Mon Jul 27 10:40:12 UTC 2020 I: starting to build igor/buster/arm64 on jenkins on '2020-07-27 10:39' Mon Jul 27 10:40:12 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/13186/console.log Mon Jul 27 10:40:12 UTC 2020 I: Downloading source for buster/igor=1.3.0+dfsg-1 --2020-07-27 10:40:12-- http://deb.debian.org/debian/pool/main/i/igor/igor_1.3.0+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1986 (1.9K) Saving to: ‘igor_1.3.0+dfsg-1.dsc’ 0K . 100% 151M=0s 2020-07-27 10:40:12 (151 MB/s) - ‘igor_1.3.0+dfsg-1.dsc’ saved [1986/1986] Mon Jul 27 10:40:13 UTC 2020 I: igor_1.3.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: igor Binary: igor Architecture: any Version: 1.3.0+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/qmarcou/IGoR/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/igor Vcs-Git: https://salsa.debian.org/med-team/igor.git Build-Depends: debhelper (>= 11), libjemalloc-dev, libgsl-dev, libatlas-base-dev | libcblas-dev Package-List: igor deb science optional arch=any Checksums-Sha1: 3c59090b6da5bda71c170a2f7204467634b15c5e 407624 igor_1.3.0+dfsg.orig.tar.xz 72152f2ccfba78b52931a8055e40d5fc335a611f 3692 igor_1.3.0+dfsg-1.debian.tar.xz Checksums-Sha256: c4cac92b4282b8c6cb7fef85eb7af1e0fbd0c27321716d46d3353b83a886f56b 407624 igor_1.3.0+dfsg.orig.tar.xz ccee38136c091011517e5a53cbd99af0a18402879f18d738f70375f9a5e9873f 3692 igor_1.3.0+dfsg-1.debian.tar.xz Files: 4a19673db9c20178e6fdafc9bc6d42a8 407624 igor_1.3.0+dfsg.orig.tar.xz f6d76091c7fe9f99816260b77ac271a8 3692 igor_1.3.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxMmuoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEqPA/9HT0I4htQQ3UtybD+5RleEY7yeuaYUMSJ a5h2p4cDaCK6j5Dvwlvni05pNVfNJClL3LvDJ9p6ZWcNlVsCQqGiQjxNGe1exjt6 Gua9e2CjbfrHH7CzCmeYCmaIWtQdEsJ5lRwRC+fbA2djx8EmOhwCqa/3g8QdxyOs n2VII4TQZQF6LqjGsIwgTSDSEWA3nPQ2gAeU+3cIUMeAUx/m2Fj3A09+yoUZXxvN wDBObIbejdl/2fOpIxvy7PijRRo3IgAikaVQix7jhIyQb47ROeqeFIklR9g5KqF9 ce+OmkRU8/uOQl+ksZtNipdKwmL1DQphoSS6n/h4sVYmOuP1IxkJQ5AHxbghsWrh WGSb6A4nmm2+5BIaE7tMQ803yDsa73GDpzBg1Gf1jnHEU2PXBnpbrwvnKvpvO/8M 8isS6iIrYTyhb5GtHa0aiCI4xf1VzbfqSDKQ+Mn4V6WCttTENFEthZUCxf3NjY0y hieF9FFxuYAGwowDsbt1QLRSA1J7hKL5wSuVewpyda2mZ1wNUJpaT/Zg/F5KJJmm dJsskBu1lqPOqu9x/TACkxO6ZzU1UO4ngQcICUkVgsROg2qJxucbYsPOH19i0rRL 3a/P1m+X7B+w5SfUbh85gftkNku4l6L/0ibyd+pokL0G0IiXwaJXOoXaCfIX1Fdw 7u/I9/DpvOo= =9d1G -----END PGP SIGNATURE----- Mon Jul 27 10:40:13 UTC 2020 I: Checking whether the package is not for us Mon Jul 27 10:40:13 UTC 2020 I: Starting 1st build on remote node codethink-sled10-arm64.debian.net. Mon Jul 27 10:40:13 UTC 2020 I: Preparing to do remote build '1' on codethink-sled10-arm64.debian.net. Mon Jul 27 10:44:53 UTC 2020 I: Deleting $TMPDIR on codethink-sled10-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 26 22:40:23 -12 2020 I: pbuilder-time-stamp: 1595846423 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_1.3.0+dfsg-1.dsc] I: copying [./igor_1.3.0+dfsg.orig.tar.xz] I: copying [./igor_1.3.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Jan 26 05:37:46 2019 -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_1.3.0+dfsg-1.dsc dpkg-source: info: extracting igor in igor-1.3.0+dfsg dpkg-source: info: unpacking igor_1.3.0+dfsg.orig.tar.xz dpkg-source: info: unpacking igor_1.3.0+dfsg-1.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3641/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='3641' 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/tmp.jQig8glF2u/pbuilderrc_ClE7 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.jQig8glF2u/b1 --logfile b1/build.log igor_1.3.0+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled10-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 25 20:26 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/3641/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11), libjemalloc-dev, libgsl-dev, libatlas-base-dev | libcblas-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 (>= 11); however: Package debhelper 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 libatlas-base-dev | libcblas-dev; however: Package libatlas-base-dev is not installed. Package libcblas-dev 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} bsdmainutils{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} libatlas-base-dev{a} libatlas3-base{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libicu63{a} libjemalloc-dev{a} libjemalloc2{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 26.5 MB of archives. After unpacking 120 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libgfortran5 arm64 8.3.0-6 [298 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libatlas3-base arm64 3.10.3-8 [2409 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libatlas-base-dev arm64 3.10.3-8 [2954 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libgslcblas0 arm64 2.5+dfsg-6 [69.5 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libgsl23 arm64 2.5+dfsg-6 [760 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libgsl-dev arm64 2.5+dfsg-6 [938 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libjemalloc2 arm64 5.1.0-3 [178 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libjemalloc-dev arm64 5.1.0-3 [315 kB] Fetched 26.5 MB in 2s (12.