Fri Aug 20 19:55:34 UTC 2021 I: starting to build phylonium/bullseye/armhf on jenkins on '2021-08-20 19:55' Fri Aug 20 19:55:34 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_8/11152/console.log Fri Aug 20 19:55:34 UTC 2021 I: Downloading source for bullseye/phylonium=1.3-1 --2021-08-20 19:55:34-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/phylonium/phylonium_1.3-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2304 (2.2K) Saving to: ‘phylonium_1.3-1.dsc’ 0K .. 100% 101M=0s 2021-08-20 19:55:34 (101 MB/s) - ‘phylonium_1.3-1.dsc’ saved [2304/2304] Fri Aug 20 19:55:34 UTC 2021 I: phylonium_1.3-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phylonium Binary: phylonium Architecture: any Version: 1.3-1 Maintainer: Debian Med Packaging Team Uploaders: Fabian Klötzl Homepage: https://github.com/EvolBioInf/phylonium Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/phylonium Vcs-Git: https://salsa.debian.org/med-team/phylonium.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libdivsufsort-dev, libgsl-dev Package-List: phylonium deb science optional arch=any Checksums-Sha1: 22133516ed6b600558926938587454ff275db64d 44071659 phylonium_1.3.orig-debian-tests-data.tar.gz 88e65e6754d761b24d72118343769c1e88fc722f 408868 phylonium_1.3.orig.tar.gz cfbcff4719d266694f25c643d7872fbfe61b8882 4804 phylonium_1.3-1.debian.tar.xz Checksums-Sha256: 2b10cc3f31ad92308280dd3886b5607e4a6922d5633b681a895332cbdf8f5e26 44071659 phylonium_1.3.orig-debian-tests-data.tar.gz f5bb3331603fd0872240ee41c220d397f8ee7ea13efa4d78699a5df6bf6d2c3e 408868 phylonium_1.3.orig.tar.gz f7a80509b91283eaca8a867a81b5ad212a9c8595f2c5d3e4d0edeca9dbc8d1bc 4804 phylonium_1.3-1.debian.tar.xz Files: a8a20e4b6fd0b2d759243f422cccd25f 44071659 phylonium_1.3.orig-debian-tests-data.tar.gz 22b8d96526c708682ffb79ac056f956f 408868 phylonium_1.3.orig.tar.gz 4aa3e048ca37b4a76743ac0ccee7b0d5 4804 phylonium_1.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAl+lJXEUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafGAYg//c5hCn+piIdUSl2tzsrkNrAbKPcN2 P9lEEcwLNtmjfr0p/JxgKk8RDeheskfMxX1stcJjlc6R9mZwm0fSC24IUlPCw8Fx xBDTGTS4qUlEYb9QtGF37tGGd+LHU5RZ4ujzbe8540NMOu6YSUpb5rRF5w6pR7U6 LQHeWTu77Q+WF4Hfmfyyqk3bd+9n8HFk5Mqi8KaByMYPcbKfymYgpJnPuVlfinfc tTOQooMZ3isKgS7hJIBCUivTeuFCegZ8OWMhrKjZNSFHvSXOh4Ns0YdcwHUZMsHe 4WXI00SQ0EgkmGOw8zY25XnDmJr1/6qcb9+RvPwACLYAzQVddR+YxtewoZ2BOv10 tlqRDAaP8SXl1bDxQJ4dqi0XErZBzIQZTb+3U864l6e2hs0IkqQnY5WcGAAt8Xx6 q7Fi4eH01Tjt6hDPqwAIU5j9qsSTOkovwaJf7/UAhtXfWsiX5jVsDsUNfYikHV22 Z/Yq/ZOvaj2a644odfX5E0U+uYRrhnluxwPV0tIhyRWHLobA7I56dZ24s3p+rN+5 eNbnEliI5HgAXBcmJC7ljDRBytLBr7ca4KJozf96MZN0jJ9RFDiY0CDQcS4ah2xs nDUxqkiG1qockGTVpgoZDJOkiE21xpN5VYo16+xXtgpzRcFIZIQZYBF6fKgLm17W MskvnF25ZMXqgNE= =zO7h -----END PGP SIGNATURE----- Fri Aug 20 19:55:34 UTC 2021 I: Checking whether the package is not for us Fri Aug 20 19:55:34 UTC 2021 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Fri Aug 20 19:55:34 UTC 2021 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Fri Aug 20 20:02:58 UTC 2021 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 20 07:55:50 -12 2021 I: pbuilder-time-stamp: 1629489350 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [phylonium_1.3-1.dsc] I: copying [./phylonium_1.3.orig-debian-tests-data.tar.gz] I: copying [./phylonium_1.3.orig.tar.gz] I: copying [./phylonium_1.3-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.tdDOdopD/trustedkeys.kbx': General error gpgv: Signature made Thu Nov 5 22:29:05 2020 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phylonium_1.3-1.dsc dpkg-source: info: extracting phylonium in phylonium-1.3 dpkg-source: info: unpacking phylonium_1.3.orig.tar.gz dpkg-source: info: unpacking phylonium_1.3.orig-debian-tests-data.tar.gz dpkg-source: info: unpacking phylonium_1.3-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5865/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='a51dc64e49a8483b92c451c181752eeb' 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='5865' 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.3y0z1fZCyZ/pbuilderrc_rcZ8 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.3y0z1fZCyZ/b1 --logfile b1/build.log phylonium_1.3-1.