Running as unit: rb-build-amd64_34-57358.service ==================================================================================== Wed Apr 23 17:51:31 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_34) on jenkins, called using "infom02-amd64 infom01-amd64" as arguments. Wed Apr 23 17:51:31 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-PIHXtMro" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Apr 23 17:51:31 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Wed Apr 23 17:51:31 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-w9CFPK' Wed Apr 23 17:51:32 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Wed Apr 23 17:51:32 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-0laOqy' ok, let's check if snpomatic is building anywhere yet… ok, snpomatic is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of snpomatic in trixie on amd64 on jenkins now. 1st build will be done on infom02-amd64.debian.net. 2nd build will be done on infom01-amd64.debian.net. ============================================================================= Wed Apr 23 17:51:43 UTC 2025 I: starting to build snpomatic/trixie/amd64 on jenkins on '2025-04-23 17:51' Wed Apr 23 17:51:43 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_34/57358/console.log 1745430703 amd64 trixie snpomatic Wed Apr 23 17:51:43 UTC 2025 I: Downloading source for trixie/snpomatic=1.0-7 --2025-04-23 17:51:44-- 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% 330M=0s 2025-04-23 17:51:44 (330 MB/s) - ‘snpomatic_1.0-7.dsc’ saved [1990/1990] --2025-04-23 17:51:44-- 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% 330M=0s 2025-04-23 17:51:44 (330 MB/s) - ‘snpomatic_1.0-7.dsc’ saved [1990/1990] Wed Apr 23 17:51:44 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----- Wed Apr 23 17:51:44 UTC 2025 I: Checking whether the package is not for us Wed Apr 23 17:51:44 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net. Wed Apr 23 17:51:44 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Wed Apr 23 17:51:44 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Wed Apr 23 17:51:44 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-rjuW6v' ==================================================================================== Wed May 27 00:14:45 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "1 snpomatic trixie /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq 1.0-7" as arguments. Wed May 27 00:14:45 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-QT6Oj8TX" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed May 27 00:14:45 UTC 2026 I: Downloading source for trixie/snpomatic=1.0-7 Reading package lists... NOTICE: 'snpomatic' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snpomatic.git Please use: git clone https://salsa.debian.org/med-team/snpomatic.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 78.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (dsc) [1990 B] Get:2 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (tar) [66.5 kB] Get:3 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (diff) [9876 B] Fetched 78.4 kB in 0s (353 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'snpomatic' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snpomatic.git Please use: git clone https://salsa.debian.org/med-team/snpomatic.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 78.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (dsc) [1990 B] Get:2 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (tar) [66.5 kB] Get:3 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (diff) [9876 B] Fetched 78.4 kB in 0s (353 kB/s) Download complete and in download only mode ============================================================================= Building snpomatic in trixie on amd64 on infom02-amd64 now. Date: Wed May 27 00:14:45 UTC 2026 Date UTC: Wed May 27 00:14:45 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue May 26 12:14:46 -12 2026 I: pbuilder-time-stamp: 1779840886 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 [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: unsupported subcommand 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/2870134/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='335686c7dd9c4ff487dec60f5a209cc9' 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='2870134' 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.9Vv3k3vq/pbuilderrc_mCth --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.9Vv3k3vq/b1 --logfile b1/build.log snpomatic_1.0-7.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 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2870134/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 ... 19840 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{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{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, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 21.2 MB of archives. After unpacking 82.2 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 openssl amd64 3.5.0-1 [1491 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 antiword amd64 0.37-16 [123 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.19 [5488 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 ruby-minitest all 5.25.4-2 [66.2 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libruby3.3 amd64 3.3.7-1 [6274 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ruby3.3 amd64 3.3.7-1 [827 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get: 28 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get: 30 http://deb.debian.org/debian trixie/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Fetched 21.2 MB in 1s (33.2 MB/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 ... 19840 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 openssl. Preparing to unpack .../01-openssl_3.5.0-1_amd64.deb ... Unpacking openssl (3.5.0-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... 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_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-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 .../08-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.41-4_amd64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package antiword. Preparing to unpack .../12-antiword_0.37-16_amd64.deb ... Unpacking antiword (0.37-16) ... 