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. 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Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/igor-1.3.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package igor dpkg-buildpackage: info: source version 1.3.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/igor-1.3.0+dfsg' dh_auto_clean rm -rf docs/latex rm -rf docs/html rm -rf config.guess config.sub make[1]: Leaving directory '/build/igor-1.3.0+dfsg' dh_clean debian/rules build dh build 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=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-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) 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 checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) 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-1.3.0+dfsg/igor_src) configure: WARNING: no configuration information is in igor_src dh_auto_build make -j8 make[1]: Entering directory '/build/igor-1.3.0+dfsg' make all-recursive make[2]: Entering directory '/build/igor-1.3.0+dfsg' Making all in igor_src make[3]: Entering directory '/build/igor-1.3.0+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-1.3.0+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-1.3.0+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-1.3.0+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-1.3.0+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-1.3.0+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-1.3.0+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-1.3.0+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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp Deletion.cpp:1590:23: warning: multi-character character constant [-Wmultichar] else if ((*iter)=='14'){ ^~~~ 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: 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)' In file included from Errorrate.h:29, from Rec_Event.h:38, from Deletion.h:29, from Deletion.cpp:26: Utils.h:67:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Seq_side)' 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: throw invalid_argument("Unknown gene for deletions : " + this->event_class); ^~~~~~~~~~~ Deletion.cpp:1173:67: note: candidate 1: 'operator+(const char*, long int)' In file included from Errorrate.h:29, from Rec_Event.h:38, from Deletion.h:29, from Deletion.cpp:26: Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)' std::string operator+(const std::string& , Gene_class ); ^~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const 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: throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); ^~~~~~~~~~~ Dinuclmarkov.cpp:147:81: note: candidate 1: 'operator+(const char*, long int)' In file included from Errorrate.h:29, from Rec_Event.h:38, from Dinuclmarkov.h:32, from Dinuclmarkov.cpp:26: Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)' 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: throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); ^~~~~~~~~~~ Dinuclmarkov.cpp:211:81: note: candidate 1: 'operator+(const char*, long int)' In file included from Errorrate.h:29, from Rec_Event.h:38, from Dinuclmarkov.h:32, from Dinuclmarkov.cpp:26: Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)' 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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp 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:566:81: 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: throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); ^~~~~~~~~~~ Dinuclmarkov.cpp:566:81: note: candidate 1: 'operator+(const char*, long int)' In file included from Errorrate.h:29, from Rec_Event.h:38, from Dinuclmarkov.h:32, from Dinuclmarkov.cpp:26: Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)' 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:140:2: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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] } ^ 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-1.3.0+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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp 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: throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class); ^~~~~~~~~~~ Genechoice.cpp:908:73: note: candidate 1: 'operator+(const char*, long int)' In file included from Errorrate.h:29, from Rec_Event.h:38, from Genechoice.h:29, from Genechoice.cpp:26: Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)' 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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.