Thu Feb 10 01:23:12 UTC 2022 I: starting to build phylonium/bullseye/amd64 on jenkins on '2022-02-10 01:22' Thu Feb 10 01:23:12 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_1/126/console.log Thu Feb 10 01:23:12 UTC 2022 I: Downloading source for bullseye/phylonium=1.3-1 --2022-02-10 01:23:12-- 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% 144M=0s 2022-02-10 01:23:12 (144 MB/s) - ‘phylonium_1.3-1.dsc’ saved [2304/2304] Thu Feb 10 01:23:12 UTC 2022 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----- Thu Feb 10 01:23:12 UTC 2022 I: Checking whether the package is not for us Thu Feb 10 01:23:12 UTC 2022 I: Starting 1st build on remote node ionos1-amd64.debian.net. Thu Feb 10 01:23:12 UTC 2022 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Thu Feb 10 01:24:42 UTC 2022 I: Deleting $TMPDIR on ionos1-amd64.debian.net. W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build I: Current time: Wed Feb 9 13:23:15 -12 2022 I: pbuilder-time-stamp: 1644456195 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.H2ct7cnS/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/2497699/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' 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='2497699' 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.RlX0yZTa71/pbuilderrc_w7MI --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RlX0yZTa71/b1 --logfile b1/build.log phylonium_1.3-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/sbin/chroot' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-11-amd64 #1 SMP Debian 5.10.92-1 (2022-01-18) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 2021 more -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Feb 6 21:25 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 2021 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/2497699/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19655 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 20.5 MB of archives. After unpacking 78.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort-dev amd64 2.0.1-5 [19.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libgsl-dev amd64 2.6+dfsg-2 [1123 kB] Fetched 20.5 MB in 0s (72.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../10-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_amd64.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) ... 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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 amd64 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 -- ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking 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 -j15 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 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 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 -mpopcnt -mssse3 -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o librevseqcmp_ssse3_a-revseqcmp_ssse3.o `test -f 'revseqcmp_ssse3.c' || echo './'`revseqcmp_ssse3.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o librevseqcmp_avx2_a-revseqcmp_avx2.o `test -f 'revseqcmp_avx2.c' || echo './'`revseqcmp_avx2.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 gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -msse2 -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqcmp_sse2_a-seqcmp_sse2.o `test -f 'seqcmp_sse2.c' || echo './'`seqcmp_sse2.c ar cru libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqcmp_avx2_a-seqcmp_avx2.o `test -f 'seqcmp_avx2.c' || echo './'`seqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx512bw -mavx512vl -g -O2 -fdebug-prefix-map=/build/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqcmp_avx512_a-seqcmp_avx512.o `test -f 'seqcmp_avx512.c' || echo './'`seqcmp_avx512.c ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcompat.a rm -f libseqcmp_sse2.a ar cru libseqcmp_sse2.a libseqcmp_sse2_a-seqcmp_sse2.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp_sse2.a rm -f librevseqcmp_ssse3.a ar cru librevseqcmp_ssse3.a librevseqcmp_ssse3_a-revseqcmp_ssse3.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib librevseqcmp_ssse3.a rm -f libseqcmp_avx512.a ar cru libseqcmp_avx512.a libseqcmp_avx512_a-seqcmp_avx512.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp_avx512.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 rm -f libseqcmp_avx2.a ar cru libseqcmp_avx2.a libseqcmp_avx2_a-seqcmp_avx2.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp_avx2.a rm -f libseqcmp.a ar cru libseqcmp.a seqcmp.o libseqcmp_sse2.a libseqcmp_avx2.a libseqcmp_avx512.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp.a rm -f librevseqcmp_avx2.a ar cru librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib librevseqcmp_avx2.a rm -f librevseqcmp.a ar cru librevseqcmp.a revseqcmp.o librevseqcmp_ssse3.a librevseqcmp_avx2.