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-did-you-mean. Preparing to unpack .../15-ruby-did-you-mean_1.6.3-2_all.deb ... Unpacking ruby-did-you-mean (1.6.3-2) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../16-ruby-minitest_5.25.4-2_all.deb ... Unpacking ruby-minitest (5.25.4-2) ... 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-power-assert. Preparing to unpack .../18-ruby-power-assert_2.0.3-1_all.deb ... Unpacking ruby-power-assert (2.0.3-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../19-ruby-test-unit_3.6.2-1_all.deb ... Unpacking ruby-test-unit (3.6.2-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../20-ruby-webrick_1.9.1-1_all.deb ... Unpacking ruby-webrick (1.9.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../21-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../22-libffi8_3.4.7-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.7-1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../23-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 .../24-libruby3.3_3.3.7-1_amd64.deb ... Unpacking libruby3.3:amd64 (3.3.7-1) ... Selecting previously unselected package ruby3.3. Preparing to unpack .../25-ruby3.3_3.3.7-1_amd64.deb ... Unpacking ruby3.3 (3.3.7-1) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../26-libruby_1%3a3.3+b1_amd64.deb ... Unpacking libruby:amd64 (1:3.3+b1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../27-ruby-rubygems_3.6.7-2_all.deb ... Unpacking ruby-rubygems (3.6.7-2) ... Selecting previously unselected package ruby. Preparing to unpack .../28-ruby_1%3a3.3+b1_amd64.deb ... Unpacking ruby (1:3.3+b1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../29-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../30-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../31-m4_1.4.19-7_amd64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../32-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../33-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../34-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../35-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../36-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../37-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../38-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../39-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 .../40-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 .../41-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 .../42-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../43-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../44-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../45-libxml2_2.12.7+dfsg+really2.9.14-0.4_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../46-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../47-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 .../48-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../49-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... Setting up ruby-power-assert (2.0.3-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up ruby-minitest (5.25.4-2) ... Setting up autotools-dev (20240727.1) ... Setting up ruby-test-unit (3.6.2-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.9.1-1) ... Setting up libffi8:amd64 (3.4.7-1) ... 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 antiword (0.37-16) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up openssl (3.5.0-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up automake (1:1.17-4) ... 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 libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. 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 rubygems-integration (1.19) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Setting up rake (13.2.1-1) ... Setting up libruby3.3:amd64 (3.3.7-1) ... Setting up ruby-rubygems (3.6.7-2) ... Setting up ruby3.3 (3.3.7-1) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.41-7) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/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 -j12 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 -j12 "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 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++ 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/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/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: 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/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/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/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/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/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/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/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/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/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/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::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/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/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/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/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 ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from src/snpomatic.h:13, from src/TChromosomeAlign.cpp:1: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const TPositionWithIndex; _Up = TPositionWithIndex; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const TPositionWithIndex*; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const TPositionWithIndex*; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*; _Tp = TPositionWithIndex]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, inlined from 'void TChromosomeAlign::run_wobble(const std::string&, const std::string&, const std::string&, const std::string&, const pwi_vector&, const pwi_vector&, uint)' at src/TChromosomeAlign.cpp:337:50: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 17 and 9223372036854775807 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = TPositionWithIndex]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = TPositionWithIndex]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:603:61, inlined from 'void TChromosomeAlign::run_wobble(const std::string&, const std::string&, const std::string&, const std::string&, const pwi_vector&, const pwi_vector&, uint)' at src/TChromosomeAlign.cpp:337:50: /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 16 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ 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-250RnVfU 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/86 objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/86/17019d7f244e102adceeb95eba7e593829f027.