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:140:2: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp 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: throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class); ^~~~~~~~~~~ Insertion.cpp:244:72: note: candidate 1: 'operator+(const char*, long int)' In file included from Errorrate.h:29, from Rec_Event.h:38, from Insertion.h:30, from Insertion.cpp:27: Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)' std::string operator+(const std::string& , Gene_class ); ^~~~~~~~ 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:140:2: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.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-1.3.0+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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp main.cpp: In function 'int main(int, char**)': main.cpp:241:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(&("man igor")[0]); ~~~~~~^~~~~~~~~~~~~~~~~~ main.cpp:265:11: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result] freopen(argv[++carg_i],"a+",stdout); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1480:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(&("mkdir " + cl_path )[0]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1631:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(&("mkdir " + cl_path + "run_demo")[0]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1665:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(&("mkdir " + cl_path + "aligns")[0]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1929:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(&("mkdir " + cl_path + batchname + "output")[0]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1933:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(&("mkdir " + cl_path + batchname + "inference")[0]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1939:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(&("mkdir " + cl_path + batchname + "evaluate")[0]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:1949:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] 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:140:2: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.3.0+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-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.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:140:2: warning: control reaches end of non-void function [-Wreturn-type] } ^ /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-1.3.0+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-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-main.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o -lgsl -lcblas -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-1.3.0+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-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-main.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o -lgsl -lcblas -ljemalloc -lpthread -ldl -fopenmp make[3]: Leaving directory '/build/igor-1.3.0+dfsg/igor_src' make[3]: Entering directory '/build/igor-1.3.0+dfsg' make[3]: Leaving directory '/build/igor-1.3.0+dfsg' make[2]: Leaving directory '/build/igor-1.3.0+dfsg' make[1]: Leaving directory '/build/igor-1.3.0+dfsg' dh_auto_test make -j8 check VERBOSE=1 make[1]: Entering directory '/build/igor-1.3.0+dfsg' Making check in igor_src make[2]: Entering directory '/build/igor-1.3.0+dfsg/igor_src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/igor-1.3.0+dfsg/igor_src' make[2]: Entering directory '/build/igor-1.3.0+dfsg' make[2]: Leaving directory '/build/igor-1.3.0+dfsg' make[1]: Leaving directory '/build/igor-1.3.0+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs dh_auto_install make -j1 install DESTDIR=/build/igor-1.3.