Running as unit: rb-build-amd64_23-51685.service ==================================================================================== Wed Apr 2 21:39:01 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_23) on jenkins, called using "ionos11-amd64 ionos15-amd64" as arguments. Wed Apr 2 21:39:02 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-WSGYVqW5" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Apr 2 21:39:02 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Wed Apr 2 21:39:02 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-obq8si' Wed Apr 2 21:39:02 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Apr 2 21:39:02 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-lvGrWJ' ok, let's check if igor is building anywhere yet… ok, igor is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of igor in trixie on amd64 on jenkins now. 1st build will be done on ionos11-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Wed Apr 2 21:39:26 UTC 2025 I: starting to build igor/trixie/amd64 on jenkins on '2025-04-02 21:39' Wed Apr 2 21:39:26 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/51685/console.log 1743629966 amd64 trixie igor Wed Apr 2 21:39:26 UTC 2025 I: Downloading source for trixie/igor=1.4.0+dfsg-5 --2025-04-02 21:39:26-- http://deb.debian.org/debian/pool/main/i/igor/igor_1.4.0%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2021 (2.0K) [text/prs.lines.tag] Saving to: ‘igor_1.4.0+dfsg-5.dsc’ 0K . 100% 340M=0s 2025-04-02 21:39:26 (340 MB/s) - ‘igor_1.4.0+dfsg-5.dsc’ saved [2021/2021] --2025-04-02 21:39:26-- http://deb.debian.org/debian/pool/main/i/igor/igor_1.4.0%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2021 (2.0K) [text/prs.lines.tag] Saving to: ‘igor_1.4.0+dfsg-5.dsc’ 0K . 100% 340M=0s 2025-04-02 21:39:26 (340 MB/s) - ‘igor_1.4.0+dfsg-5.dsc’ saved [2021/2021] Wed Apr 2 21:39:26 UTC 2025 I: igor_1.4.0+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: igor Binary: igor Architecture: any Version: 1.4.0+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/qmarcou/IGoR/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/igor Vcs-Git: https://salsa.debian.org/med-team/igor.git Testsuite: autopkgtest Testsuite-Triggers: build-essential Build-Depends: debhelper-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev | libblas.so Package-List: igor deb science optional arch=any Checksums-Sha1: 6d4cc77c4c4a6ecdf75a5c1eee86f1e8bc1c62eb 1001484 igor_1.4.0+dfsg.orig.tar.xz 742f19816a9a4f2cc63de2984fee4d24abd3b535 5324 igor_1.4.0+dfsg-5.debian.tar.xz Checksums-Sha256: eebf01e469bdcc5147d50b355d5c7890e6f4b6254596078a051f5db57cdc9449 1001484 igor_1.4.0+dfsg.orig.tar.xz 072d3461aa8e8204ce0b60f366fcaff57368ea432e46b5e7ab32e4650f857c43 5324 igor_1.4.0+dfsg-5.debian.tar.xz Files: 272f7e96c7aadd4791679d31dadf0f6f 1001484 igor_1.4.0+dfsg.orig.tar.xz d6bdbfb54dd5060fe83636bcdd72ca38 5324 igor_1.4.0+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEESjHbWh7kCWyHOZiAkDZJKUwz+bcFAmX0hQgACgkQkDZJKUwz +bdYgw//UMx9Sel3wK0560PuntnmGO1B5aCBD0TA7OMD0YPOInjJUkmSRHzI23i6 Nac78a/UaI4KkZb1g20r900eJGH9ALqcz8dPBbq9DFRA1xg+gbSP1iwfA2tQa7Tb f6q6XoLNMk4MJxTwBBId3GzxTSRsNnV3lzi2qtM734ouJaI8oduKm3JtblllYBys pDe+i0cGPnf23Q+wfvMQsZyfm3UgoLbb8UQHa2B7T/Vloau2y0rS+EguLXlMHaeF qsxr5T+PVBKWmVnTB7pkP7pCYrzoK+zL2V9FT/OogHE5B6xx0h12ZX6e0QB/PcYA LdJrkW8H1b+CfpNErlcG9eccv8aAzWR5ZllN4gIGROz3wp5/o3nlGdUrdXQtktBv u7EIFSuF3AW7YOtqwxMnkXRn4lSmSUt/HzIGBBOJu8OK35hehhEuAo3OAODsfqEE Lu9DbWV9qg/BGYFp/hvT4JOZHtAz73WuI36S9kUBtaXqkcxiRaOoAMjLM9sH+ir5 Kc7rA9OCbPfCs5WJ7Pb0Ppx7hc6GmAt0gnKh0ogSGGODCgytbErsWDDyIBjAbuOX OP6oyCY5/2GegdaAhWmqz9R/XzM83+5t1fyxCwP5yAc4nsf6J8kgoz9xCrvgz6Pw dj9B84QidRMuxh6hXFSkKY0gzGloW93uSehu808i+2fKRRFJ0zI= =/qci -----END PGP SIGNATURE----- Wed Apr 2 21:39:26 UTC 2025 I: Checking whether the package is not for us Wed Apr 2 21:39:26 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed Apr 2 21:39:26 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed Apr 2 21:39:26 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Wed Apr 2 21:39:26 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-ZjOUN3' ==================================================================================== Wed Apr 2 21:39:27 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "1 igor trixie /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq 1.4.0+dfsg-5" as arguments. Wed Apr 2 21:39:27 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-FlNzEvdX" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Apr 2 21:39:27 UTC 2025 I: Downloading source for trixie/igor=1.4.0+dfsg-5 Reading package lists... NOTICE: 'igor' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/igor.git Please use: git clone https://salsa.debian.org/med-team/igor.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1009 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (dsc) [2021 B] Get:2 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (tar) [1001 kB] Get:3 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (diff) [5324 B] Fetched 1009 kB in 0s (16.3 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'igor' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/igor.git Please use: git clone https://salsa.debian.org/med-team/igor.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1009 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (dsc) [2021 B] Get:2 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (tar) [1001 kB] Get:3 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (diff) [5324 B] Fetched 1009 kB in 0s (16.3 MB/s) Download complete and in download only mode ============================================================================= Building igor in trixie on amd64 on ionos11-amd64 now. Date: Wed Apr 2 21:39:28 UTC 2025 Date UTC: Wed Apr 2 21:39:28 UTC 2025 ============================================================================= 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 Apr 2 09:39:28 -12 2025 I: pbuilder-time-stamp: 1743629968 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 [igor_1.4.0+dfsg-5.dsc] I: copying [./igor_1.4.0+dfsg.orig.tar.xz] I: copying [./igor_1.4.0+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./igor_1.4.0+dfsg-5.dsc: unsupported subcommand dpkg-source: info: extracting igor in igor-1.4.0+dfsg dpkg-source: info: unpacking igor_1.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking igor_1.4.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying get_autoreconf_to_work.patch dpkg-source: info: applying inline_fix.patch dpkg-source: info: applying fix-gcc-10.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2238615/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='08994d864057437ca1cbc23cd62e3c3d' 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='2238615' 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.eIbAD7Nq/pbuilderrc_6e0H --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.eIbAD7Nq/b1 --logfile b1/build.log igor_1.4.0+dfsg-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2238615/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev | libblas.so dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19805 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 libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however: Package libblas-dev is not installed. Package libblas.so is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libjemalloc-dev{a} libjemalloc2{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 14.6 MB of archives. After unpacking 58.