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux virt64a 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jul 28 07:09 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 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 14 21:27 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/5865/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: armhf 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), libdivsufsort-dev, libgsl-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 ... 19398 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 libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-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} 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} libdebhelper-perl{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl25{a} libgslcblas0{a} libicu67{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, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 19.6 MB of archives. After unpacking 70.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libdivsufsort3 armhf 2.0.1-5 [44.7 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libdivsufsort-dev armhf 2.0.1-5 [19.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libgslcblas0 armhf 2.6+dfsg-2 [80.0 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libgsl25 armhf 2.6+dfsg-2 [769 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libgsl-dev armhf 2.6+dfsg-2 [963 kB] Fetched 19.6 MB in 3s (6694 kB/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 ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.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_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../25-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libdivsufsort3:armhf. Preparing to unpack .../31-libdivsufsort3_2.0.1-5_armhf.deb ... Unpacking libdivsufsort3:armhf (2.0.1-5) ... Selecting previously unselected package libdivsufsort-dev:armhf. Preparing to unpack .../32-libdivsufsort-dev_2.0.1-5_armhf.deb ... Unpacking libdivsufsort-dev:armhf (2.0.1-5) ... Selecting previously unselected package libgslcblas0:armhf. Preparing to unpack .../33-libgslcblas0_2.6+dfsg-2_armhf.deb ... Unpacking libgslcblas0:armhf (2.6+dfsg-2) ... Selecting previously unselected package libgsl25:armhf. Preparing to unpack .../34-libgsl25_2.6+dfsg-2_armhf.deb ... Unpacking libgsl25:armhf (2.6+dfsg-2) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../35-libgsl-dev_2.6+dfsg-2_armhf.deb ... Unpacking libgsl-dev (2.6+dfsg-2) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7) ... Setting up libgslcblas0:armhf (2.6+dfsg-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libgsl25:armhf (2.6+dfsg-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdivsufsort3:armhf (2.0.1-5) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up libdivsufsort-dev:armhf (2.0.1-5) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... 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/phylonium-1.3/ && 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 > ../phylonium_1.3-1_source.changes dpkg-buildpackage: info: source package phylonium dpkg-buildpackage: info: source version 1.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:11: installing './ar-lib' configure.ac:6: installing './compile' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' parallel-tests: installing './test-driver' libs/Makefile.am: installing './depcomp' test/Makefile.am:7: warning: source file '$(top_srcdir)/src/esa.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. test/Makefile.am:7: warning: source file '$(top_srcdir)/src/evo_model.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/process.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/sequence.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled debian/rules override_dh_auto_configure make[1]: Entering directory '/build/phylonium-1.3' dh_auto_configure -- --disable-x86simd ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --disable-x86simd 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 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 whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none 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 whether make sets $(MAKE)... (cached) yes checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for g++ option to support OpenMP... -fopenmp checking whether g++ supports C++14 features with -std=gnu++14... yes checking for gcc option to support OpenMP... -fopenmp checking for __attribute__((ifunc))... yes checking for cos in -lm... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -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 divsufsort.h usability... yes checking divsufsort.h presence... yes checking for divsufsort.h... yes checking for divsufsort in -ldivsufsort... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking err.h usability... yes checking err.h presence... yes checking for err.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int32_t... yes checking for uint8_t... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking for strtod... yes checking for reallocarray... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating libs/Makefile config.status: creating Makefile config.status: creating man/phylonium.1 config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/phylonium-1.3' dh_auto_build make -j3 make[1]: Entering directory '/build/phylonium-1.3' make all-recursive make[2]: Entering directory '/build/phylonium-1.3' Making all in libs make[3]: Entering directory '/build/phylonium-1.3/libs' rm -f libcompat.a ar cru libcompat.a ar: gcc -DHAVE_CONFIG_H -I. -I.. -I../opt -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c `u' modifier ignored since `D' is the default (see `U') ranlib libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o revseqcmp.o revseqcmp.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqcmp.o seqcmp.c rm -f librevseqcmp.a ar cru librevseqcmp.a revseqcmp.o ar: `u' modifier ignored since `D' is the default (see `U') rm -f libseqcmp.a ranlib librevseqcmp.a ar cru libseqcmp.a seqcmp.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp.a rm -f libpfasta.a ar cru libpfasta.a libpfasta_a-pfasta.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpfasta.a make[3]: Leaving directory '/build/phylonium-1.3/libs' Making all in src make[3]: Entering directory '/build/phylonium-1.3/src' g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-phylonium.o `test -f 'phylonium.cxx' || echo './'`phylonium.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-io.o `test -f 'io.cxx' || echo './'`io.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-sequence.o `test -f 'sequence.cxx' || echo './'`sequence.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-esa.o `test -f 'esa.cxx' || echo './'`esa.cxx esa.cxx: In constructor 'esa::esa(const sequence&)': esa.cxx:63:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'unsigned int' to 'int' [-Wnarrowing] 63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-process.o `test -f 'process.cxx' || echo './'`process.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-evo_model.o `test -f 'evo_model.cxx' || echo './'`evo_model.cxx g++ -std=gnu++14 -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phylonium phylonium-phylonium.o phylonium-io.o phylonium-sequence.o phylonium-esa.o phylonium-process.o phylonium-evo_model.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a -ldivsufsort -lm make[3]: Leaving directory '/build/phylonium-1.3/src' Making all in test make[3]: Entering directory '/build/phylonium-1.3/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/phylonium-1.3/test' Making all in . make[3]: Entering directory '/build/phylonium-1.3' make[3]: Leaving directory '/build/phylonium-1.3' make[2]: Leaving directory '/build/phylonium-1.3' make[1]: Leaving directory '/build/phylonium-1.3' dh_auto_test make -j3 check VERBOSE=1 make[1]: Entering directory '/build/phylonium-1.3' Making check in libs make[2]: Entering directory '/build/phylonium-1.3/libs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/phylonium-1.3/libs' Making check in src make[2]: Entering directory '/build/phylonium-1.3/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/phylonium-1.3/src' Making check in test make[2]: Entering directory '/build/phylonium-1.3/test' make simf unittests make[3]: Entering directory '/build/phylonium-1.3/test' g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simf-simf.o `test -f 'simf.cxx' || echo './'`simf.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-esa.o `test -f '../src/esa.cxx' || echo './'`../src/esa.