Thu Jul 27 19:50:57 UTC 2023 I: starting to build igor/bullseye/amd64 on jenkins on '2023-07-27 19:50' Thu Jul 27 19:50:58 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_9/5133/console.log Thu Jul 27 19:50:58 UTC 2023 I: Downloading source for bullseye/igor=1.4.0+dfsg-2 --2023-07-27 19:50:58-- http://cdn-fastly.deb.debian.org/debian/pool/main/i/igor/igor_1.4.0%2bdfsg-2.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-2.dsc’ 0K . 100% 94.0M=0s 2023-07-27 19:50:58 (94.0 MB/s) - ‘igor_1.4.0+dfsg-2.dsc’ saved [2046/2046] Thu Jul 27 19:50:58 UTC 2023 I: igor_1.4.0+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: igor Binary: igor Architecture: any Version: 1.4.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/qmarcou/IGoR/ Standards-Version: 4.5.0 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 0a3163c126f6df45ce35f8f2442bd78442fa177f 4988 igor_1.4.0+dfsg-2.debian.tar.xz Checksums-Sha256: eebf01e469bdcc5147d50b355d5c7890e6f4b6254596078a051f5db57cdc9449 1001484 igor_1.4.0+dfsg.orig.tar.xz 5df040205a8e17a221abf16c7e9047a82b150068c56395bdf4fc808e889022ba 4988 igor_1.4.0+dfsg-2.debian.tar.xz Files: 272f7e96c7aadd4791679d31dadf0f6f 1001484 igor_1.4.0+dfsg.orig.tar.xz 36212942a9b2034bb0f0200a9c4d6e66 4988 igor_1.4.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl8q5CIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGPXQ//VyRDZs3Jrt24A5WuCPuRX1/tlyGEsAwM fzEnE6HML74nhcWhlljNId2fOEwBcw/SMz6mOLI1ZJXD8vR9ZpsiGN0eQO9/3vUm O21+zandoEk9vzc4WGl6m+8RoNB/dzYPs0V3O8s+Bz7Y08OPvCvLcSUDbGAyqx59 u7fExbIG3k4Z5f+YDwgaxQd+EKrVpkztzRKR7Ml1yraPD45uIOWGcectjSa+wqkd BxabY/tewo2dKq3YUSU9w8XYeFbHqCLF9PnJIxCW53mC03CRzF+DwqeANqjd0v66 V6FJh3M+Rw2nX2F79i74eN6cQValr4z4EDZctng5QPO0u7YHQEu+vMpwkRuwjc5M be1iqEfc2aSF6VMu+pOVrlFZGUB4vs1i4ePnE2sf98qBLRtivIxP5lOAdgAm+YdZ OuYD79wvw00GVr4/JWxxF1v/GfRnCy9vuPun3bkB++66kUlW5RZus25U+WHFScqp 7DZIhmseVDvuO8URS4XHkXs6ygnTHzmkINS5K6b19Dcjb3S1mptOEUQrBpZJBU1G Ve/VoIFwPtsZ4pszb58ACO1+crn7FVALxoAqqjAJE0LwJfxjcWSHQRYO0FlkLk1l s6LFi68DwEpPzj2xz1RrObRN89wqY0pYDRoiRKi1hWWBZGO0Sc8/hWs0yYoRuHKk Tb1nRZTBP6I= =EwuY -----END PGP SIGNATURE----- Thu Jul 27 19:50:58 UTC 2023 I: Checking whether the package is not for us Thu Jul 27 19:50:58 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net. Thu Jul 27 19:50:58 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Thu Jul 27 19:56:46 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 27 07:51:01 -12 2023 I: pbuilder-time-stamp: 1690487461 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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-2.dsc] I: copying [./igor_1.4.0+dfsg.orig.tar.xz] I: copying [./igor_1.4.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.xULqTX5O/trustedkeys.kbx': General error gpgv: Signature made Wed Aug 5 04:53:54 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./igor_1.4.0+dfsg-2.dsc 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-2.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/1881188/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,-fixfilepath parallel=15 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='f533faeb18674c7eb94842b71058c03b' 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='1881188' 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.9ovwvntz/pbuilderrc_TsyH --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9ovwvntz/b1 --logfile b1/build.log igor_1.4.0+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-1 (2023-07-14) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 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 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 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 5898 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 8049 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/1881188/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 ... 19707 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} libgsl25{a} libgslcblas0{a} libicu67{a} libjemalloc-dev{a} libjemalloc2{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{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, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 21.5 MB of archives. After unpacking 83.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libblas-dev amd64 3.9.0-3 [161 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libgsl-dev amd64 2.6+dfsg-2 [1123 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libjemalloc2 amd64 5.2.1-3 [248 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libjemalloc-dev amd64 5.2.1-3 [437 kB] Fetched 21.5 MB in 1s (20.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_amd64.deb ... 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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/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-2_source.changes dpkg-buildpackage: info: source package igor dpkg-buildpackage: info: source version 1.4.0+dfsg-2 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 thread-safe 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 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 how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes 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 we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (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 stdbool.h that conforms to C99... no checking for _Bool... no 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 -j15 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 Deletion.cpp:1590:23: 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 -fdebug-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: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const 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:909:70: 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:909:70: 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 string&, Seq_side)' 69 | std::string operator+(const std::string& , Seq_side ); | ^~~~~~~~ Deletion.cpp:1173:67: 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:1173:67: 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:68:13: note: candidate 2: 'std::string operator+(const 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 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:244:72: 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:244:72: 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 