Running as unit: rb-build-arm64_20-38595.service ==================================================================================== Wed Sep 25 23:12:50 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_20) on jenkins, called using "codethink02-arm64 codethink04-arm64" as arguments. Wed Sep 25 23:12:50 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-N3Hhkz75" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 25 23:12:50 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Wed Sep 25 23:12:50 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-m9g4X9' Wed Sep 25 23:12:51 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Sep 25 23:12:51 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-voGtBn' 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 arm64 on jenkins now. 1st build will be done on codethink02-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Wed Sep 25 23:12:57 UTC 2024 I: starting to build snpomatic/trixie/arm64 on jenkins on '2024-09-25 23:12' Wed Sep 25 23:12:57 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/38595/console.log 1727305977 arm64 trixie snpomatic Wed Sep 25 23:12:57 UTC 2024 I: Downloading source for trixie/snpomatic=1.0-7 --2024-09-25 23:12:58-- 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% 238M=0s 2024-09-25 23:12:58 (238 MB/s) - ‘snpomatic_1.0-7.dsc’ saved [1990/1990] --2024-09-25 23:12:58-- 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% 238M=0s 2024-09-25 23:12:58 (238 MB/s) - ‘snpomatic_1.0-7.dsc’ saved [1990/1990] Wed Sep 25 23:12:58 UTC 2024 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 Sep 25 23:12:58 UTC 2024 I: Checking whether the package is not for us Wed Sep 25 23:12:58 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Wed Sep 25 23:12:58 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Wed Sep 25 23:12:58 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Wed Sep 25 23:12:58 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-66IlB4' ==================================================================================== Wed Sep 25 23:13:00 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "1 snpomatic trixie /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ 1.0-7" as arguments. Wed Sep 25 23:13:00 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-2xKxdDLp" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 25 23:13:00 UTC 2024 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 (1036 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 (1036 kB/s) Download complete and in download only mode ============================================================================= Building snpomatic in trixie on arm64 on codethink02-arm64 now. Date: Thu Sep 26 00:13:00 BST 2024 Date UTC: Wed Sep 25 23:13:00 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 25 11:13:00 -12 2024 I: pbuilder-time-stamp: 1727305980 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 gpgv: Signature made Sat Dec 23 08:22:17 2023 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: no acceptable signature found dpkg-source: info: extracting snpomatic in snpomatic-1.0 dpkg-source: info: unpacking snpomatic_1.0.orig.tar.gz dpkg-source: info: unpacking snpomatic_1.0-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_ungap dpkg-source: info: applying hardening dpkg-source: info: applying build_all_binaries I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/61293/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='26c060c19f8c4cb5bd7bfc6019262e74' 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='61293' 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.jzvft1TZ/pbuilderrc_mvOW --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.jzvft1TZ/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' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/61293/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: arm64 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 ... 19895 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} libedit2{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libpipeline1{a} libruby{a} libruby3.1t64{a} libtool{a} libuchardet0{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-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx wget zip 0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 28.0 MB of archives. After unpacking 116 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-1 [1348 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 antiword arm64 0.37-16 [119 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 ruby-sdbm arm64 1.0.0-5+b4 [14.6 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2 [95.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libruby3.1t64 arm64 3.1.2-8.4 [5266 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 ruby3.1 arm64 3.1.2-8.4 [664 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libruby arm64 1:3.1+nmu1 [4664 B] Get: 26 http://deb.debian.org/debian trixie/main arm64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 ruby arm64 1:3.1+nmu1 [5584 B] Get: 28 http://deb.debian.org/debian trixie/main arm64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 41 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Fetched 28.0 MB in 0s (129 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19895 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_3.3.2-1_arm64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package antiword. Preparing to unpack .../12-antiword_0.37-16_arm64.deb ... Unpacking antiword (0.37-16) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../13-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... 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-net-telnet. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snpomatic-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snpomatic_1.0-7_source.changes dpkg-buildpackage: info: source package snpomatic dpkg-buildpackage: info: source version 1.0-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/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(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::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/TChromosome.cpp:13:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::string)': src/TChromosome.cpp:54:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::string)': src/TChromosome.cpp:95:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::string)': src/TChromosomalIndices.cpp:33:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:37:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/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/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::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/aarch64-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:478:28, 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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-aLI0LRH9 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/a2 objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.