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-evo_model.o `test -f '../src/evo_model.cxx' || echo './'`../src/evo_model.cxx ../src/esa.cxx: In constructor 'esa::esa(const sequence&)': ../src/esa.cxx:63:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'unsigned int' to 'int' [-Wnarrowing] 63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-process.o `test -f '../src/process.cxx' || echo './'`../src/process.cxx In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/bits/random.h:34, from /usr/include/c++/10/random:49, from simf.cxx:13: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 ../src/process.cxx:420: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 420 | #pragma omp parallel for num_threads(THREADS) | ../src/process.cxx:432: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 432 | #pragma omp critical | ../src/process.cxx:435: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 435 | #pragma omp atomic | ../src/process.cxx:441: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 441 | #pragma omp critical | ../src/process.cxx:511: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 511 | #pragma omp parallel for num_threads(THREADS) | ../src/process.cxx:518: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 518 | #pragma omp atomic | ../src/process.cxx:526: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 526 | #pragma omp atomic read | ../src/process.cxx:532: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 532 | #pragma omp critical | /usr/include/c++/10/bits/vector.tcc: In function 'int main(int, char**)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tmain.o `test -f 'Tmain.cxx' || echo './'`Tmain.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tprocess.o `test -f 'Tprocess.cxx' || echo './'`Tprocess.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.cxx g++ -std=gnu++14 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort -lm In file included from /usr/include/c++/10/vector:72, from catch.hpp:521, from Tmain.cxx:3: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from catch.hpp:521, from Tmain.cxx:3: /usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -std=gnu++14 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o unittests unittests-esa.o unittests-evo_model.o unittests-process.o unittests-sequence.o unittests-Tmain.o unittests-Tprocess.o unittests-Tsequence.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a -ldivsufsort -lm make[3]: Leaving directory '/build/phylonium-1.3/test' make[2]: Leaving directory '/build/phylonium-1.3/test' Making check in . make[2]: Entering directory '/build/phylonium-1.3' make check-TESTS make[3]: Entering directory '/build/phylonium-1.3' make[4]: Entering directory '/build/phylonium-1.3' PASS: test/unittests PASS: test/simple.sh ============================================================================ Testsuite summary for phylonium 1.3 ============================================================================ # TOTAL: 2 # PASS: 2 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/phylonium-1.3' make[3]: Leaving directory '/build/phylonium-1.3' make[2]: Leaving directory '/build/phylonium-1.3' make[1]: Leaving directory '/build/phylonium-1.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j3 install DESTDIR=/build/phylonium-1.3/debian/phylonium AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/phylonium-1.3' Making install in libs make[2]: Entering directory '/build/phylonium-1.3/libs' make[3]: Entering directory '/build/phylonium-1.3/libs' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/phylonium-1.3/libs' make[2]: Leaving directory '/build/phylonium-1.3/libs' Making install in src make[2]: Entering directory '/build/phylonium-1.3/src' make[3]: Entering directory '/build/phylonium-1.3/src' /bin/mkdir -p '/build/phylonium-1.3/debian/phylonium/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c phylonium '/build/phylonium-1.3/debian/phylonium/usr/bin' make[3]: Leaving directory '/build/phylonium-1.3/src' make[2]: Leaving directory '/build/phylonium-1.3/src' Making install in test make[2]: Entering directory '/build/phylonium-1.3/test' make[3]: Entering directory '/build/phylonium-1.3/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/phylonium-1.3/test' make[2]: Leaving directory '/build/phylonium-1.3/test' Making install in . make[2]: Entering directory '/build/phylonium-1.3' make[3]: Entering directory '/build/phylonium-1.3' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/phylonium-1.3/debian/phylonium/usr/share/doc/phylonium' /usr/bin/install -c -m 644 documentation/manual.pdf '/build/phylonium-1.3/debian/phylonium/usr/share/doc/phylonium' /bin/mkdir -p '/build/phylonium-1.3/debian/phylonium/usr/share/man/man1' /usr/bin/install -c -m 644 man/phylonium.1 '/build/phylonium-1.3/debian/phylonium/usr/share/man/man1' make[3]: Leaving directory '/build/phylonium-1.3' make[2]: Leaving directory '/build/phylonium-1.3' make[1]: Leaving directory '/build/phylonium-1.3' dh_installdocs dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/phylonium/usr/bin/phylonium contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phylonium' in '../phylonium_1.3-1_armhf.deb'. dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.3-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phylonium_1.3-1_armhf.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: including full 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/5865 and its subdirectories I: Current time: Fri Aug 20 08:01:09 -12 2021 I: pbuilder-time-stamp: 1629489669 Fri Aug 20 20:03:00 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ff4a-armhf-rb.debian.net. Fri Aug 20 20:03:00 UTC 2021 I: Preparing to do remote build '2' on ff4a-armhf-rb.debian.net. Fri Aug 20 20:15:52 UTC 2021 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. Fri Aug 20 20:15:55 UTC 2021 I: phylonium_1.3-1_armhf.changes: Format: 1.8 Date: Fri, 06 Nov 2020 14:27:37 +0530 Source: phylonium Binary: phylonium phylonium-dbgsym Architecture: armhf Version: 1.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: phylonium - Fast and Accurate Estimation of Evolutionary Distances Changes: phylonium (1.3-1) unstable; urgency=medium . * Team Upload. * Multi-orig tarball for testing data * New upstream version 1.3 * Add autopkgtests * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update)\ Checksums-Sha1: 3878c6cd4e2d5108a111989d3f3211f40d9c6f40 523184 phylonium-dbgsym_1.3-1_armhf.deb 7fcc6ea48717c230a1b87cec680650b9a5538bd0 4892 phylonium_1.3-1_armhf.buildinfo c5bac75d0c69632bcdb0f836b765735bbf165378 280324 phylonium_1.3-1_armhf.deb Checksums-Sha256: 09e9e6187b13a197c521f4c697e45f29fd6c21e942476f4b11403dc40d3b190a 523184 phylonium-dbgsym_1.3-1_armhf.deb 0256c27b4800ca497ebf5ae82af55d0b967d8269e8f6c033ce05ce0d05c3ac17 4892 phylonium_1.3-1_armhf.buildinfo 357e65bd4c43f5155d99dc7edd937267276c0a1ac697264678dab87958663ed1 280324 phylonium_1.3-1_armhf.deb Files: f27c34af7d03fa648989bec2cb2fed48 523184 debug optional phylonium-dbgsym_1.3-1_armhf.deb acc2e824bdaee7f34bb965c93ffffa33 4892 science optional phylonium_1.3-1_armhf.buildinfo 3fd34739f307ebb5b3a67d21bd1056e4 280324 science optional phylonium_1.3-1_armhf.deb Fri Aug 20 20:16:01 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.3y0z1fZCyZ/phylonium_1.3-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.3y0z1fZCyZ/phylonium_1.3-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.3y0z1fZCyZ/phylonium_1.3-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.3y0z1fZCyZ/b1/phylonium_1.3-1_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.3y0z1fZCyZ/b2/phylonium_1.3-1_armhf.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: 7.992s) 7.992s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.636s) 0.636s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Aug 20 20:19:48 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 20 20:19:48 UTC 2021 I: phylonium from bullseye built successfully and reproducibly on armhf. Fri Aug 20 20:19:49 UTC 2021 I: Submitting .buildinfo files to external archives: Fri Aug 20 20:19:49 UTC 2021 I: Submitting 8.0K b1/phylonium_1.3-1_armhf.buildinfo.asc Fri Aug 20 20:19:51 UTC 2021 I: Submitting 8.0K b2/phylonium_1.3-1_armhf.buildinfo.asc Fri Aug 20 20:19:53 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Aug 20 20:19:53 UTC 2021 I: Done submitting .buildinfo files. Fri Aug 20 20:19:53 UTC 2021 I: Removing signed phylonium_1.3-1_armhf.buildinfo.asc files: removed './b1/phylonium_1.3-1_armhf.buildinfo.asc' removed './b2/phylonium_1.3-1_armhf.buildinfo.asc'