Mon Apr 17 19:04:30 UTC 2023 I: starting to build igor/bookworm/amd64 on jenkins on '2023-04-17 19:04' Mon Apr 17 19:04:30 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/31380/console.log Mon Apr 17 19:04:30 UTC 2023 I: Downloading source for bookworm/igor=1.4.0+dfsg-4 --2023-04-17 19:04:30-- http://cdn-fastly.deb.debian.org/debian/pool/main/i/igor/igor_1.4.0%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2046 (2.0K) [text/prs.lines.tag] Saving to: ‘igor_1.4.0+dfsg-4.dsc’ 0K . 100% 127M=0s 2023-04-17 19:04:30 (127 MB/s) - ‘igor_1.4.0+dfsg-4.dsc’ saved [2046/2046] Mon Apr 17 19:04:30 UTC 2023 I: igor_1.4.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: igor Binary: igor Architecture: any Version: 1.4.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/qmarcou/IGoR/ Standards-Version: 4.6.1 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 5003386f85287f87d50662fcfb3fe96b9ae0102d 5200 igor_1.4.0+dfsg-4.debian.tar.xz Checksums-Sha256: eebf01e469bdcc5147d50b355d5c7890e6f4b6254596078a051f5db57cdc9449 1001484 igor_1.4.0+dfsg.orig.tar.xz 951c0b83d26b3499481797a85462b52c941b1bb5e3026427744e9a20ac595dfc 5200 igor_1.4.0+dfsg-4.debian.tar.xz Files: 272f7e96c7aadd4791679d31dadf0f6f 1001484 igor_1.4.0+dfsg.orig.tar.xz 245d7f388afd522f707a0e8cd00b4869 5200 igor_1.4.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNmvlARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEziRAAmlup9P+gyEF+tnH+vOWYMjU03QoRt/HA wtmzW/gKUcZnv0l7D9alV+5E8IZ8nzd+wO4YaaERrjUrEOom2d5CpUbMUW5N4ZaK olTm8WVyNLRiMK3sr/Pvuq7AkuZbYFfgnWEl7hZVsvyRuLXrPv6ShdjJNJk13Pge JVc3Uj2yp4Mbb7V5Osept2T2pK30wIb1cdeHceVSDHp++hEKY1wURX6w3akC9dir 76I3cPEaC7gk91Yg7TCDAGjeOwK4ig4oWhHgjUkp7ssP2QFJ6grQCLAJIIpZYBjt Dt+Vl57q+7Oj6k9A+VkyOLWZTNnUWKa/WS5yDtj02DcwANU1TN4O4UpjJGliTGHX pVgQPIMTTB0+F59t+F3YCj2dSVSproNyE4kD2jZSRaJCpD9zyJ83QPLGsFf1ksMj mY2EM5t+PH8sdPJfx05tGCGKuI3SG/XOFzHvayMXsl2rSocMX6pY/KIxVHAT1Hlm Xt0cdIvQLeM+XHWl5YMQAKbBxvJooW64Ze/dPf18NCFPmmR+GrUay6gbTdjrUiId rBMugzaWkqCkPb30nt8U2gA8QXG6gbnqtyQ/CTwt0ChKEOwIeIf/k9ucyf11otLj kQCizsPPZFOZ+cAU8vRYZ8fcTggVHK+jCpnd/smCZsLEYtohI2tULs1oKdn6yCak AbAaykFPbc8= =+T0U -----END PGP SIGNATURE----- Mon Apr 17 19:04:30 UTC 2023 I: Checking whether the package is not for us Mon Apr 17 19:04:30 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net. Mon Apr 17 19:04:30 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Mon Apr 17 19:11:35 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 19 13:27:39 -12 2024 I: pbuilder-time-stamp: 1716168459 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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-4.dsc] I: copying [./igor_1.4.0+dfsg.orig.tar.xz] I: copying [./igor_1.4.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 5 07:49:36 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./igor_1.4.0+dfsg-4.dsc: no acceptable signature found 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-4.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/3118553/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='064130a567ff4717bcc99514977bd6e9' 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='3118553' 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.FBLVfMPC/pbuilderrc_keK9 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FBLVfMPC/b1 --logfile b1/build.log igor_1.4.0+dfsg-4.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://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3118553/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 ... 19596 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} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu72{a} libjemalloc-dev{a} libjemalloc2{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{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, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 22.0 MB of archives. After unpacking 88.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libblas-dev amd64 3.11.0-2 [158 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-3+b1 [116 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-3+b1 [948 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libgsl-dev amd64 2.7.1+dfsg-3+b1 [1152 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libjemalloc2 amd64 5.3.0-1 [275 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libjemalloc-dev amd64 5.3.0-1 [494 kB] Fetched 22.0 MB in 1s (31.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... 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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/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-4_source.changes dpkg-buildpackage: info: source package igor dpkg-buildpackage: info: source version 1.4.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/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/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 build environment is sane... yes checking for a race-free mkdir -p... /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 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... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /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 ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /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... 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/igor-1.4.0+dfsg/igor_src) configure: WARNING: no configuration information is in igor_src dh_auto_build make -j16 make[1]: Entering directory '/build/igor-1.4.0+dfsg' make all-recursive make[2]: Entering directory '/build/igor-1.4.0+dfsg' Making all in igor_src make[3]: Entering directory '/build/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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.