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/igor-1.3.0+dfsg' Making install in igor_src make[2]: Entering directory '/build/igor-1.3.0+dfsg/igor_src' make[3]: Entering directory '/build/igor-1.3.0+dfsg/igor_src' /bin/mkdir -p '/build/igor-1.3.0+dfsg/debian/igor/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c igor '/build/igor-1.3.0+dfsg/debian/igor/usr/bin' libtool: install: /usr/bin/install -c igor /build/igor-1.3.0+dfsg/debian/igor/usr/bin/igor make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/igor-1.3.0+dfsg/igor_src' make[2]: Leaving directory '/build/igor-1.3.0+dfsg/igor_src' make[2]: Entering directory '/build/igor-1.3.0+dfsg' make[3]: Entering directory '/build/igor-1.3.0+dfsg' make[3]: Nothing to be done for 'install-exec-am'. mkdir -p /build/igor-1.3.0+dfsg/debian/igor/usr/share/igor/models cp -r models/* /build/igor-1.3.0+dfsg/debian/igor/usr/share/igor/models /bin/mkdir -p '/build/igor-1.3.0+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-1.3.0+dfsg/debian/igor/usr/share/igor/demo' make[3]: Leaving directory '/build/igor-1.3.0+dfsg' make[2]: Leaving directory '/build/igor-1.3.0+dfsg' make[1]: Leaving directory '/build/igor-1.3.0+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/igor/usr/bin/igor was not linked against libcblas.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_1.3.0+dfsg-1_arm64.deb'. dpkg-deb: building package 'igor' in '../igor_1.3.0+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../igor_1.3.0+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/3641 and its subdirectories I: Current time: Sun Jul 26 22:44:50 -12 2020 I: pbuilder-time-stamp: 1595846690 Mon Jul 27 10:44:54 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled15-arm64.debian.net. Mon Jul 27 10:44:54 UTC 2020 I: Preparing to do remote build '2' on codethink-sled15-arm64.debian.net. Mon Jul 27 10:47:10 UTC 2020 I: Deleting $TMPDIR on codethink-sled15-arm64.debian.net. Mon Jul 27 10:47:11 UTC 2020 I: igor_1.3.0+dfsg-1_arm64.changes: Format: 1.8 Date: Sat, 26 Jan 2019 17:21:02 +0100 Source: igor Binary: igor igor-dbgsym Architecture: arm64 Version: 1.3.0+dfsg-1 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 (1.3.0+dfsg-1) unstable; urgency=medium . * Team upload. * Debian Med team maintenance * Fix watch file * Standards-Version: 4.2.1 * Add missing Build-Depends: libatlas-base-dev | libcblas-dev * Fix for gcc-8 does not expose inline definitions to other source files * hardening=+all Checksums-Sha1: d7aefa96dea6658bcde2c0e641955c033ba88e95 6228676 igor-dbgsym_1.3.0+dfsg-1_arm64.deb 1c8cb53dad6c0880d11a2d211221641f866252f7 4791 igor_1.3.0+dfsg-1_arm64.buildinfo b56d79a4d6449b457c4d50638be75e5ecc757787 483908 igor_1.3.0+dfsg-1_arm64.deb Checksums-Sha256: 697b6193218b1a39cfb97c8cc65f41a2a34bac66c12972ea31f47545c46d63cc 6228676 igor-dbgsym_1.3.0+dfsg-1_arm64.deb 78e1e87888a5a00faa8645ea0b4caaf7f1e886e637dfb60d40fccfcb02a34d0d 4791 igor_1.3.0+dfsg-1_arm64.buildinfo 16326a154dabf1e40e34ed079ae0daaf96340701a11d8e39e81dbe2aff72239e 483908 igor_1.3.0+dfsg-1_arm64.deb Files: 8f471c03e752f851c6cfa3537e1fd800 6228676 debug optional igor-dbgsym_1.3.0+dfsg-1_arm64.deb 5940a30de8c693bb2e7d737ec0933702 4791 science optional igor_1.3.0+dfsg-1_arm64.buildinfo 91e560ea80d9e5c3ee1186176ab56c07 483908 science optional igor_1.3.0+dfsg-1_arm64.deb Mon Jul 27 10:47:12 UTC 2020 I: diffoscope 153 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.jQig8glF2u/igor_1.3.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.jQig8glF2u/igor_1.3.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.jQig8glF2u/igor_1.3.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.jQig8glF2u/b1/igor_1.3.0+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.jQig8glF2u/b2/igor_1.3.0+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.314s) 0.314s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.090s) 0.090s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 27 10:47:14 UTC 2020 I: diffoscope 153 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 27 10:47:14 UTC 2020 I: igor from buster built successfully and reproducibly on arm64. Mon Jul 27 10:47:15 UTC 2020 I: Submitting .buildinfo files to external archives: Mon Jul 27 10:47:15 UTC 2020 I: Submitting 8.0K b1/igor_1.3.0+dfsg-1_arm64.buildinfo.asc Mon Jul 27 10:47:16 UTC 2020 I: Submitting 8.0K b2/igor_1.3.0+dfsg-1_arm64.buildinfo.asc Mon Jul 27 10:47:17 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 27 10:47:17 UTC 2020 I: Done submitting .buildinfo files. Mon Jul 27 10:47:17 UTC 2020 I: Removing signed igor_1.3.0+dfsg-1_arm64.buildinfo.asc files: removed './b1/igor_1.3.0+dfsg-1_arm64.buildinfo.asc' removed './b2/igor_1.3.0+dfsg-1_arm64.buildinfo.asc'