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB] Fetched 14.6 MB in 5s (2683 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19805 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-5_amd64.deb ... Unpacking bsdextrautils (2.40.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-7_amd64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/igor-1.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../igor_1.4.0+dfsg-5_source.changes dpkg-buildpackage: info: source package igor dpkg-buildpackage: info: source version 1.4.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_auto_clean rm -rf docs/latex rm -rf docs/html rm -rf config.guess config.sub make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:14: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:7: installing './install-sh' configure.ac:7: installing './missing' igor_src/Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking whether g++ supports C++11 features by default... yes checking for g++ option to support OpenMP... -fopenmp checking for _Bool... no checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for size_t... yes checking for pow... yes checking for sqrt... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating igor_src/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in igor_src (/build/reproducible-path/igor-1.4.0+dfsg/igor_src) configure: WARNING: no configuration information is in igor_src dh_auto_build make -j20 make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making all in igor_src make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Bestscenarioscounter.o `test -f 'Bestscenarioscounter.cpp' || echo './'`Bestscenarioscounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-CDR3SeqData.o `test -f 'CDR3SeqData.cpp' || echo './'`CDR3SeqData.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Counter.o `test -f 'Counter.cpp' || echo './'`Counter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Coverageerrcounter.o `test -f 'Coverageerrcounter.cpp' || echo './'`Coverageerrcounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp Deletion.cpp:1590:44: warning: multi-character character constant [-Wmultichar] 1590 | else if ((*iter)=='14'){ | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Genechoice.cpp:908:94: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class); | ^~~~~~~~~~~ Genechoice.cpp:908:94: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Genechoice.h:29, from Genechoice.cpp:26: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Deletion.cpp:909:98: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used | ^~~~~~~~~~ Deletion.cpp:909:98: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Deletion.h:29, from Deletion.cpp:26: Utils.h:69:13: note: candidate 2: 'std::string operator+(const std::string&, Seq_side)' 69 | std::string operator+(const std::string& , Seq_side ); | ^~~~~~~~ Deletion.cpp:1173:88: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class); | ^~~~~~~~~~~ Deletion.cpp:1173:88: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Insertion.cpp: In member function 'virtual void Insertion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Insertion.cpp:244:93: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 244 | throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class); | ^~~~~~~~~~~ Insertion.cpp:244:93: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Insertion.h:30, from Insertion.cpp:27: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Dinuclmarkov.cpp:147:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 147 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:147:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Dinuclmarkov.h:32, from Dinuclmarkov.cpp:26: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual std::queue Dinucl_markov::draw_random_realization(const Marginal_array_p&, std::unordered_map, int>&, const std::unordered_map, std::vector, int> > >&, std::unordered_map >&, std::mt19937_64&) const': Dinuclmarkov.cpp:211:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 211 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:211:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate_initialize_Len_proba(Seq_type, std::map&, std::queue >&, double&, const Marginal_array_p&, Index_map&, Seq_type_str_p_map&, int&) const': Dinuclmarkov.cpp:565:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 565 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:565:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const': Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type] 1705 | } | ^ Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ In file included from Errorrate.h:29, from HypermutationfullNmererrorrate.h:30, from HypermutationfullNmererrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ In file included from Errorrate.h:29, from Singleerrorrate.h:30, from Singleerrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ In file included from Errorrate.h:29, from Hypermutationglobalerrorrate.h:30, from Hypermutationglobalerrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ main.cpp: In function 'int main(int, char**)': main.cpp:257:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 257 | system(&("man igor")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~ main.cpp:289:32: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | freopen(argv[++carg_i],"a+",stdout); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1565:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1565 | system(&("mkdir " + cl_path )[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1716:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1716 | system(&("mkdir " + cl_path + "run_demo")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1750:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1750 | system(&("mkdir " + cl_path + "aligns")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2058:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2058 | system(&("mkdir " + cl_path + batchname + "output")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2062:39: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2062 | system(&("mkdir " + cl_path + batchname + "inference")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2068:39: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2068 | system(&("mkdir " + cl_path + batchname + "evaluate")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2078:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2078 | system(&("mkdir " + cl_path + batchname + "generated")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Errorrate.h:29, from Rec_Event.h:38, from Deletion.h:29, from main.cpp:28: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl libtool: link: g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl -fopenmp make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_auto_test make -j20 check "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making check in igor_src make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/igor/ make -j1 install DESTDIR=/build/reproducible-path/igor-1.4.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making install in igor_src make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c igor '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' libtool: install: /usr/bin/install -c igor /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin/igor make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' /usr/bin/install -c scripts/igor-compute_pgen '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' mkdir -p /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models cp -r models/* /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' /usr/bin/install -c -m 644 demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJs_all_curated.fasta demo/murugan_naive1_noncoding_demo_seqs.txt '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' cp debian/igor1 debian/igor.1 dh_installman make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_fixperms find debian -name "*.fasta" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/igor/usr/bin/igor was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'igor' in '../igor_1.4.