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/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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=a20d3cba6fd2c4010f1c05bbc73d05be91f518c8 -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_arm64.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-7_arm64.buildinfo dpkg-genchanges --build=binary -O../snpomatic_1.0-7_arm64.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/61293 and its subdirectories I: Current time: Wed Sep 25 11:13:33 -12 2024 I: pbuilder-time-stamp: 1727306013 Wed Sep 25 23:13:33 UTC 2024 I: Signing ./b1/snpomatic_1.0-7_arm64.buildinfo as snpomatic_1.0-7_arm64.buildinfo.asc Wed Sep 25 23:13:33 UTC 2024 I: Signed ./b1/snpomatic_1.0-7_arm64.buildinfo as ./b1/snpomatic_1.0-7_arm64.buildinfo.asc Wed Sep 25 23:13:33 UTC 2024 - build #1 for snpomatic/trixie/arm64 on codethink02-arm64 done. Starting cleanup. All cleanup done. Wed Sep 25 23:13:33 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-2xKxdDLp, removing. /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Sep 25 23:13 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 25 23:12 b2 -rw------- 1 jenkins jenkins 3100 Sep 25 23:12 rbuildlog.TRot4EI -rw-r--r-- 1 jenkins jenkins 1990 Dec 23 2023 snpomatic_1.0-7.dsc /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/b1: total 1016 -rw-r--r-- 1 jenkins jenkins 62197 Sep 25 23:13 build.log -rw-r--r-- 1 jenkins jenkins 854080 Sep 25 23:13 snpomatic-dbgsym_1.0-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 9876 Sep 25 23:13 snpomatic_1.0-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1990 Sep 25 23:13 snpomatic_1.0-7.dsc -rw-r--r-- 1 jenkins jenkins 5399 Sep 25 23:13 snpomatic_1.0-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6281 Sep 25 23:13 snpomatic_1.0-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1383 Sep 25 23:13 snpomatic_1.0-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 73844 Sep 25 23:13 snpomatic_1.0-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 1244 Sep 25 23:13 snpomatic_1.0-7_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/b2: total 0 Wed Sep 25 23:13:34 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 25 11:13:00 -12 2024 I: pbuilder-time-stamp: 1727305980 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 gpgv: Signature made Sat Dec 23 08:22:17 2023 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: no acceptable signature found dpkg-source: info: extracting snpomatic in snpomatic-1.0 dpkg-source: info: unpacking snpomatic_1.0.orig.tar.gz dpkg-source: info: unpacking snpomatic_1.0-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_ungap dpkg-source: info: applying hardening dpkg-source: info: applying build_all_binaries I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/61293/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='26c060c19f8c4cb5bd7bfc6019262e74' 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='61293' 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.jzvft1TZ/pbuilderrc_mvOW --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.jzvft1TZ/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' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/61293/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: arm64 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 ... 19895 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} libedit2{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libpipeline1{a} libruby{a} libruby3.1t64{a} libtool{a} libuchardet0{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-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx wget zip 0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 28.0 MB of archives. After unpacking 116 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-1 [1348 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 antiword arm64 0.37-16 [119 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 ruby-sdbm arm64 1.0.0-5+b4 [14.6 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2 [95.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libruby3.1t64 arm64 3.1.2-8.4 [5266 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 ruby3.1 arm64 3.1.2-8.4 [664 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libruby arm64 1:3.1+nmu1 [4664 B] Get: 26 http://deb.debian.org/debian trixie/main arm64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 ruby arm64 1:3.1+nmu1 [5584 B] Get: 28 http://deb.debian.org/debian trixie/main arm64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 41 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Fetched 28.0 MB in 0s (129 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19895 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_3.3.2-1_arm64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package antiword. Preparing to unpack .../12-antiword_0.37-16_arm64.deb ... Unpacking antiword (0.37-16) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../13-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... 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-net-telnet. Preparing to unpack .../15-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../16-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../17-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package ruby-sdbm:arm64. Preparing to unpack .../18-ruby-sdbm_1.0.0-5+b4_arm64.deb ... Unpacking ruby-sdbm:arm64 (1.0.0-5+b4) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../19-libedit2_3.1-20240808-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20240808-1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../20-libncurses6_6.5-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5-2) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../21-libyaml-0-2_0.2.5-1+b1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:arm64. Preparing to unpack .../22-libruby3.1t64_3.1.2-8.4_arm64.deb ... Unpacking libruby3.1t64:arm64 (3.1.2-8.4) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../23-ruby3.1_3.1.2-8.4_arm64.deb ... Unpacking ruby3.1 (3.1.2-8.4) ... Selecting previously unselected package libruby:arm64. Preparing to unpack .../24-libruby_1%3a3.1+nmu1_arm64.deb ... Unpacking