Thu Sep 11 05:46:28 UTC 2025 I: starting to build snpomatic/forky/amd64 on jenkins on '2025-09-11 05:46' Thu Sep 11 05:46:28 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/54386/console.log Thu Sep 11 05:46:28 UTC 2025 I: Downloading source for forky/snpomatic=1.0-7 --2025-09-11 05:46:28-- http://deb.debian.org/debian/pool/main/s/snpomatic/snpomatic_1.0-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1990 (1.9K) [text/prs.lines.tag] Saving to: ‘snpomatic_1.0-7.dsc’ 0K . 100% 187M=0s 2025-09-11 05:46:28 (187 MB/s) - ‘snpomatic_1.0-7.dsc’ saved [1990/1990] Thu Sep 11 05:46:28 UTC 2025 I: snpomatic_1.0-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: snpomatic Binary: snpomatic Architecture: any Version: 1.0-7 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://github.com/magnusmanske/snpomatic Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/snpomatic Vcs-Git: https://salsa.debian.org/med-team/snpomatic.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 13), asciidoctor, antiword Package-List: snpomatic deb science optional arch=any Checksums-Sha1: ce873229b63a44cf210a7c41ef866642bed72d1f 66546 snpomatic_1.0.orig.tar.gz 8faf78e650eecc34cac38723ba1f4428249ed176 9876 snpomatic_1.0-7.debian.tar.xz Checksums-Sha256: b90123226e24edfa5c2ca296f9414b5aa005d3da77ad80b5c576adddbb38a094 66546 snpomatic_1.0.orig.tar.gz 903f7fbf8f286aafb8de26bec1a40df648ca1c40f5dcc1512b3c6e6e257972eb 9876 snpomatic_1.0-7.debian.tar.xz Files: bac27c60847ad8036faafd7c9a335b5c 66546 snpomatic_1.0.orig.tar.gz 8b47bba755e345c86070eea001b3b167 9876 snpomatic_1.0-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmWGmLkACgkQ6NN64vCf SHJ7Ig//fwpaQyd1cWhPKbJc6B5vMNCCoQeV3qGZieZ4lTbzEuQ8guqXKIMm7Dcn DzVbpguH6xjTdjhu5C3fY+ZGrLsuNceOoD6O8W8NFfjKlEPiIdE8Ckw50wFMCzej upWRWIMovkhyb6Yd1zL9I1CNakKu46ECVIcW3CC0snimk6STnFEiTYvCLjHlKUnp karPUsQOm/tYR/Szetxv+zwsXzh8tNZTg9dUOFFo63ylNjbNcfxIsrLq55Y4HKEQ LTN0tFV2Wbpc7rntYT2rBnP/juR3F9/UicwteoK0ykgOaAieghgHf79Sp8c0Ibg0 AJvHTcWfc9hUhNBUQnqvMQKQqFeQZDPplgnjpDf556/2cbcye9ELSFqZrKKz3tVg MZo0tAQX23+FuDqyG8I5QsnOAh4yyj9/AMM2Itc8Cp9qw6w/S32FHAHNkWpyuME2 1ZQDybzBfqYft9EP2wLi0jtvrP05oXHQx0kPPWf6B1pKOoK1adhs17VfAffP7E5h AuFS8STirI7JCmbXCksQg+c/V9LUayDfgdxDl1pvMJDRXKakss4Tnnp2DVUdKXhH MR9XMrkWoSnbztsc3WcDtwD2ifwrESyVU6mTJaGb1bBYLiyIM/h0CizoueLlCo/z EZKWrN0vSZr727kMnX0jJetWc/U8GclH5sAjnUr7kn8Alj1B5XU= =leI9 -----END PGP SIGNATURE----- Thu Sep 11 05:46:28 UTC 2025 I: Checking whether the package is not for us Thu Sep 11 05:46:28 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Thu Sep 11 05:46:28 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Thu Sep 11 05:49:12 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 10 17:46:29 -12 2025 I: pbuilder-time-stamp: 1757569589 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [snpomatic_1.0-7.dsc] I: copying [./snpomatic_1.0.orig.tar.gz] I: copying [./snpomatic_1.0-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: no acceptable signature found dpkg-source: info: extracting snpomatic in snpomatic-1.0 dpkg-source: info: unpacking snpomatic_1.0.orig.tar.gz dpkg-source: info: unpacking snpomatic_1.0-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_ungap dpkg-source: info: applying hardening dpkg-source: info: applying build_all_binaries I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1196753/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=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5f9baf32cecd4e689d53a014f4fba54f' 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='1196753' 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.nfdrNq13/pbuilderrc_HdIU --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nfdrNq13/b1 --logfile b1/build.log snpomatic_1.0-7.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1196753/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), asciidoctor, antiword dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 21054 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 asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on antiword; however: Package antiword 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: antiword{a} asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{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} libffi8{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libruby{a} libruby3.3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} ruby{a} ruby-asciidoctor{a} ruby-csv{a} ruby-did-you-mean{a} ruby-net-telnet{a} ruby-ruby2-keywords{a} ruby-rubygems{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.3{a} rubygems-integration{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libjs-jquery libltdl-dev libmail-sendmail-perl lynx ruby-sdbm wget zip 0 packages upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 21.2 MB of archives. After unpacking 82.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 ca-certificates all 20250419 [162 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-2 [95.