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 ); | ^~~~~~~~ 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 ); | ^~~~~~~~ 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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp 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 ); | ^~~~~~~~ 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 | } | ^ 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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp 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 | } | ^ 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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp 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 | } | ^ 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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/igor-1.4.0+dfsg' make[3]: Leaving directory '/build/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/igor-1.4.0+dfsg' dh_auto_test make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 make[1]: Entering directory '/build/igor-1.4.0+dfsg' Making check in igor_src make[2]: Entering directory '/build/igor-1.4.0+dfsg/igor_src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/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/igor-1.4.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/igor-1.4.0+dfsg' Making install in igor_src make[2]: Entering directory '/build/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/igor-1.4.0+dfsg/igor_src' /bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c igor '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' libtool: install: /usr/bin/install -c igor /build/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/igor-1.4.0+dfsg/igor_src' make[2]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/igor-1.4.0+dfsg' make[3]: Entering directory '/build/igor-1.4.0+dfsg' /bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' /usr/bin/install -c scripts/igor-compute_pgen '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' mkdir -p /build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models cp -r models/* /build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models /bin/mkdir -p '/build/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/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' make[3]: Leaving directory '/build/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/igor-1.4.0+dfsg' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/igor-1.4.0+dfsg' mv debian/igor1 debian/igor.1 dh_installman make[1]: Leaving directory '/build/igor-1.4.0+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/igor-1.4.0+dfsg' dh_fixperms find debian -name "*.fasta" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/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-4_amd64.deb'. dpkg-deb: building package 'igor' in '../igor_1.4.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../igor_1.4.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../igor_1.4.0+dfsg-4_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/3118553 and its subdirectories I: Current time: Sun May 19 13:34:36 -12 2024 I: pbuilder-time-stamp: 1716168876 Mon Apr 17 19:11:35 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Mon Apr 17 19:11:35 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Mon Apr 17 19:16:38 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Mon Apr 17 19:16:38 UTC 2023 I: igor_1.4.0+dfsg-4_amd64.changes: Format: 1.8 Date: Sat, 05 Nov 2022 20:40:47 +0100 Source: igor Binary: igor igor-dbgsym Architecture: amd64 Version: 1.4.0+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: igor - infers V(D)J recombination processes from sequencing data Changes: igor (1.4.0+dfsg-4) unstable; urgency=medium . * Team upload. * Fix watch file * Standards-Version: 4.6.1 (routine-update) * lintian-overrides (see lintian bug #1017966) Checksums-Sha1: 141fcfcaaad10fb93f4d772438185e57278b3609 5886532 igor-dbgsym_1.4.0+dfsg-4_amd64.deb ce36be36c5de0abc83d3032733ab047c00d102f0 5337 igor_1.4.0+dfsg-4_amd64.buildinfo 92daeb1aa4a9285b9fc77642614ab3bf49ce2dbc 566608 igor_1.4.0+dfsg-4_amd64.deb Checksums-Sha256: d2b1e5566449f1b31d0d583da585d45f82b38e9105a186e975733442d5525be2 5886532 igor-dbgsym_1.4.0+dfsg-4_amd64.deb a5e8f612fed43ba4e6d434503854d0d7378736b8550eb1b6d8094f77b979ddd6 5337 igor_1.4.0+dfsg-4_amd64.buildinfo ccd7b3a2b0c9eafe5236ccfd6d515158fc32cbe000626ca52ec8ff8d208623bd 566608 igor_1.4.0+dfsg-4_amd64.deb Files: b7abf95d249ed0122b8c6aa5507a8d5c 5886532 debug optional igor-dbgsym_1.4.0+dfsg-4_amd64.deb 945be80b9c17317bfc015d495c44aac0 5337 science optional igor_1.4.0+dfsg-4_amd64.buildinfo 9e4cd0cf14444effe98b8d29d80e6f41 566608 science optional igor_1.4.0+dfsg-4_amd64.deb Mon Apr 17 19:16:39 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.FBLVfMPC/igor_1.4.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.FBLVfMPC/igor_1.4.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.FBLVfMPC/igor_1.4.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.FBLVfMPC/b1/igor_1.4.0+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.FBLVfMPC/b2/igor_1.4.0+dfsg-4_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 abc.DotChangesFile ## main (total time: 0.413s) 0.413s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.087s) 0.086s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon Apr 17 19:16:40 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 17 19:16:40 UTC 2023 I: igor from bookworm built successfully and reproducibly on amd64. Mon Apr 17 19:16:41 UTC 2023 I: Submitting .buildinfo files to external archives: Mon Apr 17 19:16:41 UTC 2023 I: Submitting 8.0K b1/igor_1.4.0+dfsg-4_amd64.buildinfo.asc Mon Apr 17 19:16:42 UTC 2023 I: Submitting 8.0K b2/igor_1.4.0+dfsg-4_amd64.buildinfo.asc Mon Apr 17 19:16:43 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 17 19:16:43 UTC 2023 I: Done submitting .buildinfo files. Mon Apr 17 19:16:43 UTC 2023 I: Removing signed igor_1.4.0+dfsg-4_amd64.buildinfo.asc files: removed './b1/igor_1.4.0+dfsg-4_amd64.buildinfo.asc' removed './b2/igor_1.4.0+dfsg-4_amd64.buildinfo.asc'