libruby:arm64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../25-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../26-ruby_1%3a3.1+nmu1_arm64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../27-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../28-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../29-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../30-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../31-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../32-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../33-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../34-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../35-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../36-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../37-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 .../38-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../39-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../40-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../41-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../42-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../43-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../44-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../45-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snpomatic-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snpomatic_1.0-7_source.changes dpkg-buildpackage: info: source package snpomatic dpkg-buildpackage: info: source version 1.0-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/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(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::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/TChromosome.cpp:13:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::string)': src/TChromosome.cpp:54:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::string)': src/TChromosome.cpp:95:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::string)': src/TChromosomalIndices.cpp:33:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:37:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/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/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::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/aarch64-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:478:28, 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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-aLI0LRH9 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/a2 objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.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/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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=a20d3cba6fd2c4010f1c05bbc73d05be91f518c8 -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_arm64.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-7_arm64.buildinfo dpkg-genchanges --build=binary -O../snpomatic_1.0-7_arm64.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/61293 and its subdirectories I: Current time: Wed Sep 25 11:13:33 -12 2024 I: pbuilder-time-stamp: 1727306013 Wed Sep 25 23:13:35 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Wed Sep 25 23:13:35 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Wed Sep 25 23:13:35 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Sep 25 23:13:35 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-RSq8QO' ==================================================================================== Wed Sep 25 23:13:37 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 snpomatic trixie /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ 1.0-7" as arguments. Wed Sep 25 23:13:37 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-XC07rAz6" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 25 23:13:37 UTC 2024 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 (7075 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 (7075 kB/s) Download complete and in download only mode ============================================================================= Re-Building snpomatic in trixie on arm64 on codethink04-arm64 now. Date: Thu Sep 26 00:13:37 BST 2024 Date UTC: Wed Sep 25 23:13:37 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/pbuilderrc_2AiU + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${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.jzvft1TZ/pbuilderrc_2AiU --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.jzvft1TZ/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 Sep 26 13:13:37 +14 2024 I: pbuilder-time-stamp: 1727306017 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 gpgv: Signature made Sat Dec 23 08:22:17 2023 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: no acceptable signature found dpkg-source: info: extracting snpomatic in snpomatic-1.0 dpkg-source: info: unpacking snpomatic_1.0.orig.tar.gz dpkg-source: info: unpacking snpomatic_1.0-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_ungap dpkg-source: info: applying hardening dpkg-source: info: applying build_all_binaries I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/691025/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. 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 Sep 25 23:13 /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/691025/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/691025/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 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=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=c06244b7b6c446e6ad979b934d8915b8 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=691025 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.jzvft1TZ/pbuilderrc_2AiU --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.jzvft1TZ/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' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/691025/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: arm64 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 ... 19895 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} libedit2{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libpipeline1{a} libruby{a} libruby3.1t64{a} libtool{a} libuchardet0{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-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx wget zip 0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 28.0 MB of archives. After unpacking 116 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-1 [1348 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 antiword arm64 0.37-16 [119 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 ruby-sdbm arm64 1.0.0-5+b4 [14.6 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2 [95.