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/86/17019d7f244e102adceeb95eba7e593829f027.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/86/17019d7f244e102adceeb95eba7e593829f027.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=8617019d7f244e102adceeb95eba7e593829f027 -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' in '../snpomatic_1.0-7_amd64.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_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/2870134 and its subdirectories I: Current time: Tue May 26 12:15:32 -12 2026 I: pbuilder-time-stamp: 1779840932 Wed May 27 00:15:32 UTC 2026 I: Signing ./b1/snpomatic_1.0-7_amd64.buildinfo as snpomatic_1.0-7_amd64.buildinfo.asc Wed May 27 00:15:32 UTC 2026 I: Signed ./b1/snpomatic_1.0-7_amd64.buildinfo as ./b1/snpomatic_1.0-7_amd64.buildinfo.asc Wed May 27 00:15:32 UTC 2026 - build #1 for snpomatic/trixie/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Wed May 27 00:15:32 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-QT6Oj8TX, removing. /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 17:52 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 17:51 b2 -rw------- 1 jenkins jenkins 3092 Apr 23 17:51 rbuildlog.NsdKF47 -rw-r--r-- 1 jenkins jenkins 1990 Dec 23 2023 snpomatic_1.0-7.dsc /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b1: total 1060 -rw-r--r-- 1 jenkins jenkins 62122 Apr 23 17:52 build.log -rw-r--r-- 1 jenkins jenkins 885972 Apr 23 17:52 snpomatic-dbgsym_1.0-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 9876 Apr 23 17:52 snpomatic_1.0-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1990 Apr 23 17:52 snpomatic_1.0-7.dsc -rw-r--r-- 1 jenkins jenkins 5424 Apr 23 17:52 snpomatic_1.0-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6306 Apr 23 17:52 snpomatic_1.0-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1383 Apr 23 17:52 snpomatic_1.0-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 86564 Apr 23 17:52 snpomatic_1.0-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 1244 Apr 23 17:52 snpomatic_1.0-7_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b2: total 0 Wed Apr 23 17:52:33 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 26 12:14:46 -12 2026 I: pbuilder-time-stamp: 1779840886 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 [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: unsupported subcommand 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/2870134/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='335686c7dd9c4ff487dec60f5a209cc9' 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='2870134' 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.9Vv3k3vq/pbuilderrc_mCth --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.9Vv3k3vq/b1 --logfile b1/build.log snpomatic_1.0-7.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 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2870134/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 ... 19840 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{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{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, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 21.2 MB of archives. After unpacking 82.2 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 openssl amd64 3.5.0-1 [1491 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 antiword amd64 0.37-16 [123 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.19 [5488 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 ruby-minitest all 5.25.4-2 [66.2 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libruby3.3 amd64 3.3.7-1 [6274 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ruby3.3 amd64 3.3.7-1 [827 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get: 28 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get: 30 http://deb.debian.org/debian trixie/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Fetched 21.2 MB in 1s (33.2 MB/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 ... 19840 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 openssl. Preparing to unpack .../01-openssl_3.5.0-1_amd64.deb ... Unpacking openssl (3.5.0-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... 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_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-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 .../08-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.41-4_amd64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package antiword. Preparing to unpack .../12-antiword_0.37-16_amd64.deb ... Unpacking antiword (0.37-16) ... 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-did-you-mean. Preparing to unpack .../15-ruby-did-you-mean_1.6.3-2_all.deb ... Unpacking ruby-did-you-mean (1.6.3-2) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../16-ruby-minitest_5.25.4-2_all.deb ... Unpacking ruby-minitest (5.25.4-2) ... 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-power-assert. Preparing to unpack .../18-ruby-power-assert_2.0.3-1_all.deb ... Unpacking ruby-power-assert (2.0.3-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../19-ruby-test-unit_3.6.2-1_all.deb ... Unpacking ruby-test-unit (3.6.2-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../20-ruby-webrick_1.9.1-1_all.deb ... Unpacking ruby-webrick (1.9.