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib librevseqcmp.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 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 esa.cxx: In constructor 'esa::esa(const sequence&)': esa.cxx:63:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'int' [-Wnarrowing] 63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ 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 ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.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 -j15 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 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 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 ../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 | ../src/esa.cxx: In constructor 'esa::esa(const sequence&)': ../src/esa.cxx:63:55: warning: narrowing conversion of '(((& seq)->sequence::size() * 2) + 1)' from 'long unsigned int' to 'int' [-Wnarrowing] 63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ 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 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 ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.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 -j15 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' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/phylonium-1.3/debian/phylonium/usr/bin' /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' /bin/mkdir -p '/build/phylonium-1.3/debian/phylonium/usr/share/man/man1' /usr/bin/install -c -m 644 documentation/manual.pdf '/build/phylonium-1.3/debian/phylonium/usr/share/doc/phylonium' /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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phylonium' in '../phylonium_1.3-1_amd64.deb'. dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.3-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phylonium_1.3-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/2497699 and its subdirectories I: Current time: Wed Feb 9 13:24:41 -12 2022 I: pbuilder-time-stamp: 1644456281 Thu Feb 10 01:24:42 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Thu Feb 10 01:24:42 UTC 2022 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Thu Feb 10 01:26:35 UTC 2022 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Thu Feb 10 01:26:35 UTC 2022 I: phylonium_1.3-1_amd64.changes: Format: 1.8 Date: Fri, 06 Nov 2020 14:27:37 +0530 Source: phylonium Binary: phylonium phylonium-dbgsym Architecture: amd64 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: 73873f63afac8cdbbc2d7409345a856a521c8ee6 528916 phylonium-dbgsym_1.3-1_amd64.deb 94e819eb103539acba1270586f3636ba6932f19e 5153 phylonium_1.3-1_amd64.buildinfo fdfbfbc9693557d5c907abab786f998f2e47ef1f 287792 phylonium_1.3-1_amd64.deb Checksums-Sha256: ddd25a2fa27bf72c4c09af616ad2a714a39756bc31db83733cc876f8d2c25143 528916 phylonium-dbgsym_1.3-1_amd64.deb 88b3fd53fe5fa6330d6b3d4bb0496e4583de792beb745658f0283463867b661d 5153 phylonium_1.3-1_amd64.buildinfo 68dc469cda15036e06610f5bfadf12ea905920c9c158449b53c18dd9abd0c303 287792 phylonium_1.3-1_amd64.deb Files: e1010225994e83fd4e3902197210d0a6 528916 debug optional phylonium-dbgsym_1.3-1_amd64.deb fffcbdd52f87b8114da1c9c10de98d84 5153 science optional phylonium_1.3-1_amd64.buildinfo 5943d540febdbac71085145f50398040 287792 science optional phylonium_1.3-1_amd64.deb Thu Feb 10 01:26:38 UTC 2022 I: diffoscope 203 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 5400 --html /srv/reproducible-results/rbuild-debian/tmp.RlX0yZTa71/phylonium_1.3-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.RlX0yZTa71/phylonium_1.3-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.RlX0yZTa71/phylonium_1.3-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.RlX0yZTa71/b1/phylonium_1.3-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.RlX0yZTa71/b2/phylonium_1.3-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.484s) 0.483s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.040s) 0.039s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Thu Feb 10 01:26:41 UTC 2022 I: diffoscope 203 found no differences in the changes files, and a .buildinfo file also exists. Thu Feb 10 01:26:41 UTC 2022 I: phylonium from bullseye built successfully and reproducibly on amd64. Thu Feb 10 01:26:42 UTC 2022 I: Submitting .buildinfo files to external archives: Thu Feb 10 01:26:43 UTC 2022 I: Submitting 8.0K b1/phylonium_1.3-1_amd64.buildinfo.asc Thu Feb 10 01:26:44 UTC 2022 I: Submitting 8.0K b2/phylonium_1.3-1_amd64.buildinfo.asc Thu Feb 10 01:26:45 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Feb 10 01:26:45 UTC 2022 I: Done submitting .buildinfo files. Thu Feb 10 01:26:45 UTC 2022 I: Removing signed phylonium_1.3-1_amd64.buildinfo.asc files: removed './b1/phylonium_1.3-1_amd64.buildinfo.asc' removed './b2/phylonium_1.3-1_amd64.buildinfo.asc'