXBjMS2e6wATj9zWy3nJIlkvDgTHw kjot7YoMQSs2YRPNFdHkaa5ZM1/TqQkSJGzv6ivgAHYVFWlmd4pbv6jVagSgOxOU 35Ih+jRx6GeZbpC22yPZTIsWC8GGA1IGdEwERadLVZyNaHnhaO1oywjU+FcRYM6n 3MmaXOc+nfvVhs3eiaCJ3q9uzU/weMELbu1jnCNvy2NA6QUlKHYJirwsFj1q98ig SigKSgoWfE3eEjioIg/pw7Ms7v4jPCfMJ7kgdM0d4CBn0tZXoBh8B4ko63SRJ+8n EjKPxK8aOQr1epPoXQMdp3oxR0bLRg8iH/WT9zY6/m4EsgIpNy7l8vvLBJhsw8gT hxoz6oHGcxpmEoc1W9eljuQI/Wyypy8rluZVCkn0zZbJJxQDbEXvoruPTEu/9WMK fT/YaQktyhs= =DnsR -----END PGP SIGNATURE----- Fri Feb 28 15:53:29 UTC 2025 I: Checking whether the package is not for us Fri Feb 28 15:53:29 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net. Fri Feb 28 15:53:29 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Fri Feb 28 16:04:57 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 2 10:16:31 -12 2026 I: pbuilder-time-stamp: 1775168191 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [art-nextgen-simulation-tools_20160605+dfsg-5.dsc] I: copying [./art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz] I: copying [./art-nextgen-simulation-tools_20160605+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./art-nextgen-simulation-tools_20160605+dfsg-5.dsc: unsupported subcommand 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-5.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2300861/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='36215a241dfd4c1c9d3eb85a585dca3e' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2300861' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TPaCJwHb/pbuilderrc_8Wne --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TPaCJwHb/b1 --logfile b1/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2300861/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libgsl-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19802 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 22.9 MB of archives. After unpacking 89.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Fetched 22.9 MB in 3s (7453 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19802 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-4_amd64.deb ... Unpacking bsdextrautils (2.40.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../30-libgslcblas0_2.8+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../31-libgsl28_2.8+dfsg-5_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../32-libgsl-dev_2.8+dfsg-5_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-4) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:8: installing './compile' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' Makefile.am: installing './INSTALL' Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... 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 or later... yes checking for inline... inline checking for size_t... yes checking for floor... yes checking for pow... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make all-am make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o art_illumina_src/seqRead.o art_illumina_src/seqRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o art_454_src/samRead.o art_454_src/samRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o art_SOLiD_src/samRead.o art_SOLiD_src/samRead.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o art_454 art_454_src/art_454.o art_454_src/art.o art_454_src/read_profile.o art_454_src/readSeqFile.o art_454_src/seqRead.o art_454_src/samRead.o -lgsl -lgslcblas -lm g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[2]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/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: 0.037752 The random seed for the run: 1775168309 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: 0.037337 The random seed for the run: 1775168309 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: 0.032516 The random seed for the run: 1775168309 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: 6.58176 The random seed for the run: 1775168310 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: 5.50652 The random seed for the run: 1775168321 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: 0.035474 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: 0.037746 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: 0.060659 The random seed for the run: 1775168336 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: 0.073346 The random seed for the run: 1775168336 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: 0.126299 The random seed for the run: 1775168336 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: 0.046402 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: 0.04559 The random seed for the run: 777 Parameters Settings fold of read coverage: 10X F3 read length: 50 R3 read length: 50 fragment length mean: 1500 std: 50 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./matepair_fs2_R3.fq the 2nd reads: ./matepair_fs2_F3.fq MAP Alignment Files: the 1st reads: ./matepair_fs2_R3.map the 2nd reads: ./matepair_fs2_F3.map SAM Alignment File: ./matepair_fs2.sam compare two simulation datasets 4c4 < @PG ID:03 PN:ART_SOLiD CL:../art_SOLiD -r 777 -s testSeq.fa ./matepair_fs1 50 10 1500 50 --- > @PG ID:03 PN:ART_SOLiD CL:../art_SOLiD -r 777 -s testSeq.fa ./matepair_fs2 50 10 1500 50 ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Paired-end (F3-F5) simulation Total CPU time used: 0.162314 The random seed for the run: 1775168337 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: 152.004 The random seed for the run: 1775168337 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: 84.1581 The random seed for the run: 1775168699 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: 57.2559 The random seed for the run: 1775168793 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: 0.042943 The random seed for the run: 1775168855 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: 0.028794 The random seed for the run: 1775168855 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: 0.021995 The random seed for the run: 1775168855 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: 0.030687 The random seed for the run: 1775168855 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: 0.022709 The random seed for the run: 1775168855 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 2500 Standard Deviation: 50 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeq 2500 Length 126 R1 (built-in profile) First Read: HiSeq 2500 Length 126 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./matepair_com1.fq the 2nd reads: ./matepair_com2.fq ALN Alignment Files: the 1st reads: ./matepair_com1.aln the 2nd reads: ./matepair_com2.aln SAM Alignment File: ./matepair_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon 5'-end sequencing simulation Total CPU time used: 0.205409 The random seed for the run: 1775168855 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 # Reads per Amplion: 2 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeqX v2.5 TruSeq Length 151 R1 (built-in profile) Output files FASTQ Sequence File: ./amp_5_end_com.fq ALN Alignment File: ./amp_5_end_com.aln SAM Alignment File: ./amp_5_end_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon paired-end sequencing simulation Total CPU time used: 0.287845 The random seed for the run: 1775168855 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 # Read Pairs per Amplion: 1 Profile Type: Combined ID Tag: Quality Profile(s) First Read: MiSeq v1 Length 250 R1 (built-in profile) First Read: MiSeq v1 Length 250 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./amp_pair1.fq the 2nd reads: ./amp_pair2.fq ALN Alignment Files: the 1st reads: ./amp_pair1.aln the 2nd reads: ./amp_pair2.aln SAM Alignment File: ./amp_pair.