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 -fdebug-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 -fdebug-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 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:147:81: 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:147:81: 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 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:211:81: 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:211:81: 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 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 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:908:73: 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:908:73: 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 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:565:81: 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:565:81: 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 string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ In file included from Errorrate.h:29, from Rec_Event.h:38, from Dinuclmarkov.h:32, from Dinuclmarkov.cpp:26: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:2: 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 -fdebug-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 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 -fdebug-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 HypermutationfullNmererrorrate.h:30, from HypermutationfullNmererrorrate.cpp:27: Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': Utils.h:142:2: 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:142:2: 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 -fdebug-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 -fdebug-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 -fdebug-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:142:2: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ main.cpp: In function 'int main(int, char**)': main.cpp:257:10: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 257 | system(&("man igor")[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~ main.cpp:289:11: 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:1565:9: 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:1716:9: 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:1750:10: 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:2058:10: 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:2062:11: 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:2068:11: 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:2078:10: 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:142:2: 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 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -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 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -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 -j15 check 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 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' in '../igor_1.4.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'igor-dbgsym' in '../igor-dbgsym_1.4.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../igor_1.4.0+dfsg-2_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/1881188 and its subdirectories I: Current time: Thu Jul 27 07:56:45 -12 2023 I: pbuilder-time-stamp: 1690487805 Thu Jul 27 19:56:47 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Thu Jul 27 19:56:47 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Thu Jul 27 19:57:58 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Thu Jul 27 19:57:58 UTC 2023 I: igor_1.4.0+dfsg-2_amd64.changes: Format: 1.8 Date: Wed, 05 Aug 2020 18:37:57 +0200 Source: igor Binary: igor igor-dbgsym Architecture: amd64 Version: 1.4.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: igor - infers V(D)J recombination processes from sequencing data Closes: 966868 Changes: igor (1.4.0+dfsg-2) unstable; urgency=medium . * Team upload. * Fix gcc-10 build Closes: #966868 * debhelper-compat 13 (routine-update) * Do not use outdated libcblas any more Checksums-Sha1: d4c69a884aede22933fa008dc3d4b278feee54e9 5817216 igor-dbgsym_1.4.0+dfsg-2_amd64.deb c445822ab09a6c5c544b7b307f267d3f5ff1359b 5419 igor_1.4.0+dfsg-2_amd64.buildinfo ac07c1c1dc34f07fc833288546a9de0a9c5a6e55 558112 igor_1.4.0+dfsg-2_amd64.deb Checksums-Sha256: aa3e73467b6aea61beb8ff24ab943d3ebfc46e0e7bff179416b81b29ed600f7a 5817216 igor-dbgsym_1.4.0+dfsg-2_amd64.deb 7d80cac6f527ee3dab1ef0a2b4f88d9e86039a51d73c4895f364f38392e3118a 5419 igor_1.4.0+dfsg-2_amd64.buildinfo 125a853bfd386b7c82817e58a13831218c1c2f90adc73b8b6a7463c0fa96e265 558112 igor_1.4.0+dfsg-2_amd64.deb Files: 16303797918b5d6aa84275e467a89a0c 5817216 debug optional igor-dbgsym_1.4.0+dfsg-2_amd64.deb 43166a2c7e98b45fb61a35fae8ea9e82 5419 science optional igor_1.4.0+dfsg-2_amd64.buildinfo 265cef8b2d5efeda6733a57465ca7507 558112 science optional igor_1.4.0+dfsg-2_amd64.deb Thu Jul 27 19:58:00 UTC 2023 I: diffoscope 243 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.9ovwvntz/igor_1.4.0+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9ovwvntz/igor_1.4.0+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9ovwvntz/igor_1.4.0+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9ovwvntz/b1/igor_1.4.0+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.9ovwvntz/b2/igor_1.4.0+dfsg-2_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: 0.304s) 0.304s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.072s) 0.072s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Thu Jul 27 20:01:16 UTC 2023 I: diffoscope 243 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 27 20:01:16 UTC 2023 I: igor from bullseye built successfully and reproducibly on amd64. Thu Jul 27 20:01:18 UTC 2023 I: Submitting .buildinfo files to external archives: Thu Jul 27 20:01:19 UTC 2023 I: Submitting 8.0K b1/igor_1.4.0+dfsg-2_amd64.buildinfo.asc Thu Jul 27 20:01:21 UTC 2023 I: Submitting 8.0K b2/igor_1.4.0+dfsg-2_amd64.buildinfo.asc Thu Jul 27 20:01:22 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jul 27 20:01:22 UTC 2023 I: Done submitting .buildinfo files. Thu Jul 27 20:01:22 UTC 2023 I: Removing signed igor_1.4.0+dfsg-2_amd64.buildinfo.asc files: removed './b1/igor_1.4.0+dfsg-2_amd64.buildinfo.asc' removed './b2/igor_1.4.0+dfsg-2_amd64.buildinfo.asc'