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libruby3.1t64 arm64 3.1.2-8.4 [5266 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 ruby3.1 arm64 3.1.2-8.4 [664 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libruby arm64 1:3.1+nmu1 [4664 B] Get: 26 http://deb.debian.org/debian trixie/main arm64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 ruby arm64 1:3.1+nmu1 [5584 B] Get: 28 http://deb.debian.org/debian trixie/main arm64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 41 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Fetched 28.0 MB in 1s (40.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19895 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_3.3.2-1_arm64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package antiword. Preparing to unpack .../12-antiword_0.37-16_arm64.deb ... Unpacking antiword (0.37-16) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../13-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... 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-net-telnet. Preparing to unpack .../15-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../16-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../17-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package ruby-sdbm:arm64. Preparing to unpack .../18-ruby-sdbm_1.0.0-5+b4_arm64.deb ... Unpacking ruby-sdbm:arm64 (1.0.0-5+b4) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../19-libedit2_3.1-20240808-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20240808-1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../20-libncurses6_6.5-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5-2) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../21-libyaml-0-2_0.2.5-1+b1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:arm64. Preparing to unpack .../22-libruby3.1t64_3.1.2-8.4_arm64.deb ... Unpacking libruby3.1t64:arm64 (3.1.2-8.4) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../23-ruby3.1_3.1.2-8.4_arm64.deb ... Unpacking ruby3.1 (3.1.2-8.4) ... Selecting previously unselected package libruby:arm64. Preparing to unpack .../24-libruby_1%3a3.1+nmu1_arm64.deb ... Unpacking libruby:arm64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../25-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../26-ruby_1%3a3.1+nmu1_arm64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../27-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../28-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../29-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../30-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../31-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../32-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../33-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../34-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../35-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../36-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../37-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 .../38-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../39-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../40-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../41-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../42-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../43-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../44-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../45-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 .../46-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../47-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up libdebhelper-perl (13.20) ... Setting up libedit2:arm64 (3.1-20240808-1) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up autotools-dev (20220109.1) ... Setting up libncurses6:arm64 (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up antiword (0.37-16) ... Setting up openssl (3.3.2-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Setting up rake (13.2.1-1) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b4) ... Setting up libruby3.1t64:arm64 (3.1.2-8.4) ... Setting up libruby:arm64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.40-2) ... Processing triggers for ca-certificates (20240203) ... 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/691025/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/691025/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 arm64 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosome.cpp -o src/TChromosome.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.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++ 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.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++ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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++ 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/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/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/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::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/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::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/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/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::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/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::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/aarch64-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:478:28, 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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-PKem2lQI 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/a2 objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.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/a2/0d3cba6fd2c4010f1c05bbc73d05be91f518c8.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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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=a20d3cba6fd2c4010f1c05bbc73d05be91f518c8 -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/.debhelper/snpomatic/dbgsym-root .. dpkg-deb --root-owner-group --build debian/snpomatic .. dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-7_arm64.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-7_arm64.buildinfo dpkg-genchanges --build=binary -O../snpomatic_1.0-7_arm64.