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 antiword amd64 0.37-17 [123 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 rubygems-integration all 1.19 [5488 B] Get: 15 http://deb.debian.org/debian forky/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 ruby-csv all 3.3.4-1 [42.2 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 ruby-ruby2-keywords all 0.0.5-1 [4300 B] Get: 20 http://deb.debian.org/debian forky/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libruby3.3 amd64 3.3.8-2 [6301 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 ruby3.3 amd64 3.3.8-2 [834 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get: 27 http://deb.debian.org/debian forky/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get: 29 http://deb.debian.org/debian forky/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 42 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Fetched 21.2 MB in 11s (1989 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 ... 21054 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package openssl. Preparing to unpack .../01-openssl_3.5.2-1_amd64.deb ... Unpacking openssl (3.5.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.41.1-2_amd64.deb ... Unpacking bsdextrautils (2.41.1-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../10-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package antiword. Preparing to unpack .../12-antiword_0.37-17_amd64.deb ... Unpacking antiword (0.37-17) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../13-rubygems-integration_1.19_all.deb ... Unpacking rubygems-integration (1.19) ... Selecting previously unselected package rake. Preparing to unpack .../14-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-csv. Preparing to unpack .../15-ruby-csv_3.3.4-1_all.deb ... Unpacking ruby-csv (3.3.4-1) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../16-ruby-did-you-mean_1.6.3-2_all.deb ... Unpacking ruby-did-you-mean (1.6.3-2) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../17-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-ruby2-keywords. Preparing to unpack .../18-ruby-ruby2-keywords_0.0.5-1_all.deb ... Unpacking ruby-ruby2-keywords (0.0.5-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../19-ruby-webrick_1.9.1-1_all.deb ... Unpacking ruby-webrick (1.9.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../20-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../21-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../22-libyaml-0-2_0.2.5-2_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-2) ... Selecting previously unselected package libruby3.3:amd64. Preparing to unpack .../23-libruby3.3_3.3.8-2_amd64.deb ... Unpacking libruby3.3:amd64 (3.3.8-2) ... Selecting previously unselected package ruby3.3. Preparing to unpack .../24-ruby3.3_3.3.8-2_amd64.deb ... Unpacking ruby3.3 (3.3.8-2) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../25-libruby_1%3a3.3+b1_amd64.deb ... Unpacking libruby:amd64 (1:3.3+b1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../26-ruby-rubygems_3.6.7-2_all.deb ... Unpacking ruby-rubygems (3.6.7-2) ... Selecting previously unselected package ruby. Preparing to unpack .../27-ruby_1%3a3.3+b1_amd64.deb ... Unpacking ruby (1:3.3+b1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../28-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../29-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../30-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../31-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../32-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../33-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../34-autopoint_0.23.1-2_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snpomatic-1.0/ && 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 > ../snpomatic_1.0-7_source.changes dpkg-buildpackage: info: source package snpomatic dpkg-buildpackage: info: source version 1.0-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0' /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/snpomatic-1.0' rm -f *.o rm -f src/*.o rm -f findknownsnps rm -f variety make[2]: Leaving directory '/build/reproducible-path/snpomatic-1.0' rm -rf debian/findknownsnps.1 rm -rf debian/findknownsnps.1.html rm -f mapcontigs reassemble ungap rm -f doc/Manual.txt dh_auto_clean -- make -j40 clean make[2]: Entering directory '/build/reproducible-path/snpomatic-1.0' rm -f *.o rm -f src/*.o rm -f findknownsnps rm -f variety make[2]: Leaving directory '/build/reproducible-path/snpomatic-1.0' make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/snpomatic.substvars debian/files rm -fr -- debian/snpomatic/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j40 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0' g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/findknownsnps.cpp -o src/findknownsnps.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/global_functions.cpp -o src/global_functions.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosome.cpp -o src/TChromosome.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/mapcontigs.cpp -o src/mapcontigs.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/ungap.cpp -o src/ungap.