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'igor-dbgsym' in '../igor-dbgsym_1.4.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../igor_1.4.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../igor_1.4.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2238615 and its subdirectories I: Current time: Wed Apr 2 09:42:37 -12 2025 I: pbuilder-time-stamp: 1743630157 Wed Apr 2 21:42:37 UTC 2025 I: Signing ./b1/igor_1.4.0+dfsg-5_amd64.buildinfo as igor_1.4.0+dfsg-5_amd64.buildinfo.asc Wed Apr 2 21:42:37 UTC 2025 I: Signed ./b1/igor_1.4.0+dfsg-5_amd64.buildinfo as ./b1/igor_1.4.0+dfsg-5_amd64.buildinfo.asc Wed Apr 2 21:42:37 UTC 2025 - build #1 for igor/trixie/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Wed Apr 2 21:42:37 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-FlNzEvdX, removing. /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Apr 2 21:42 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 2 21:39 b2 -rw-r--r-- 1 jenkins jenkins 2021 Mar 15 2024 igor_1.4.0+dfsg-5.dsc -rw------- 1 jenkins jenkins 3125 Apr 2 21:39 rbuildlog.Galk04M /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/b1: total 6640 -rw-r--r-- 1 jenkins jenkins 55529 Apr 2 21:42 build.log -rw-r--r-- 1 jenkins jenkins 6101612 Apr 2 21:42 igor-dbgsym_1.4.0+dfsg-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 5324 Apr 2 21:42 igor_1.4.0+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2021 Apr 2 21:42 igor_1.4.0+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 5037 Apr 2 21:42 igor_1.4.0+dfsg-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5919 Apr 2 21:42 igor_1.4.0+dfsg-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1454 Apr 2 21:42 igor_1.4.0+dfsg-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 598920 Apr 2 21:42 igor_1.4.0+dfsg-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 1305 Apr 2 21:42 igor_1.4.0+dfsg-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/b2: total 0 Wed Apr 2 21:42:38 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 2 09:39:28 -12 2025 I: pbuilder-time-stamp: 1743629968 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 [igor_1.4.0+dfsg-5.dsc] I: copying [./igor_1.4.0+dfsg.orig.tar.xz] I: copying [./igor_1.4.0+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./igor_1.4.0+dfsg-5.dsc: unsupported subcommand dpkg-source: info: extracting igor in igor-1.4.0+dfsg dpkg-source: info: unpacking igor_1.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking igor_1.4.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying get_autoreconf_to_work.patch dpkg-source: info: applying inline_fix.patch dpkg-source: info: applying fix-gcc-10.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2238615/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='08994d864057437ca1cbc23cd62e3c3d' 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='2238615' 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.eIbAD7Nq/pbuilderrc_6e0H --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.eIbAD7Nq/b1 --logfile b1/build.log igor_1.4.0+dfsg-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2238615/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev | libblas.so dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19805 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 libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however: Package libblas-dev is not installed. Package libblas.so is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libjemalloc-dev{a} libjemalloc2{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 14.6 MB of archives. After unpacking 58.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB] Fetched 14.6 MB in 5s (2683 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19805 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-5_amd64.deb ... Unpacking bsdextrautils (2.40.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-7_amd64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.4_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../29-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../30-libblas-dev_3.12.1-2_amd64.deb ... Unpacking libblas-dev:amd64 (3.12.1-2) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../31-libgslcblas0_2.8+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../32-libgsl28_2.8+dfsg-5_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../33-libgsl-dev_2.8+dfsg-5_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5) ... Selecting previously unselected package libjemalloc2:amd64. Preparing to unpack .../34-libjemalloc2_5.3.0-3_amd64.deb ... Unpacking libjemalloc2:amd64 (5.3.0-3) ... Selecting previously unselected package libjemalloc-dev. Preparing to unpack .../35-libjemalloc-dev_5.3.0-3_amd64.deb ... Unpacking libjemalloc-dev (5.3.0-3) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.40.4-5) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up file (1:5.45-3+b1) ... Setting up libjemalloc2:amd64 (5.3.0-3) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libjemalloc-dev (5.3.0-3) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libblas-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.41-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/igor-1.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../igor_1.4.0+dfsg-5_source.changes dpkg-buildpackage: info: source package igor dpkg-buildpackage: info: source version 1.4.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_auto_clean rm -rf docs/latex rm -rf docs/html rm -rf config.guess config.sub make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:14: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:7: installing './install-sh' configure.ac:7: installing './missing' igor_src/Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking whether g++ supports C++11 features by default... yes checking for g++ option to support OpenMP... -fopenmp checking for _Bool... no checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for size_t... yes checking for pow... yes checking for sqrt... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating igor_src/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in igor_src (/build/reproducible-path/igor-1.4.0+dfsg/igor_src) configure: WARNING: no configuration information is in igor_src dh_auto_build make -j20 make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making all in igor_src make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Bestscenarioscounter.o `test -f 'Bestscenarioscounter.cpp' || echo './'`Bestscenarioscounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-CDR3SeqData.o `test -f 'CDR3SeqData.cpp' || echo './'`CDR3SeqData.