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/691025/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/691025/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/691025 and its subdirectories I: Current time: Thu Sep 26 13:15:49 +14 2024 I: pbuilder-time-stamp: 1727306149 + false + set +x Wed Sep 25 23:15:49 UTC 2024 I: Signing ./b2/snpomatic_1.0-7_arm64.buildinfo as snpomatic_1.0-7_arm64.buildinfo.asc Wed Sep 25 23:15:49 UTC 2024 I: Signed ./b2/snpomatic_1.0-7_arm64.buildinfo as ./b2/snpomatic_1.0-7_arm64.buildinfo.asc Wed Sep 25 23:15:49 UTC 2024 - build #2 for snpomatic/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Wed Sep 25 23:15:49 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-XC07rAz6, removing. /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ: total 84 drwxr-xr-x 2 jenkins jenkins 4096 Sep 25 23:13 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 25 23:15 b2 -rw------- 1 jenkins jenkins 65598 Sep 25 23:13 rbuildlog.TRot4EI -rw-r--r-- 1 jenkins jenkins 1990 Dec 23 2023 snpomatic_1.0-7.dsc /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/b1: total 1028 -rw-r--r-- 1 jenkins jenkins 62197 Sep 25 23:13 build.log -rw-r--r-- 1 jenkins jenkins 854080 Sep 25 23:13 snpomatic-dbgsym_1.0-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 9876 Sep 25 23:13 snpomatic_1.0-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1990 Sep 25 23:13 snpomatic_1.0-7.dsc -rw-r--r-- 1 jenkins jenkins 5399 Sep 25 23:13 snpomatic_1.0-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6281 Sep 25 23:13 snpomatic_1.0-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1383 Sep 25 23:13 snpomatic_1.0-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 73844 Sep 25 23:13 snpomatic_1.0-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 1244 Sep 25 23:13 snpomatic_1.0-7_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/b2: total 1016 -rw-r--r-- 1 jenkins jenkins 64139 Sep 25 23:15 build.log -rw-r--r-- 1 jenkins jenkins 854080 Sep 25 23:15 snpomatic-dbgsym_1.0-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 9876 Sep 25 23:15 snpomatic_1.0-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1990 Sep 25 23:15 snpomatic_1.0-7.dsc -rw-r--r-- 1 jenkins jenkins 5399 Sep 25 23:15 snpomatic_1.0-7_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6281 Sep 25 23:15 snpomatic_1.0-7_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1383 Sep 25 23:15 snpomatic_1.0-7_arm64.changes -rw-r--r-- 1 jenkins jenkins 73844 Sep 25 23:15 snpomatic_1.0-7_arm64.deb -rw-r--r-- 1 jenkins jenkins 1244 Sep 25 23:15 snpomatic_1.0-7_source.changes Wed Sep 25 23:15:50 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Wed Sep 25 23:15:51 UTC 2024 I: snpomatic_1.0-7_arm64.changes: Format: 1.8 Date: Sat, 23 Dec 2023 09:19:24 +0100 Source: snpomatic Binary: snpomatic snpomatic-dbgsym Architecture: arm64 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: 17de01baaf488ab39561de4a2c2b901002ed576d 854080 snpomatic-dbgsym_1.0-7_arm64.deb 5097f34398dedb5361237aab0c513af256bc265f 5399 snpomatic_1.0-7_arm64.buildinfo bcf57ec1ed9c64812d1727b0f90d438466a74d3e 73844 snpomatic_1.0-7_arm64.deb Checksums-Sha256: 8cce48265f42f8818d34bba3022b4a3d23f2e26bc17b1f10dc89920f3ad7b28c 854080 snpomatic-dbgsym_1.0-7_arm64.deb 672855ccd14cc32f754da5b3653ba35116bb6e1161f227e5d8bb5214b0d63b32 5399 snpomatic_1.0-7_arm64.buildinfo b6eba4ddff2a8a8fa57096766acef642d72625c66078a2669bf3fd76ea34f99a 73844 snpomatic_1.0-7_arm64.deb Files: 04dc22e8d50e4fc5f923ad64762eb5fe 854080 debug optional snpomatic-dbgsym_1.0-7_arm64.deb 66419463941e7a96c37c4b9ae3e0c931 5399 science optional snpomatic_1.0-7_arm64.buildinfo 61778c798749da1e1eb6b5c765dc8595 73844 science optional snpomatic_1.0-7_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/snpomatic_1.0-7.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/snpomatic_1.0-7.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/snpomatic_1.0-7.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/snpomatic_1.0-7.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/snpomatic_1.0-7_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/snpomatic_1.0-7.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-09-25 23:13:34.476702815 +0000 +++ b2/build.log 2024-09-25 23:15:50.046937099 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 25 11:13:00 -12 2024 -I: pbuilder-time-stamp: 1727305980 +I: Current time: Thu Sep 26 13:13:37 +14 2024 +I: pbuilder-time-stamp: 1727306017 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ 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/61293/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/691025/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +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 Sep 25 23:13 /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/691025/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/691025/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='arm64' - 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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='26c060c19f8c4cb5bd7bfc6019262e74' - 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='61293' - PS1='# ' - PS2='> ' + INVOCATION_ID=c06244b7b6c446e6ad979b934d8915b8 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=691025 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.jzvft1TZ/pbuilderrc_mvOW --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.jzvft1TZ/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' - http_proxy='http://192.168.101.4:3128' + 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.jzvft1TZ/pbuilderrc_2AiU --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.jzvft1TZ/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' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/61293/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/691025/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -162,7 +194,7 @@ Get: 46 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] -Fetched 28.0 MB in 0s (129 MB/s) +Fetched 28.0 MB in 1s (40.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19895 files and directories currently installed.) @@ -376,7 +408,11 @@ 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/691025/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/691025/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 @@ -431,30 +467,23 @@ 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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++ +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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.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++ +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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.