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::init()': src/TChromosomeAlign.cpp:83:58: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 83 | fprintf ( sam , "@SQ\tSN:%s\tLN:%d\n" , (*chrs)[i].name.c_str() , (*chrs)[i].sequence.length() ) ; | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %ld src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)': src/TChromosomeAlign.cpp:956:98: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 956 | fprintf ( sqlite , "INSERT INTO chromosomes ( name , size ) VALUES ( \"%s\" , \"%d\") ;\n" , (*chrs)[a].name.c_str() , (*chrs)[a].sequence.length() ) ; | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %ld src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_cigar_sqlite(const std::string&, const std::string&, uint, uint, char)': src/TChromosomeAlign.cpp:1583:43: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 1583 | fprintf ( cigar , "%s %d %d %c %s %d %d + %d %s\n" , | ~^ | | | int | %ld ...... 1586 | sequence.length() , // Read end | ~~~~~~~~~~~~~~~~~ | | | std::__cxx11::basic_string::size_type {aka long unsigned int} src/TChromosomeAlign.cpp:1583:55: warning: format '%d' expects argument of type 'int', but argument 9 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 1583 | fprintf ( cigar , "%s %d %d %c %s %d %d + %d %s\n" , | ~^ | | | int | %ld ...... 1590 | position + sequence.length() , // End on chromosome | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | std::__cxx11::basic_string::size_type {aka long unsigned int} src/global_functions.cpp: In function 'void load_all_chromosomes(std::string, std::vector&, bool)': src/global_functions.cpp:146:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] 146 | if ( DEBUGGING ) { fprintf ( stdout , "read %d chromosomes.\n" , chrs.size() ) ; fflush(stdout); } | ~^ ~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run(chrvec*)': src/TChromosomalIndices.cpp:262:87: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] 262 | if ( index_from == 0 && index_to == 0 ) fprintf ( stdout , "Indexing %d chromosomes ... " , chrs->size() ) ; | ~^ ~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld src/TChromosomalIndices.cpp:263:52: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] 263 | else fprintf ( stdout , "Indexing %d chromosomes (%d-%d) ... " , chrs->size() , index_from , index_to ) ; | ~^ ~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld src/global_functions.cpp:116:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 116 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/global_functions.cpp: In function 'void incorporate_all_gff(std::string, std::vector&)': src/global_functions.cpp:165:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 165 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::read_chromosome(std::string, std::string)': src/TChromosome.cpp:41:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 41 | if ( DEBUGGING ) { fprintf ( stdout , "read %d nucleotides.\n" , sequence.length() ) ; fflush(stdout); } | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %ld src/global_functions.cpp: In function 'void incorporate_simple_snps(std::string, std::vector&)': src/global_functions.cpp:220:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 220 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_nono_list(std::string)': src/TChromosomeAlign.cpp:93:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp:13:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::string)': src/TChromosome.cpp:54:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::string)': src/TChromosome.cpp:95:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::string)': src/TChromosomalIndices.cpp:33:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:37:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)': src/TChromosomeAlign.cpp:972:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 972 | fgets ( dummy , READ_CHAR_BUFFER , sqlite_cache ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_paired(std::string, std::string, uint, uint, uint)': src/TChromosomeAlign.cpp:1070:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1070 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1075:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1075 | fgets ( c1 , READ_CHAR_BUFFER , file2 ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::reassemble_reads(FILE*, uint, index2type, index2type)': src/TChromosomalIndices.cpp:126:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 126 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:127:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_regions(chrvec*, std::string)': src/TChromosomalIndices.cpp:167:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 167 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq(std::string)': src/TChromosomeAlign.cpp:1296:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1296 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1306:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1306 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1316:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1316 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1325:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1325 