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Counter.o `test -f 'Counter.cpp' || echo './'`Counter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Coverageerrcounter.o `test -f 'Coverageerrcounter.cpp' || echo './'`Coverageerrcounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp Deletion.cpp:1590:44: warning: multi-character character constant [-Wmultichar] 1590 | else if ((*iter)=='14'){ | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Genechoice.cpp:908:94: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class); | ^~~~~~~~~~~ Genechoice.cpp:908:94: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Genechoice.h:29, from Genechoice.cpp:26: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Deletion.cpp:909:98: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used | ^~~~~~~~~~ Deletion.cpp:909:98: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Deletion.h:29, from Deletion.cpp:26: Utils.h:69:13: note: candidate 2: 'std::string operator+(const std::string&, Seq_side)' 69 | std::string operator+(const std::string& , Seq_side ); | ^~~~~~~~ Deletion.cpp:1173:88: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class); | ^~~~~~~~~~~ Deletion.cpp:1173:88: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Insertion.cpp: In member function 'virtual void Insertion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Insertion.cpp:244:93: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 244 | throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class); | ^~~~~~~~~~~ Insertion.cpp:244:93: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Insertion.h:30, from Insertion.cpp:27: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Dinuclmarkov.cpp:147:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 147 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:147:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Dinuclmarkov.h:32, from Dinuclmarkov.cpp:26: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual std::queue Dinucl_markov::draw_random_realization(const Marginal_array_p&, std::unordered_map, int>&, const std::unordered_map, std::vector, int> > >&, std::unordered_map >&, std::mt19937_64&) const': Dinuclmarkov.cpp:211:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 211 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:211:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate_initialize_Len_proba(Seq_type, std::map&, std::queue >&, double&, const Marginal_array_p&, Index_map&, Seq_type_str_p_map&, int&) const': Dinuclmarkov.cpp:565:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 565 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:565:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const': Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type] 1705 | } | ^ Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ In file included from Errorrate.h:29, from HypermutationfullNmererrorrate.h:30, from HypermutationfullNmererrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ In file included from Errorrate.h:29, from Singleerrorrate.h:30, from Singleerrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ In file included from Errorrate.h:29, from Hypermutationglobalerrorrate.h:30, from Hypermutationglobalerrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ main.cpp: In function 'int main(int, char**)': main.cpp:257:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 257 | system(&("man igor")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~ main.cpp:289:32: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | freopen(argv[++carg_i],"a+",stdout); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1565:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1565 | system(&("mkdir " + cl_path )[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1716:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1716 | system(&("mkdir " + cl_path + "run_demo")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1750:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1750 | system(&("mkdir " + cl_path + "aligns")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2058:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2058 | system(&("mkdir " + cl_path + batchname + "output")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2062:39: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2062 | system(&("mkdir " + cl_path + batchname + "inference")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2068:39: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2068 | system(&("mkdir " + cl_path + batchname + "evaluate")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2078:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2078 | system(&("mkdir " + cl_path + batchname + "generated")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Errorrate.h:29, from Rec_Event.h:38, from Deletion.h:29, from main.cpp:28: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl libtool: link: g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl -fopenmp make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_auto_test make -j20 check "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making check in igor_src make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/igor/ make -j1 install DESTDIR=/build/reproducible-path/igor-1.4.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making install in igor_src make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c igor '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' libtool: install: /usr/bin/install -c igor /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin/igor make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' /usr/bin/install -c scripts/igor-compute_pgen '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' mkdir -p /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models cp -r models/* /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' /usr/bin/install -c -m 644 demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJs_all_curated.fasta demo/murugan_naive1_noncoding_demo_seqs.txt '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' cp debian/igor1 debian/igor.1 dh_installman make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_fixperms find debian -name "*.fasta" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/igor/usr/bin/igor was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'igor' in '../igor_1.4.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'igor-dbgsym' in '../igor-dbgsym_1.4.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../igor_1.4.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../igor_1.4.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2238615 and its subdirectories I: Current time: Wed Apr 2 09:42:37 -12 2025 I: pbuilder-time-stamp: 1743630157 Wed Apr 2 21:42:38 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed Apr 2 21:42:38 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed Apr 2 21:42:38 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Apr 2 21:42:38 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-l01nGt' ==================================================================================== Wed May 6 04:05:39 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 igor trixie /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq 1.4.0+dfsg-5" as arguments. Wed May 6 04:05:39 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-y6pCvooP" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed May 6 04:05:39 UTC 2026 I: Downloading source for trixie/igor=1.4.0+dfsg-5 Reading package lists... NOTICE: 'igor' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/igor.git Please use: git clone https://salsa.debian.org/med-team/igor.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1009 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (dsc) [2021 B] Get:2 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (tar) [1001 kB] Get:3 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (diff) [5324 B] Fetched 1009 kB in 0s (10.