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++ +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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++ -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); } @@ -462,13 +491,6 @@ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %ld -src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)': -src/TChromosomeAlign.cpp:956:98: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] - 956 | fprintf ( sqlite , "INSERT INTO chromosomes ( name , size ) VALUES ( \"%s\" , \"%d\") ;\n" , (*chrs)[a].name.c_str() , (*chrs)[a].sequence.length() ) ; - | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | int std::__cxx11::basic_string::size_type {aka long unsigned int} - | %ld src/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() ) ; @@ -476,12 +498,37 @@ | | | | 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/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/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::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/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); } @@ -512,17 +559,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | std::__cxx11::basic_string::size_type {aka long unsigned int} -src/TChromosome.cpp:13:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 13 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::string)': -src/TChromosome.cpp:54:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 54 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::string)': -src/TChromosome.cpp:95:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 95 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::string)': src/TChromosomalIndices.cpp:33:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; @@ -578,10 +614,6 @@ 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 ) ; @@ -593,6 +625,10 @@ 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/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::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 ) ; @@ -664,7 +700,7 @@ 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 -mbranch-protection=standard -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-aLI0LRH9 + rm -fr -- /tmp/dh-xdg-rundir-PKem2lQI create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/snpomatic.substvars @@ -758,8 +794,8 @@ 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 --root-owner-group --build debian/snpomatic .. dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-7_arm64.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-7_arm64.buildinfo @@ -769,12 +805,14 @@ 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/691025/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/691025/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/61293 and its subdirectories -I: Current time: Wed Sep 25 11:13:33 -12 2024 -I: pbuilder-time-stamp: 1727306013 +I: removing directory /srv/workspace/pbuilder/691025 and its subdirectories +I: Current time: Thu Sep 26 13:15:49 +14 2024 +I: pbuilder-time-stamp: 1727306149 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/snpomatic_1.0-7.diff: 82.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/snpomatic_1.0-7.diff.gz b2/build.log: 82.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.0% -- replaced with stdout Wed Sep 25 23:15:52 UTC 2024 I: diffoscope 277 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_snpomatic_trixie_arm64_1727306152 + touch /var/log/reproducible-builds/diffoscope_stamp_snpomatic_trixie_arm64_1727306152 + RESULT=0 + systemd-run '--description=diffoscope on snpomatic/1.0-7 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_20-38595 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ --run-session -c jenkins-reproducible-trixie-diffoscope-a7db18c8-d099-4b82-9093-d08c745a2121 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/dbd-tmp-hrINk8h ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/snpomatic_1.0-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/snpomatic_1.0-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/snpomatic_1.0-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/b1/snpomatic_1.0-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/b2/snpomatic_1.0-7_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_20-38595.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/snpomatic_1.0-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/snpomatic_1.0-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/snpomatic_1.0-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/b1/snpomatic_1.0-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.jzvft1TZ/b2/snpomatic_1.0-7_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.399s) 0.399s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.027s) 0.027s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 741ms CPU time consumed: 742ms _ _ ___ _ __ _ __ ___ _ __ ___ __ _| |_(_) ___ / __| '_ \| '_ \ / _ \| '_ ` _ \ / _` | __| |/ __| \__ \ | | | |_) | (_) | | | | | | (_| | |_| | (__ |___/_| |_| .__/ \___/|_| |_| |_|\__,_|\__|_|\___| |_| Wed Sep 25 23:15:53 UTC 2024 I: diffoscope 277 found no differences in the changes files, and a .buildinfo file also exists. Wed Sep 25 23:15:53 UTC 2024 I: snpomatic from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-25 23:15:53] INFO: Starting at 2024-09-25 23:15:53.983675 [2024-09-25 23:15:54] INFO: Generating the pages of 1 package(s) [2024-09-25 23:15:54] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/snpomatic didn't produce a buildlog, even though it has been built. [2024-09-25 23:15:54] INFO: Finished at 2024-09-25 23:15:54.519377, took: 0:00:00.535707 Wed Sep 25 23:15:54 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/snpomatic.html Wed Sep 25 23:15:54 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Sep 25 23:15:54 UTC 2024 I: Submitting 8.0K b1/snpomatic_1.0-7_arm64.buildinfo.asc https://buildinfo.debian.net/5097f34398dedb5361237aab0c513af256bc265f/snpomatic_1.0-7_arm64 Wed Sep 25 23:15:55 UTC 2024 I: Submitting 8.0K b2/snpomatic_1.0-7_arm64.buildinfo.asc https://buildinfo.debian.net/c48c4d829ef89b9842242048d533ca83c530b995/snpomatic_1.0-7_arm64 Wed Sep 25 23:15:56 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Sep 25 23:15:56 UTC 2024 I: Done submitting .buildinfo files. Wed Sep 25 23:15:56 UTC 2024 I: Removing signed snpomatic_1.0-7_arm64.buildinfo.asc files: removed './b1/snpomatic_1.0-7_arm64.buildinfo.asc' removed './b2/snpomatic_1.0-7_arm64.buildinfo.asc' 1727306156 arm64 trixie snpomatic Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/snpomatic_1.0-7.rbuild.log: 80.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/snpomatic_1.0-7.rbuild.log.gz [2024-09-25 23:15:56] INFO: Starting at 2024-09-25 23:15:56.526877 [2024-09-25 23:15:56] INFO: Generating the pages of 1 package(s) [2024-09-25 23:15:57] INFO: Finished at 2024-09-25 23:15:57.060295, took: 0:00:00.533427 All cleanup done. Wed Sep 25 23:15:57 UTC 2024 - total duration: 0h 3m 3s. Wed Sep 25 23:15:57 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-N3Hhkz75, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 6.624s CPU time consumed: 8.946s