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::load_index(std::string)': src/TChromosomalIndices.cpp:409:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 409 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Version | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:410:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 410 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // position size | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fasta(std::string)': src/TChromosomeAlign.cpp:1374:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1374 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:415:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 415 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Sub-index size | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:419:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 419 | fread ( &i.index2 , sizeof ( i.index2 ) , 1 , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:420:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 420 | fread ( &i.position , sizeof ( i.position ) , 1 , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:421:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 421 | fread ( &i.chromosome , sizeof ( i.chromosome ) , 1 , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:422:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 422 | fread ( &i.reverse_complement , sizeof ( i.reverse_complement ) , 1 , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq_variety(std::string)': src/TChromosomeAlign.cpp:1628:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1628 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1637:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1637 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1647:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1647 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1655:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1655 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/reassemble.cpp: In function 'void read_fastq(std::string, std::vector&, int)': src/reassemble.cpp:319:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 319 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o findknownsnps g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o reassemble g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o variety g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o mapcontigs g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o ungap make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0' dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-CvEmjBFE create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/snpomatic.substvars rm -fr -- debian/.debhelper/generated/snpomatic/ debian/snpomatic/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0' mkdir -p /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin install -p findknownsnps /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin # -- we don't install the others as they seem unmaintained/undocumented #cp reassemble /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin #cp variety /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin #cp mapcontigs /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin #cp ungap /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0' debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0' antiword doc/Manual.doc > doc/Manual.txt mkdir -p debian/snpomatic/usr/share/doc/snpomatic cp doc/Manual.txt debian/snpomatic/usr/share/doc/snpomatic dh_installdocs -- install -p -m0644 debian/copyright debian/snpomatic/usr/share/doc/snpomatic/copyright install -m0755 -d debian/snpomatic/usr/share/doc-base/ install -p -m0644 debian/doc-base debian/snpomatic/usr/share/doc-base/snpomatic.snpomatic make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0' dh_installchangelogs install -m0755 -d debian/snpomatic/usr/share/doc/snpomatic install -p -m0644 debian/.debhelper/generated/snpomatic/dh_installchangelogs.dch.trimmed debian/snpomatic/usr/share/doc/snpomatic/changelog.Debian rm -f debian/snpomatic.debhelper.log debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0' asciidoctor -a docdate='' -b manpage debian/findknownsnps.1.adoc dh_installman -- install -m0755 -d debian/snpomatic/usr/share/man/man1/ install -p -m0644 ./debian/findknownsnps.1 debian/snpomatic/usr/share/man/man1/findknownsnps.1 man-recode --to-code UTF-8 --suffix .dh-new debian/snpomatic/usr/share/man/man1/findknownsnps.1 mv debian/snpomatic/usr/share/man/man1/findknownsnps.1.dh-new debian/snpomatic/usr/share/man/man1/findknownsnps.1 chmod 0644 -- debian/snpomatic/usr/share/man/man1/findknownsnps.1 make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0' dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/snpomatic chmod a-x usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1 gzip -9nf usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1 cd '/build/reproducible-path/snpomatic-1.0' dh_fixperms find debian/snpomatic ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/snpomatic/usr/share/doc -type f -a -true -a ! -regex 'debian/snpomatic/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/snpomatic/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/snpomatic/usr/bin/findknownsnps dh_strip -a install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a1 objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a1/edf78850cff1f6263c103eca6a119bb1448701.