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'igor' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/igor.git Please use: git clone https://salsa.debian.org/med-team/igor.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1009 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (dsc) [2021 B] Get:2 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (tar) [1001 kB] Get:3 http://deb.debian.org/debian trixie/main igor 1.4.0+dfsg-5 (diff) [5324 B] Fetched 1009 kB in 0s (10.4 MB/s) Download complete and in download only mode ============================================================================= Re-Building igor in trixie on amd64 on ionos15-amd64 now. Date: Wed May 6 04:05:39 UTC 2026 Date UTC: Wed May 6 04:05:39 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/pbuilderrc_qL0G + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' igor = debian-installer -o igor = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' igor = u-boot ']' + case "${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.eIbAD7Nq/pbuilderrc_qL0G --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.eIbAD7Nq/b2 --logfile b2/build.log igor_1.4.0+dfsg-5.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: Wed May 6 18:05:40 +14 2026 I: pbuilder-time-stamp: 1778040340 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 [igor_1.4.0+dfsg-5.dsc] I: copying [./igor_1.4.0+dfsg.orig.tar.xz] I: copying [./igor_1.4.0+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./igor_1.4.0+dfsg-5.dsc: unsupported subcommand dpkg-source: info: extracting igor in igor-1.4.0+dfsg dpkg-source: info: unpacking igor_1.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking igor_1.4.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying get_autoreconf_to_work.patch dpkg-source: info: applying inline_fix.patch dpkg-source: info: applying fix-gcc-10.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 6 04:05 /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/1071690/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=9389f5bd44b348908879a57eee604d21 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1071690 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.eIbAD7Nq/pbuilderrc_qL0G --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.eIbAD7Nq/b2 --logfile b2/build.log igor_1.4.0+dfsg-5.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev | libblas.so dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19805 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 libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however: Package libblas-dev is not installed. Package libblas.so is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libjemalloc-dev{a} libjemalloc2{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 14.6 MB of archives. After unpacking 58.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB] Fetched 14.6 MB in 0s (115 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19805 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. 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Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../29-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../30-libblas-dev_3.12.1-2_amd64.deb ... Unpacking libblas-dev:amd64 (3.12.1-2) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../31-libgslcblas0_2.8+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../32-libgsl28_2.8+dfsg-5_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5) ... 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Setting up libjemalloc-dev (5.3.0-3) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libblas-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.41-6) ... 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/1071690/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/igor-1.4.0+dfsg/ && 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 > ../igor_1.4.0+dfsg-5_source.changes dpkg-buildpackage: info: source package igor dpkg-buildpackage: info: source version 1.4.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_auto_clean rm -rf docs/latex rm -rf docs/html rm -rf config.guess config.sub make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:14: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:7: installing './install-sh' configure.ac:7: installing './missing' igor_src/Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking whether g++ supports C++11 features by default... yes checking for g++ option to support OpenMP... -fopenmp checking for _Bool... no checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for size_t... yes checking for pow... yes checking for sqrt... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating igor_src/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in igor_src (/build/reproducible-path/igor-1.4.0+dfsg/igor_src) configure: WARNING: no configuration information is in igor_src dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making all in igor_src make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Bestscenarioscounter.o `test -f 'Bestscenarioscounter.cpp' || echo './'`Bestscenarioscounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-CDR3SeqData.o `test -f 'CDR3SeqData.cpp' || echo './'`CDR3SeqData.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Counter.o `test -f 'Counter.cpp' || echo './'`Counter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Coverageerrcounter.o `test -f 'Coverageerrcounter.cpp' || echo './'`Coverageerrcounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp Deletion.cpp:1590:44: warning: multi-character character constant [-Wmultichar] 1590 | else if ((*iter)=='14'){ | ^~~~ Insertion.cpp: In member function 'virtual void Insertion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Insertion.cpp:244:93: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 244 | throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class); | ^~~~~~~~~~~ Insertion.cpp:244:93: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Insertion.h:30, from Insertion.cpp:27: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Dinuclmarkov.cpp:147:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 147 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:147:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Dinuclmarkov.h:32, from Dinuclmarkov.cpp:26: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ In file included from Errorrate.h:29, from Singleerrorrate.h:30, from Singleerrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Deletion.cpp:909:98: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used | ^~~~~~~~~~ Deletion.cpp:909:98: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Deletion.h:29, from Deletion.cpp:26: Utils.h:69:13: note: candidate 2: 'std::string operator+(const std::string&, Seq_side)' 69 | std::string operator+(const std::string& , Seq_side ); | ^~~~~~~~ Deletion.cpp:1173:88: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class); | ^~~~~~~~~~~ Deletion.cpp:1173:88: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual std::queue Dinucl_markov::draw_random_realization(const Marginal_array_p&, std::unordered_map, int>&, const std::unordered_map, std::vector, int> > >&, std::unordered_map >&, std::mt19937_64&) const': Dinuclmarkov.cpp:211:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 211 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:211:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Genechoice.cpp:908:94: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class); | ^~~~~~~~~~~ Genechoice.cpp:908:94: note: candidate 1: 