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../21-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../22-libffi8_3.4.7-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.7-1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../23-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 .../24-libruby3.3_3.3.7-1_amd64.deb ... Unpacking libruby3.3:amd64 (3.3.7-1) ... Selecting previously unselected package ruby3.3. Preparing to unpack .../25-ruby3.3_3.3.7-1_amd64.deb ... Unpacking ruby3.3 (3.3.7-1) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../26-libruby_1%3a3.3+b1_amd64.deb ... Unpacking libruby:amd64 (1:3.3+b1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../27-ruby-rubygems_3.6.7-2_all.deb ... Unpacking ruby-rubygems (3.6.7-2) ... Selecting previously unselected package ruby. Preparing to unpack .../28-ruby_1%3a3.3+b1_amd64.deb ... Unpacking ruby (1:3.3+b1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../29-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../30-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../31-m4_1.4.19-7_amd64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../32-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../33-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../34-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../35-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../36-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../37-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../38-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../39-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 .../40-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 .../41-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 .../42-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../43-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../44-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../45-libxml2_2.12.7+dfsg+really2.9.14-0.4_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../46-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../47-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 .../48-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../49-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... Setting up ruby-power-assert (2.0.3-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up ruby-minitest (5.25.4-2) ... Setting up autotools-dev (20240727.1) ... Setting up ruby-test-unit (3.6.2-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.9.1-1) ... Setting up libffi8:amd64 (3.4.7-1) ... 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 antiword (0.37-16) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up openssl (3.5.0-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up automake (1:1.17-4) ... 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 libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. 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 rubygems-integration (1.19) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Setting up rake (13.2.1-1) ... Setting up libruby3.3:amd64 (3.3.7-1) ... Setting up ruby-rubygems (3.6.7-2) ... Setting up ruby3.3 (3.3.7-1) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.41-7) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/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 -j12 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 -j12 "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 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++ 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/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/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: 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/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/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/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/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/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/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/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/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/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/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::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/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/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/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/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 ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from src/snpomatic.h:13, from src/TChromosomeAlign.cpp:1: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const TPositionWithIndex; _Up = TPositionWithIndex; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const TPositionWithIndex*; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const TPositionWithIndex*; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*; _Tp = TPositionWithIndex]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, inlined from 'void TChromosomeAlign::run_wobble(const std::string&, const std::string&, const std::string&, const std::string&, const pwi_vector&, const pwi_vector&, uint)' at src/TChromosomeAlign.cpp:337:50: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 17 and 9223372036854775807 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = TPositionWithIndex]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = TPositionWithIndex]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:603:61, inlined from 'void TChromosomeAlign::run_wobble(const std::string&, const std::string&, const std::string&, const std::string&, const pwi_vector&, const pwi_vector&, uint)' at src/TChromosomeAlign.cpp:337:50: /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 16 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ 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-250RnVfU 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/86 objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/86/17019d7f244e102adceeb95eba7e593829f027.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/86/17019d7f244e102adceeb95eba7e593829f027.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/86/17019d7f244e102adceeb95eba7e593829f027.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=8617019d7f244e102adceeb95eba7e593829f027 -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' in '../snpomatic_1.0-7_amd64.