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon matepair sequencing simulation Total CPU time used: 0.386154 The random seed for the run: 1775168856 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: 0.019581 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: 0.019335 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: 0.022951 The random seed for the run: 1775168856 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: 0.021804 The random seed for the run: 1775168856 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 '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' /usr/bin/mkdir -p '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/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 '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c art_illumina art_454 art_SOLiD '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' make[2]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/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 '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' dh_install -Nart-nextgen-simulation-tools dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' dh_installchangelogs ChangeLog make[1]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_installexamples-arch make[1]: Entering directory '/build/reproducible-path/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 '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' dh_installexamples -Nart-nextgen-simulation-tools dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools-profiles: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_amd64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2300861 and its subdirectories I: Current time: Thu Apr 2 10:27:56 -12 2026 I: pbuilder-time-stamp: 1775168876 Fri Feb 28 16:04:58 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Fri Feb 28 16:04:58 UTC 2025 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Fri Feb 28 16:10:35 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. Fri Feb 28 16:10:35 UTC 2025 I: art-nextgen-simulation-tools_20160605+dfsg-5_amd64.changes: Format: 1.8 Date: Mon, 18 Dec 2023 18:59:24 +0100 Source: art-nextgen-simulation-tools Binary: art-nextgen-simulation-tools art-nextgen-simulation-tools-dbgsym art-nextgen-simulation-tools-profiles Architecture: amd64 all Version: 20160605+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: art-nextgen-simulation-tools - simulation tools to generate synthetic next-generation sequencing art-nextgen-simulation-tools-profiles - profiles for art simulation tools Closes: 1043622 Changes: art-nextgen-simulation-tools (20160605+dfsg-5) unstable; urgency=medium . * Fix clean target Closes: #1043622 * Standards-Version: 4.6.2 (routine-update) * debhelper-compat 13 (routine-update) * Update lintian override info format * Apply multi-arch hints. Checksums-Sha1: c4ab22e9015220118888d5e6a19aa301c59d18c5 1711680 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_amd64.deb a7ef4174eb2400ef3c24cd8e3fff2628e6a9c2d0 1848492 art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb 40adf52261059c181043016029c9e891d9673db8 5634 art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo 462e0ec325981220d0dea5d69536fe2792e55171 1687780 art-nextgen-simulation-tools_20160605+dfsg-5_amd64.deb Checksums-Sha256: 9b8d7484731ea90d648b343bcdbf7168be743014df196e05e61e4772036b9d6c 1711680 art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_amd64.deb f1a297fd5dced8a0045115191fdddc62576ccc067eb00c005aa43627341fcf57 1848492 art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb 2f124c62d50f61fc37cc5b829ca675cb0c67cbeeb2aa72c342d11fb05bf580c2 5634 art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo 9dd0593ab1d65bc7a344dbdd6233cc276ec8ff3078c598a85ea188508b26098a 1687780 art-nextgen-simulation-tools_20160605+dfsg-5_amd64.deb Files: 4407652b3700b1c95c1d1aaf271f0fff 1711680 debug optional art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_amd64.deb 8dd1a5a5c45ef6e51b671480dbfab76b 1848492 science optional art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb ca70ee581473314cca9bb5d2b31cacec 5634 science optional art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo 350853cd8651f3aae589d41e6bbdcfb0 1687780 science optional art-nextgen-simulation-tools_20160605+dfsg-5_amd64.deb Fri Feb 28 16:10:36 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_36-50198.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.TPaCJwHb/art-nextgen-simulation-tools_20160605+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TPaCJwHb/art-nextgen-simulation-tools_20160605+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TPaCJwHb/art-nextgen-simulation-tools_20160605+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TPaCJwHb/b1/art-nextgen-simulation-tools_20160605+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.TPaCJwHb/b2/art-nextgen-simulation-tools_20160605+dfsg-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 222ms CPU time consumed: 222ms Fri Feb 28 16:10:41 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Fri Feb 28 16:10:41 UTC 2025 I: art-nextgen-simulation-tools from trixie built successfully and reproducibly on amd64. Fri Feb 28 16:10:42 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Feb 28 16:10:42 UTC 2025 I: Submitting 8.0K b1/art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo.asc Fri Feb 28 16:10:43 UTC 2025 I: Submitting 8.0K b2/art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo.asc Fri Feb 28 16:10:44 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Feb 28 16:10:44 UTC 2025 I: Done submitting .buildinfo files. Fri Feb 28 16:10:44 UTC 2025 I: Removing signed art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo.asc files: removed './b1/art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo.asc' removed './b2/art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo.asc'