'operator+(const char*, long int)' (built-in) In file included from Errorrate.h:29, from Rec_Event.h:38, from Genechoice.h:29, from Genechoice.cpp:26: Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate_initialize_Len_proba(Seq_type, std::map&, std::queue >&, double&, const Marginal_array_p&, Index_map&, Seq_type_str_p_map&, int&) const': Dinuclmarkov.cpp:565:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 565 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); | ^~~~~~~~~~~ Dinuclmarkov.cpp:565:95: note: candidate 1: 'operator+(const char*, long int)' (built-in) Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ In file included from Errorrate.h:29, from HypermutationfullNmererrorrate.h:30, from HypermutationfullNmererrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const': Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type] 1705 | } | ^ In file included from Errorrate.h:29, from Hypermutationglobalerrorrate.h:30, from Hypermutationglobalerrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ main.cpp: In function 'int main(int, char**)': main.cpp:257:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 257 | system(&("man igor")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~ main.cpp:289:32: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | freopen(argv[++carg_i],"a+",stdout); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1565:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1565 | system(&("mkdir " + cl_path )[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1716:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1716 | system(&("mkdir " + cl_path + "run_demo")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1750:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1750 | system(&("mkdir " + cl_path + "aligns")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2058:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2058 | system(&("mkdir " + cl_path + batchname + "output")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2062:39: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2062 | system(&("mkdir " + cl_path + batchname + "inference")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2068:39: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2068 | system(&("mkdir " + cl_path + batchname + "evaluate")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:2078:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2078 | system(&("mkdir " + cl_path + batchname + "generated")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Errorrate.h:29, from Rec_Event.h:38, from Deletion.h:29, from main.cpp:28: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ /bin/sh ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl libtool: link: g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl -fopenmp make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_auto_test make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making check in igor_src make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/igor/ make -j1 install DESTDIR=/build/reproducible-path/igor-1.4.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making install in igor_src make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c igor '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' libtool: install: /usr/bin/install -c igor /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin/igor make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' /usr/bin/install -c scripts/igor-compute_pgen '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' mkdir -p /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models cp -r models/* /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' /usr/bin/install -c -m 644 demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJs_all_curated.fasta demo/murugan_naive1_noncoding_demo_seqs.txt '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' cp debian/igor1 debian/igor.1 dh_installman make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_fixperms find debian -name "*.fasta" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/igor/usr/bin/igor was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'igor-dbgsym' in '../igor-dbgsym_1.4.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'igor' in '../igor_1.4.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../igor_1.4.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../igor_1.4.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1071690/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/1071690 and its subdirectories I: Current time: Wed May 6 18:06:49 +14 2026 I: pbuilder-time-stamp: 1778040409 + false + set +x Wed May 6 04:06:49 UTC 2026 I: Signing ./b2/igor_1.4.0+dfsg-5_amd64.buildinfo as igor_1.4.0+dfsg-5_amd64.buildinfo.asc Wed May 6 04:06:49 UTC 2026 I: Signed ./b2/igor_1.4.0+dfsg-5_amd64.buildinfo as ./b2/igor_1.4.0+dfsg-5_amd64.buildinfo.asc Wed May 6 04:06:49 UTC 2026 - build #2 for igor/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Wed May 6 04:06:49 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-y6pCvooP, removing. /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq: total 76 drwxr-xr-x 2 jenkins jenkins 4096 Apr 2 21:42 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 2 21:43 b2 -rw-r--r-- 1 jenkins jenkins 2021 Mar 15 2024 igor_1.4.0+dfsg-5.dsc -rw------- 1 jenkins jenkins 58943 Apr 2 21:42 rbuildlog.Galk04M /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/b1: total 6660 -rw-r--r-- 1 jenkins jenkins 55529 Apr 2 21:42 build.log -rw-r--r-- 1 jenkins jenkins 6101612 Apr 2 21:42 igor-dbgsym_1.4.0+dfsg-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 5324 Apr 2 21:42 igor_1.4.0+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2021 Apr 2 21:42 igor_1.4.0+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 5037 Apr 2 21:42 igor_1.4.0+dfsg-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5919 Apr 2 21:42 igor_1.4.0+dfsg-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1454 Apr 2 21:42 igor_1.4.0+dfsg-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 598920 Apr 2 21:42 igor_1.4.0+dfsg-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 1305 Apr 2 21:42 igor_1.4.0+dfsg-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/b2: total 6644 -rw-r--r-- 1 jenkins jenkins 57467 Apr 2 21:43 build.log -rw-r--r-- 1 jenkins jenkins 6101612 Apr 2 21:43 igor-dbgsym_1.4.0+dfsg-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 5324 Apr 2 21:43 igor_1.4.0+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2021 Apr 2 21:43 igor_1.4.0+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 5048 Apr 2 21:43 igor_1.4.0+dfsg-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5930 Apr 2 21:43 igor_1.4.0+dfsg-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1454 Apr 2 21:43 igor_1.4.0+dfsg-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 598920 Apr 2 21:43 igor_1.4.0+dfsg-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 1305 Apr 2 21:43 igor_1.4.0+dfsg-5_source.changes Wed Apr 2 21:43:50 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed Apr 2 21:43:51 UTC 2025 I: igor_1.4.0+dfsg-5_amd64.changes: Format: 1.8 Date: Fri, 15 Mar 2024 23:03:10 +0700 Source: igor Binary: igor igor-dbgsym Architecture: amd64 Version: 1.4.0+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Lance Lin Description: igor - infers V(D)J recombination processes from sequencing data Closes: 1049535 Changes: igor (1.4.0+dfsg-5) unstable; urgency=medium . * Team upload. * Standards-Version: 4.6.2 (routine-update) * d/rules: Copy manpage instead of moving it (Closes: #1049535) Checksums-Sha1: aa432b489478ee987bd76408ef7d4b5250e73341 6101612 igor-dbgsym_1.4.0+dfsg-5_amd64.deb 17a03e6e99b12dd10aab930b3d9bdd2a691c78bb 5037 igor_1.4.0+dfsg-5_amd64.buildinfo 887559965f85e361dfb6e1e6351ab2ba8abdd1e0 598920 igor_1.4.0+dfsg-5_amd64.deb Checksums-Sha256: d9343ff94b15e65c43761c475450044f31d3bf3bf6def1cd6a3c28c388182b15 6101612 igor-dbgsym_1.4.0+dfsg-5_amd64.deb f1fd322b6b3413dde7f7be2c96fc66609eb83026a39fc52c67948598c7086d16 5037 igor_1.4.0+dfsg-5_amd64.buildinfo 250ad46d01b3a9764b06f5578424832a54f9d835b2bf6579806dd39c3111e439 598920 igor_1.4.0+dfsg-5_amd64.deb Files: 2abd790f0ff640b6b7d7e16fd7c8a7f8 6101612 debug optional igor-dbgsym_1.4.0+dfsg-5_amd64.deb 1050f97033e0ce8c302f833c967e873f 5037 science optional igor_1.4.0+dfsg-5_amd64.buildinfo e09e16d1ae62ec07a72d5350c1f72151 598920 science optional igor_1.4.0+dfsg-5_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/igor_1.4.0+dfsg-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/igor_1.4.0+dfsg-5.