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_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/2870134 and its subdirectories I: Current time: Tue May 26 12:15:32 -12 2026 I: pbuilder-time-stamp: 1779840932 Wed Apr 23 17:52:33 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Wed Apr 23 17:52:33 UTC 2025 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Wed Apr 23 17:52:33 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Wed Apr 23 17:52:33 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-hbejUM' ==================================================================================== Wed Apr 23 17:52:34 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "2 snpomatic trixie /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq 1.0-7" as arguments. Wed Apr 23 17:52:34 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-UqwQTtzU" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Apr 23 17:52:34 UTC 2025 I: Downloading source for trixie/snpomatic=1.0-7 Reading package lists... NOTICE: 'snpomatic' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snpomatic.git Please use: git clone https://salsa.debian.org/med-team/snpomatic.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 78.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (dsc) [1990 B] Get:2 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (tar) [66.5 kB] Get:3 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (diff) [9876 B] Fetched 78.4 kB in 0s (1643 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'snpomatic' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snpomatic.git Please use: git clone https://salsa.debian.org/med-team/snpomatic.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 78.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (dsc) [1990 B] Get:2 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (tar) [66.5 kB] Get:3 http://deb.debian.org/debian trixie/main snpomatic 1.0-7 (diff) [9876 B] Fetched 78.4 kB in 0s (1643 kB/s) Download complete and in download only mode ============================================================================= Re-Building snpomatic in trixie on amd64 on infom01-amd64 now. Date: Wed Apr 23 17:52:35 UTC 2025 Date UTC: Wed Apr 23 17:52:35 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/pbuilderrc_agij + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' snpomatic = debian-installer -o snpomatic = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' snpomatic = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/pbuilderrc_agij --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b2 --logfile b2/build.log snpomatic_1.0-7.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 24 07:52:35 +14 2025 I: pbuilder-time-stamp: 1745430755 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 [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: unsupported subcommand 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/201909/tmp/hooks/D01_modify_environment starting debug: Running on infom01-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 23 17:52 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/201909/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/201909/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=7a213a672e5f490fa22fe1591802b4c4 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=201909 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/pbuilderrc_agij --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b2 --logfile b2/build.log snpomatic_1.0-7.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-33-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.133-1 (2025-04-10) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/201909/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 ... 19840 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{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{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, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 21.2 MB of archives. After unpacking 82.2 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 openssl amd64 3.5.0-1 [1491 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 antiword amd64 0.37-16 [123 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.19 [5488 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 ruby-minitest all 5.25.4-2 [66.2 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libruby3.3 amd64 3.3.7-1 [6274 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ruby3.3 amd64 3.3.7-1 [827 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get: 28 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get: 30 http://deb.debian.org/debian trixie/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Fetched 21.2 MB in 1s (23.5 MB/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 ... 19840 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 openssl. Preparing to unpack .../01-openssl_3.5.0-1_amd64.deb ... Unpacking openssl (3.5.0-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... 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_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-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 .../08-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.41-4_amd64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package antiword. Preparing to unpack .../12-antiword_0.37-16_amd64.deb ... Unpacking antiword (0.37-16) ... 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-did-you-mean. Preparing to unpack .../15-ruby-did-you-mean_1.6.3-2_all.deb ... Unpacking ruby-did-you-mean (1.6.3-2) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../16-ruby-minitest_5.25.4-2_all.deb ... Unpacking ruby-minitest (5.25.4-2) ... 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-power-assert. Preparing to unpack .../18-ruby-power-assert_2.0.3-1_all.deb ... Unpacking ruby-power-assert (2.0.3-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../19-ruby-test-unit_3.6.2-1_all.deb ... Unpacking ruby-test-unit (3.6.2-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../20-ruby-webrick_1.9.1-1_all.deb ... Unpacking ruby-webrick (1.9.