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a1/edf78850cff1f6263c103eca6a119bb1448701.debug strip --remove-section=.comment --remove-section=.note debian/snpomatic/usr/bin/findknownsnps objcopy --add-gnu-debuglink debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a1/edf78850cff1f6263c103eca6a119bb1448701.debug debian/snpomatic/usr/bin/findknownsnps install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc ln -s snpomatic debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc/snpomatic-dbgsym install -m0755 -d debian/.debhelper/snpomatic dh_makeshlibs -a rm -f debian/snpomatic/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/snpomatic/DEBIAN dpkg-shlibdeps -Tdebian/snpomatic.substvars debian/snpomatic/usr/bin/findknownsnps dh_installdeb install -m0755 -d debian/snpomatic/DEBIAN dh_gencontrol install -m0755 -d debian/snpomatic/DEBIAN echo misc:Depends= >> debian/snpomatic.substvars echo misc:Pre-Depends= >> debian/snpomatic.substvars install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/DEBIAN dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -cdebian/control -Pdebian/.debhelper/snpomatic/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=snpomatic-dbgsym "-DDepends=snpomatic (= \${binary:Version})" "-DDescription=debug symbols for snpomatic" -DBuild-Ids=a1edf78850cff1f6263c103eca6a119bb1448701 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/control dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -cdebian/control -Pdebian/snpomatic chmod 0644 -- debian/snpomatic/DEBIAN/control dh_md5sums install -m0755 -d debian/snpomatic/DEBIAN cd debian/snpomatic >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/snpomatic/DEBIAN/md5sums install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/DEBIAN cd debian/.debhelper/snpomatic/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/snpomatic .. dpkg-deb --root-owner-group --build debian/.debhelper/snpomatic/dbgsym-root .. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-7_amd64.deb'. dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-7_amd64.buildinfo dpkg-genchanges --build=binary -O../snpomatic_1.0-7_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/1196753 and its subdirectories I: Current time: Wed Sep 10 17:49:12 -12 2025 I: pbuilder-time-stamp: 1757569752 Thu Sep 11 05:49:12 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Sep 11 05:49:12 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Sep 11 05:50:28 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Thu Sep 11 05:50:28 UTC 2025 I: snpomatic_1.0-7_amd64.changes: Format: 1.8 Date: Sat, 23 Dec 2023 09:19:24 +0100 Source: snpomatic Binary: snpomatic snpomatic-dbgsym Architecture: amd64 Version: 1.0-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: snpomatic - fast, stringent short-read mapping software Closes: 1046157 Changes: snpomatic (1.0-7) unstable; urgency=medium . * Enable building twice in a row by cleaning antiword output. Closes: #1046157 Checksums-Sha1: 9af68006f21e00952c65489e646851efb127296a 894676 snpomatic-dbgsym_1.0-7_amd64.deb 33fe5c2cee3776acccb08e7f6d5f1d66418e4fc5 5554 snpomatic_1.0-7_amd64.buildinfo adc637744550d0f20f0c08c028760e51345b38bc 91448 snpomatic_1.0-7_amd64.deb Checksums-Sha256: aefc65a282d0105398c7eae26cea160b097231b0f6ebeadd9743b02a74038d8e 894676 snpomatic-dbgsym_1.0-7_amd64.deb 3d8146d608e76d928ad1c5a4adc414fd21eed4b298c8cb173e41209aa0f115c3 5554 snpomatic_1.0-7_amd64.buildinfo ae5584b16135d17c16f07b6c2818c773e3e325c39186c73a9e451adbc8625c4a 91448 snpomatic_1.0-7_amd64.deb Files: a1d542088b5fa3efe12722a2f81efcc1 894676 debug optional snpomatic-dbgsym_1.0-7_amd64.deb 01ab44f988241234a1d3ac07fb0433a0 5554 science optional snpomatic_1.0-7_amd64.buildinfo 1b4c264b4abb826f229ca6323c701fee 91448 science optional snpomatic_1.0-7_amd64.deb Thu Sep 11 05:50:29 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_29-54386.service; invocation ID: d4b0269a0e6949bc9fba9e29696d9840 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.nfdrNq13/snpomatic_1.0-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.nfdrNq13/snpomatic_1.0-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.nfdrNq13/snpomatic_1.0-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.nfdrNq13/b1/snpomatic_1.0-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.nfdrNq13/b2/snpomatic_1.0-7_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/SUCCESS Service runtime: 226ms CPU time consumed: 180ms Memory peak: 18.7M (swap: 0B) Thu Sep 11 05:58:30 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 11 05:58:30 UTC 2025 I: snpomatic from forky built successfully and reproducibly on amd64. Thu Sep 11 05:58:31 UTC 2025 I: Removing signed snpomatic_1.0-7_amd64.buildinfo.asc files: removed './b1/snpomatic_1.0-7_amd64.buildinfo.asc' removed './b2/snpomatic_1.0-7_amd64.buildinfo.asc'