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/igor_1.4.0+dfsg-5.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/igor_1.4.0+dfsg-5.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/igor_1.4.0+dfsg-5_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/igor_1.4.0+dfsg-5.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-04-02 21:42:38.063877046 +0000 +++ b2/build.log 2025-04-02 21:43:50.486262793 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 2 09:39:28 -12 2025 -I: pbuilder-time-stamp: 1743629968 +I: Current time: Wed May 6 18:05:40 +14 2026 +I: pbuilder-time-stamp: 1778040340 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying fix-gcc-10.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2238615/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 6 04:05 /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/1071690/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='08994d864057437ca1cbc23cd62e3c3d' - 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='2238615' - PS1='# ' - PS2='> ' + INVOCATION_ID=9389f5bd44b348908879a57eee604d21 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1071690 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.eIbAD7Nq/pbuilderrc_6e0H --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.eIbAD7Nq/b1 --logfile b1/build.log igor_1.4.0+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.eIbAD7Nq/pbuilderrc_qL0G --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.eIbAD7Nq/b2 --logfile b2/build.log igor_1.4.0+dfsg-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2238615/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -150,7 +182,7 @@ Get: 34 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB] -Fetched 14.6 MB in 5s (2683 kB/s) +Fetched 14.6 MB in 0s (115 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19805 files and directories currently installed.) @@ -311,7 +343,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/igor-1.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../igor_1.4.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1071690/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/igor-1.4.0+dfsg/ && 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 > ../igor_1.4.0+dfsg-5_source.changes dpkg-buildpackage: info: source package igor dpkg-buildpackage: info: source version 1.4.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -467,7 +503,7 @@ === configuring in igor_src (/build/reproducible-path/igor-1.4.0+dfsg/igor_src) configure: WARNING: no configuration information is in igor_src dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' @@ -493,42 +529,12 @@ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp Deletion.cpp:1590:44: warning: multi-character character constant [-Wmultichar] 1590 | else if ((*iter)=='14'){ | ^~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp -Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': -Genechoice.cpp:908:94: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: - 908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class); - | ^~~~~~~~~~~ -Genechoice.cpp:908:94: note: candidate 1: 'operator+(const char*, long int)' (built-in) -In file included from Errorrate.h:29, - from Rec_Event.h:38, - from Genechoice.h:29, - from Genechoice.cpp:26: -Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' - 68 | std::string operator+(const std::string& , Gene_class ); - | ^~~~~~~~ -Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': -Deletion.cpp:909:98: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: - 909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used - | ^~~~~~~~~~ -Deletion.cpp:909:98: note: candidate 1: 'operator+(const char*, long int)' (built-in) -In file included from Errorrate.h:29, - from Rec_Event.h:38, - from Deletion.h:29, - from Deletion.cpp:26: -Utils.h:69:13: note: candidate 2: 'std::string operator+(const std::string&, Seq_side)' - 69 | std::string operator+(const std::string& , Seq_side ); - | ^~~~~~~~ -Deletion.cpp:1173:88: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: - 1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class); - | ^~~~~~~~~~~ -Deletion.cpp:1173:88: note: candidate 1: 'operator+(const char*, long int)' (built-in) -Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' - 68 | std::string operator+(const std::string& , Gene_class ); - | ^~~~~~~~ Insertion.cpp: In member function 'virtual void Insertion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Insertion.cpp:244:93: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 244 | throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class); @@ -541,7 +547,6 @@ Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Dinuclmarkov.cpp:147:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 147 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); @@ -554,6 +559,32 @@ Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ +In file included from Errorrate.h:29, + from Singleerrorrate.h:30, + from Singleerrorrate.cpp:27: +Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': +Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] + 142 | } + | ^ +Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': +Deletion.cpp:909:98: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: + 909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used + | ^~~~~~~~~~ +Deletion.cpp:909:98: note: candidate 1: 'operator+(const char*, long int)' (built-in) +In file included from Errorrate.h:29, + from Rec_Event.h:38, + from Deletion.h:29, + from Deletion.cpp:26: +Utils.h:69:13: note: candidate 2: 'std::string operator+(const std::string&, Seq_side)' + 69 | std::string operator+(const std::string& , Seq_side ); + | ^~~~~~~~ +Deletion.cpp:1173:88: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: + 1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class); + | ^~~~~~~~~~~ +Deletion.cpp:1173:88: note: candidate 1: 'operator+(const char*, long int)' (built-in) +Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' + 68 | std::string operator+(const std::string& , Gene_class ); + | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual std::queue Dinucl_markov::draw_random_realization(const Marginal_array_p&, std::unordered_map, int>&, const std::unordered_map, std::vector, int> > >&, std::unordered_map >&, std::mt19937_64&) const': Dinuclmarkov.cpp:211:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 211 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); @@ -562,6 +593,18 @@ Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ +Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': +Genechoice.cpp:908:94: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: + 908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class); + | ^~~~~~~~~~~ +Genechoice.cpp:908:94: note: candidate 1: 'operator+(const char*, long int)' (built-in) +In file included from Errorrate.h:29, + from Rec_Event.h:38, + from Genechoice.h:29, + from Genechoice.cpp:26: +Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' + 68 | std::string operator+(const std::string& , Gene_class ); + | ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate_initialize_Len_proba(Seq_type, std::map&, std::queue >&, double&, const Marginal_array_p&, Index_map&, Seq_type_str_p_map&, int&) const': Dinuclmarkov.cpp:565:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 565 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); @@ -570,10 +613,6 @@ Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ -Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const': -Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type] - 1705 | } - | ^ Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } @@ -585,13 +624,10 @@ Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ -In file included from Errorrate.h:29, - from Singleerrorrate.h:30, - from Singleerrorrate.cpp:27: -Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': -Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] - 142 | } - | ^ +Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const': +Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type] + 1705 | } + | ^ In file included from Errorrate.h:29, from Hypermutationglobalerrorrate.h:30, from Hypermutationglobalerrorrate.cpp:27: @@ -635,7 +671,7 @@ Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ -/bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl +/bin/sh ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl libtool: link: g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/reproducible-path/igor-1.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl -fopenmp make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' @@ -643,7 +679,7 @@ make[2]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg' dh_auto_test - make -j20 check "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 + make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg' Making check in igor_src make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' @@ -662,7 +698,7 @@ make[2]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' /usr/bin/mkdir -p '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c igor '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c igor '/build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin' libtool: install: /usr/bin/install -c igor /build/reproducible-path/igor-1.4.0+dfsg/debian/igor/usr/bin/igor make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/igor-1.4.0+dfsg/igor_src' @@ -705,8 +741,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'igor' in '../igor_1.4.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'igor-dbgsym' in '../igor-dbgsym_1.4.0+dfsg-5_amd64.deb'. +dpkg-deb: building package 'igor' in '../igor_1.4.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../igor_1.4.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../igor_1.4.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -714,12 +750,14 @@ 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/1071690/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1071690/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/2238615 and its subdirectories -I: Current time: Wed Apr 2 09:42:37 -12 2025 -I: pbuilder-time-stamp: 1743630157 +I: removing directory /srv/workspace/pbuilder/1071690 and its subdirectories +I: Current time: Wed May 6 18:06:49 +14 2026 +I: pbuilder-time-stamp: 1778040409 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/igor_1.4.0+dfsg-5.diff: 81.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/igor_1.4.0+dfsg-5.diff.gz b2/build.log: 81.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.2% -- replaced with stdout Wed Apr 2 21:43:52 UTC 2025 I: diffoscope 293 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_igor_trixie_amd64_1743630232 + touch /var/log/reproducible-builds/diffoscope_stamp_igor_trixie_amd64_1743630232 + RESULT=0 + systemd-run '--description=diffoscope on igor/1.4.0+dfsg-5 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_23-51685 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq --run-session -c jenkins-reproducible-trixie-diffoscope-54836c52-09b9-4d68-8d33-0c8c698f3b90 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/dbd-tmp-Bletwyk ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/igor_1.4.0+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/igor_1.4.0+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/igor_1.4.0+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/b1/igor_1.4.0+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/b2/igor_1.4.0+dfsg-5_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_23-51685.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/igor_1.4.0+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/igor_1.4.0+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/igor_1.4.0+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/b1/igor_1.4.0+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.eIbAD7Nq/b2/igor_1.4.0+dfsg-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 231ms CPU time consumed: 232ms _ (_) __ _ ___ _ __ | |/ _` |/ _ \| '__| | | (_| | (_) | | |_|\__, |\___/|_| |___/ Wed Apr 2 21:43:52 UTC 2025 I: diffoscope 293 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 2 21:43:52 UTC 2025 I: igor from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-04-02 21:43:53] INFO: Starting at 2025-04-02 21:43:53.206958 [2025-04-02 21:43:53] INFO: Generating the pages of 1 package(s) [2025-04-02 21:43:53] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/igor didn't produce a buildlog, even though it has been built. [2025-04-02 21:43:53] INFO: Finished at 2025-04-02 21:43:53.612313, took: 0:00:00.405365 Wed Apr 2 21:43:53 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/igor.html Wed Apr 2 21:43:53 UTC 2025 I: Submitting .buildinfo files to external archives: Wed Apr 2 21:43:53 UTC 2025 I: Submitting 8.0K b1/igor_1.4.0+dfsg-5_amd64.buildinfo.asc https://buildinfo.debian.net/17a03e6e99b12dd10aab930b3d9bdd2a691c78bb/igor_1.4.0+dfsg-5_amd64 Wed Apr 2 21:43:55 UTC 2025 I: Submitting 8.0K b2/igor_1.4.0+dfsg-5_amd64.buildinfo.asc https://buildinfo.debian.net/be5266cef82bec59df916d6672aa641217b95587/igor_1.4.0+dfsg-5_amd64 Wed Apr 2 21:43:55 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 2 21:43:55 UTC 2025 I: Done submitting .buildinfo files. Wed Apr 2 21:43:55 UTC 2025 I: Removing signed igor_1.4.0+dfsg-5_amd64.buildinfo.asc files: removed './b1/igor_1.4.0+dfsg-5_amd64.buildinfo.asc' removed './b2/igor_1.4.0+dfsg-5_amd64.buildinfo.asc' 1743630235 amd64 trixie igor Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/igor_1.4.0+dfsg-5.rbuild.log: 79.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/igor_1.4.0+dfsg-5.rbuild.log.gz [2025-04-02 21:43:56] INFO: Starting at 2025-04-02 21:43:56.351411 [2025-04-02 21:43:56] INFO: Generating the pages of 1 package(s) [2025-04-02 21:43:56] INFO: Finished at 2025-04-02 21:43:56.918723, took: 0:00:00.567323 All cleanup done. Wed Apr 2 21:43:57 UTC 2025 - total duration: 0h 4m 50s. Wed Apr 2 21:43:57 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-WSGYVqW5, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 4min 55.076s CPU time consumed: 7.435s