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../21-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../22-libffi8_3.4.7-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.7-1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../23-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 .../24-libruby3.3_3.3.7-1_amd64.deb ... Unpacking libruby3.3:amd64 (3.3.7-1) ... Selecting previously unselected package ruby3.3. Preparing to unpack .../25-ruby3.3_3.3.7-1_amd64.deb ... Unpacking ruby3.3 (3.3.7-1) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../26-libruby_1%3a3.3+b1_amd64.deb ... Unpacking libruby:amd64 (1:3.3+b1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../27-ruby-rubygems_3.6.7-2_all.deb ... Unpacking ruby-rubygems (3.6.7-2) ... Selecting previously unselected package ruby. Preparing to unpack .../28-ruby_1%3a3.3+b1_amd64.deb ... Unpacking ruby (1:3.3+b1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../29-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../30-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../31-m4_1.4.19-7_amd64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../32-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../33-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../34-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../35-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../36-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../37-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../38-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../39-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 .../40-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 .../41-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 .../42-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../43-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../44-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../45-libxml2_2.12.7+dfsg+really2.9.14-0.4_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../46-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../47-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 .../48-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../49-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... Setting up ruby-power-assert (2.0.3-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up ruby-minitest (5.25.4-2) ... Setting up autotools-dev (20240727.1) ... Setting up ruby-test-unit (3.6.2-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.9.1-1) ... Setting up libffi8:amd64 (3.4.7-1) ... 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 antiword (0.37-16) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up openssl (3.5.0-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up automake (1:1.17-4) ... 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 libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. 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 rubygems-integration (1.19) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Setting up rake (13.2.1-1) ... Setting up libruby3.3:amd64 (3.3.7-1) ... Setting up ruby-rubygems (3.6.7-2) ... Setting up ruby3.3 (3.3.7-1) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.41-7) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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: user script /srv/workspace/pbuilder/201909/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/201909/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/snpomatic-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 -j12 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 -j12 "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 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++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 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/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/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/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/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::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/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::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/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/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/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::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/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 ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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/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/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 ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from src/snpomatic.h:13, from src/TChromosomeAlign.cpp:1: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const TPositionWithIndex; _Up = TPositionWithIndex; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const TPositionWithIndex*; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const TPositionWithIndex*; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = TPositionWithIndex*; _Tp = TPositionWithIndex]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, inlined from 'void TChromosomeAlign::run_wobble(const std::string&, const std::string&, const std::string&, const std::string&, const pwi_vector&, const pwi_vector&, uint)' at src/TChromosomeAlign.cpp:337:50: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 17 and 9223372036854775807 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = TPositionWithIndex]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = TPositionWithIndex]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:603:61, inlined from 'void TChromosomeAlign::run_wobble(const std::string&, const std::string&, const std::string&, const std::string&, const pwi_vector&, const pwi_vector&, uint)' at src/TChromosomeAlign.cpp:337:50: /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 16 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ 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-ULKQ1mpQ 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/86 objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/86/17019d7f244e102adceeb95eba7e593829f027.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/86/17019d7f244e102adceeb95eba7e593829f027.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/86/17019d7f244e102adceeb95eba7e593829f027.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=8617019d7f244e102adceeb95eba7e593829f027 -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' in '../snpomatic_1.0-7_amd64.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_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: user script /srv/workspace/pbuilder/201909/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/201909/tmp/hooks/B01_cleanup finished 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/201909 and its subdirectories I: Current time: Thu Apr 24 07:54:19 +14 2025 I: pbuilder-time-stamp: 1745430859 + false + set +x Wed Apr 23 17:54:19 UTC 2025 I: Signing ./b2/snpomatic_1.0-7_amd64.buildinfo as snpomatic_1.0-7_amd64.buildinfo.asc Wed Apr 23 17:54:19 UTC 2025 I: Signed ./b2/snpomatic_1.0-7_amd64.buildinfo as ./b2/snpomatic_1.0-7_amd64.buildinfo.asc Wed Apr 23 17:54:19 UTC 2025 - build #2 for snpomatic/trixie/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Wed Apr 23 17:54:19 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-UqwQTtzU, removing. /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq: total 80 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 17:52 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 17:54 b2 -rw------- 1 jenkins jenkins 65503 Apr 23 17:52 rbuildlog.NsdKF47 -rw-r--r-- 1 jenkins jenkins 1990 Dec 23 2023 snpomatic_1.0-7.dsc /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b1: total 1072 -rw-r--r-- 1 jenkins jenkins 62122 Apr 23 17:52 build.log -rw-r--r-- 1 jenkins jenkins 885972 Apr 23 17:52 snpomatic-dbgsym_1.0-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 9876 Apr 23 17:52 snpomatic_1.0-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1990 Apr 23 17:52 snpomatic_1.0-7.dsc -rw-r--r-- 1 jenkins jenkins 5424 Apr 23 17:52 snpomatic_1.0-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6306 Apr 23 17:52 snpomatic_1.0-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1383 Apr 23 17:52 snpomatic_1.0-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 86564 Apr 23 17:52 snpomatic_1.0-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 1244 Apr 23 17:52 snpomatic_1.0-7_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b2: total 1060 -rw-r--r-- 1 jenkins jenkins 64039 Apr 23 17:54 build.log -rw-r--r-- 1 jenkins jenkins 885972 Apr 23 17:54 snpomatic-dbgsym_1.0-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 9876 Apr 23 17:54 snpomatic_1.0-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1990 Apr 23 17:54 snpomatic_1.0-7.dsc -rw-r--r-- 1 jenkins jenkins 5419 Apr 23 17:54 snpomatic_1.0-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6301 Apr 23 17:54 snpomatic_1.0-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1383 Apr 23 17:54 snpomatic_1.0-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 86564 Apr 23 17:54 snpomatic_1.0-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 1244 Apr 23 17:54 snpomatic_1.0-7_source.changes Wed Apr 23 17:54:19 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. Wed Apr 23 17:54:20 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: 6fb1630b574045843a027f1629ce0246d6a4462e 885972 snpomatic-dbgsym_1.0-7_amd64.deb e55ca8be34973ed1c224fcd8504536c1d3ff1ad3 5424 snpomatic_1.0-7_amd64.buildinfo 502a48c5d77f718e0b4bc89eb9b2e0cf62f35658 86564 snpomatic_1.0-7_amd64.deb Checksums-Sha256: 1ea63ef5759c396a47bb14c3ff5db6327694c14996e46d8decad22d5b253efcd 885972 snpomatic-dbgsym_1.0-7_amd64.deb 50e9d940e66a05d471d7ca93742bd495ce55fd125406ef35b77bce107e8042f2 5424 snpomatic_1.0-7_amd64.buildinfo 8b642396d638fb2f88ad9ce90d9a7a71668fefb2ec74a8e31f6804ea22fddcf3 86564 snpomatic_1.0-7_amd64.deb Files: 07199b44fcb7d9d8ad4f2571bd093ab8 885972 debug optional snpomatic-dbgsym_1.0-7_amd64.deb bcb8efac3726f04c5970447863dfd6c7 5424 science optional snpomatic_1.0-7_amd64.buildinfo 0923562f70d94dd29ef8bfd962c6362c 86564 science optional snpomatic_1.0-7_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snpomatic_1.0-7.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snpomatic_1.0-7.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/snpomatic_1.0-7.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/snpomatic_1.0-7.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/snpomatic_1.0-7_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snpomatic_1.0-7.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-04-23 17:52:32.934731669 +0000 +++ b2/build.log 2025-04-23 17:54:19.720452935 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 26 12:14:46 -12 2026 -I: pbuilder-time-stamp: 1779840886 +I: Current time: Thu Apr 24 07:52:35 +14 2025 +I: pbuilder-time-stamp: 1745430755 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,51 +26,83 @@ 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/2870134/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/201909/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 23 17:52 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/201909/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/201909/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='335686c7dd9c4ff487dec60f5a209cc9' - 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='2870134' - PS1='# ' - PS2='> ' + INVOCATION_ID=7a213a672e5f490fa22fe1591802b4c4 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=201909 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.9Vv3k3vq/pbuilderrc_mCth --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.9Vv3k3vq/b1 --logfile b1/build.log snpomatic_1.0-7.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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/pbuilderrc_agij --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b2 --logfile b2/build.log snpomatic_1.0-7.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-33-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.133-1 (2025-04-10) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2870134/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/201909/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -160,7 +192,7 @@ Get: 48 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] -Fetched 21.2 MB in 1s (33.2 MB/s) +Fetched 21.2 MB in 1s (23.5 MB/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 ... 19840 files and directories currently installed.) @@ -382,7 +414,11 @@ 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 +I: user script /srv/workspace/pbuilder/201909/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/201909/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpomatic-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -454,13 +490,6 @@ 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/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); } @@ -468,6 +497,13 @@ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %ld +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() ) ; @@ -481,20 +517,13 @@ | | | | int std::vector::size_type {aka long unsigned int} | %ld -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/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::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/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 ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -506,6 +535,31 @@ 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/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/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::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/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::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" , @@ -529,16 +583,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | std::__cxx11::basic_string::size_type {aka long unsigned int} -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/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/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 ) ; @@ -550,14 +594,6 @@ 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/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/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/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 @@ -584,6 +620,10 @@ 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/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 ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ) ; @@ -625,10 +665,6 @@ 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 ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -670,7 +706,7 @@ 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-250RnVfU + rm -fr -- /tmp/dh-xdg-rundir-ULKQ1mpQ create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/snpomatic.substvars @@ -771,12 +807,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/201909/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/201909/tmp/hooks/B01_cleanup finished 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/2870134 and its subdirectories -I: Current time: Tue May 26 12:15:32 -12 2026 -I: pbuilder-time-stamp: 1779840932 +I: removing directory /srv/workspace/pbuilder/201909 and its subdirectories +I: Current time: Thu Apr 24 07:54:19 +14 2025 +I: pbuilder-time-stamp: 1745430859 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snpomatic_1.0-7.diff: 80.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snpomatic_1.0-7.diff.gz b2/build.log: 82.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.2% -- replaced with stdout Wed Apr 23 17:54:21 UTC 2025 I: diffoscope 294 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_snpomatic_trixie_amd64_1745430861 + touch /var/log/reproducible-builds/diffoscope_stamp_snpomatic_trixie_amd64_1745430861 + RESULT=0 + systemd-run '--description=diffoscope on snpomatic/1.0-7 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_34-57358 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq --run-session -c jenkins-reproducible-trixie-diffoscope-f1ed6b12-9b24-4017-a5b4-4c05d7e1f1be -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/dbd-tmp-lSeohLT ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/snpomatic_1.0-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/snpomatic_1.0-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/snpomatic_1.0-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b1/snpomatic_1.0-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b2/snpomatic_1.0-7_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_34-57358.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/snpomatic_1.0-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/snpomatic_1.0-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/snpomatic_1.0-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/b1/snpomatic_1.0-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.9Vv3k3vq/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 Service runtime: 218ms CPU time consumed: 219ms _ _ ___ _ __ _ __ ___ _ __ ___ __ _| |_(_) ___ / __| '_ \| '_ \ / _ \| '_ ` _ \ / _` | __| |/ __| \__ \ | | | |_) | (_) | | | | | | (_| | |_| | (__ |___/_| |_| .__/ \___/|_| |_| |_|\__,_|\__|_|\___| |_| Wed Apr 23 17:54:21 UTC 2025 I: diffoscope 294 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 23 17:54:21 UTC 2025 I: snpomatic from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-04-23 17:54:22] INFO: Starting at 2025-04-23 17:54:22.396569 [2025-04-23 17:54:22] INFO: Generating the pages of 1 package(s) [2025-04-23 17:54:22] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/snpomatic didn't produce a buildlog, even though it has been built. [2025-04-23 17:54:22] INFO: Finished at 2025-04-23 17:54:22.849832, took: 0:00:00.453267 Wed Apr 23 17:54:22 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/snpomatic.html Wed Apr 23 17:54:22 UTC 2025 I: Submitting .buildinfo files to external archives: Wed Apr 23 17:54:22 UTC 2025 I: Submitting 8.0K b1/snpomatic_1.0-7_amd64.buildinfo.asc https://buildinfo.debian.net/e55ca8be34973ed1c224fcd8504536c1d3ff1ad3/snpomatic_1.0-7_amd64 Wed Apr 23 17:54:45 UTC 2025 I: Submitting 8.0K b2/snpomatic_1.0-7_amd64.buildinfo.asc https://buildinfo.debian.net/f4d12705a38956033c373b24561a8719cc81db10/snpomatic_1.0-7_amd64 Wed Apr 23 17:55:06 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 23 17:55:06 UTC 2025 I: Done submitting .buildinfo files. Wed Apr 23 17:55:06 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' 1745430906 amd64 trixie snpomatic Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snpomatic_1.0-7.rbuild.log: 80.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snpomatic_1.0-7.rbuild.log.gz [2025-04-23 17:55:06] INFO: Starting at 2025-04-23 17:55:06.971231 [2025-04-23 17:55:07] INFO: Generating the pages of 1 package(s) [2025-04-23 17:55:07] INFO: Finished at 2025-04-23 17:55:07.391329, took: 0:00:00.420107 All cleanup done. Wed Apr 23 17:55:07 UTC 2025 - total duration: 0h 2m 50s. Wed Apr 23 17:55:07 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-PIHXtMro, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 35.771s CPU time consumed: 6.893s