Sat Aug 21 14:53:35 UTC 2021 I: starting to build proteinortho/bullseye/arm64 on jenkins on '2021-08-21 14:53' Sat Aug 21 14:53:35 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/46931/console.log Sat Aug 21 14:53:35 UTC 2021 I: Downloading source for bullseye/proteinortho=6.0.28+dfsg-1 --2021-08-21 14:53:35-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/proteinortho/proteinortho_6.0.28%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2184 (2.1K) Saving to: ‘proteinortho_6.0.28+dfsg-1.dsc’ 0K .. 100% 15.3M=0s 2021-08-21 14:53:35 (15.3 MB/s) - ‘proteinortho_6.0.28+dfsg-1.dsc’ saved [2184/2184] Sat Aug 21 14:53:35 UTC 2021 I: proteinortho_6.0.28+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: proteinortho Binary: proteinortho Architecture: any Version: 6.0.28+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra Homepage: https://gitlab.com/paulklemm_PHD/proteinortho Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/proteinortho Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner, procps Package-List: proteinortho deb science optional arch=any Checksums-Sha1: 1a7a107de669c298311ea9b4cbd6ed35f78af829 511280 proteinortho_6.0.28+dfsg.orig.tar.xz 18f6971318cba96f4f7b450db1f70fc46f07e71a 7028 proteinortho_6.0.28+dfsg-1.debian.tar.xz Checksums-Sha256: 8313be7b13b1ce86c9b80b85ed7dbcd7d856adafb31f563b4b1add526050e1af 511280 proteinortho_6.0.28+dfsg.orig.tar.xz 27dbeded20a55fe619377c119f8132622fce324a9be43869d1a19362e38d66d5 7028 proteinortho_6.0.28+dfsg-1.debian.tar.xz Files: e3e0060b37d2069b080249d31c733872 511280 proteinortho_6.0.28+dfsg.orig.tar.xz cd6c344e6c64a38efb5f0018ac5cfd2a 7028 proteinortho_6.0.28+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmAX2DoUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafHVwRAAtVu5y/8DYnq4m4qGSE68uWDnfWPz cO9SivNhZxhGiwmg4mtvkdKn1G1z+M4c99IqCBtQn8Y4ZZ1IhH9hE8zW5/P3u2nd l7tS5HppiXPUtVm066dKYIf62LOw/fUyxIsgkXLQVkH3I1Sbe4PL06Pa05GMScmo SSaATttTXYj+Rmc4sODaIHa3kfLCaKyXZ1ETflW3ipj8f4AaPuekTDkVGaOLbsIa Ug4VLDGt6eUMjV8La+KbaBuRkU6K47q2kkpUiNR/IljfvsKg/7/aFp1PHmCN2JHL eWv79HGrxLOijtTOAYIIV8Bslza81wgcOH4DQaNMFPpn0k8pkvg8fMmkbXmdymOX qdj0wDAiqmlTg3y8WwPANadfuo2iaZcpVbCLWc0X44fRRNMit+MTH4khbC+iQn7S wzlHTLhZBFXqNe6xye51kODA7EvYD4wx4j2IxgrkbaRQKZCsHYGPyl7CkkLuYWXu txXsqVObXH9np1HPzglAXKnoeSVdDq1sRr+x+dubkJMI6uG0rnLgbVFK4HD70gTE UpqklWTH+iLrrxM4jx536cPtsZ/CTgVT5zZxmmhenwRmDSGQEDMVYoPoYPK859Rs TSFvnONZ/LbSRn+DkPN5bU5LR4pl7JrH8523VwT+eQXSyxhDgMWskgTsSl3okkfL P/qrfGvHjAh0/4s= =r5QD -----END PGP SIGNATURE----- Sat Aug 21 14:53:35 UTC 2021 I: Checking whether the package is not for us Sat Aug 21 14:53:35 UTC 2021 I: Starting 1st build on remote node codethink12-arm64.debian.net. Sat Aug 21 14:53:35 UTC 2021 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Sat Aug 21 14:57:27 UTC 2021 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 21 02:53:39 -12 2021 I: pbuilder-time-stamp: 1629557619 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 [proteinortho_6.0.28+dfsg-1.dsc] I: copying [./proteinortho_6.0.28+dfsg.orig.tar.xz] I: copying [./proteinortho_6.0.28+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.BnqIg50y/trustedkeys.kbx': General error gpgv: Signature made Sun Jan 31 22:30:18 2021 -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 ./proteinortho_6.0.28+dfsg-1.dsc dpkg-source: info: extracting proteinortho in proteinortho-6.0.28+dfsg dpkg-source: info: unpacking proteinortho_6.0.28+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_6.0.28+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb_diamond dpkg-source: info: applying baseline.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3029/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3029' 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.KPm7iKMdny/pbuilderrc_eyFC --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.KPm7iKMdny/b1 --logfile b1/build.log proteinortho_6.0.28+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink12-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 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 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 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 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 134808 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 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 20 21:24 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 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/3029/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner, procps dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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 ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev | libatlas-base-dev | liblapack.so; however: Package liblapack-dev is not installed. Package libatlas-base-dev is not installed. Package liblapack.so is not installed. pbuilder-satisfydepends-dummy depends on diamond-aligner; however: Package diamond-aligner is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps 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} diamond-aligner{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu67{a} liblapack-dev{a} liblapack3{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmpdec3{a} libncurses6{a} libpipeline1{a} libprocps8{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx med-config psmisc wget 0 packages upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 44.1 MB of archives. After unpacking 197 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 diamond-aligner arm64 2.0.7-1 [1114 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libblas3 arm64 3.9.0-3 [101 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libblas-dev arm64 3.9.0-3 [107 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3 [1541 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 liblapack-dev arm64 3.9.0-3 [2758 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 liblmdb0 arm64 0.9.24-1 [43.7 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libmbedcrypto3 arm64 2.16.9-0.1 [211 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libmbedx509-0 arm64 2.16.9-0.1 [108 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libmbedtls12 arm64 2.16.9-0.1 [132 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 ncbi-blast+ arm64 2.11.0+ds-1 [10.2 MB] Fetched 44.1 MB in 3s (16.4 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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... 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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/proteinortho-6.0.28+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../proteinortho_6.0.28+dfsg-1_source.changes dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 6.0.28+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j8 clean make[1]: Entering directory '/build/proteinortho-6.0.28+dfsg' rm -rf src/BUILD test/C.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.* rm -rf src/lapack-3.8.0/ make[1]: Leaving directory '/build/proteinortho-6.0.28+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/proteinortho-6.0.28+dfsg' Creating build directory ... [ 10%] Prepare proteinortho_clustering ... [ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking) g++ -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proteinortho-6.0.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -o src/BUILD/Linux_aarch64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive [ 25%] Building **graphMinusRemovegraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proteinortho-6.0.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_aarch64/proteinortho_graphMinusRemovegraph src/graphMinusRemovegraph.cpp -Wl,-z,relro -Wl,-z,now [ 50%] Building **cleanupblastgraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proteinortho-6.0.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_aarch64/proteinortho_cleanupblastgraph src/cleanupblastgraph.cpp -Wl,-z,relro -Wl,-z,now [ 75%] Building **po_tree** cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/proteinortho-6.0.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o src/BUILD/Linux_aarch64/proteinortho_treeBuilderCore src/po_tree.c -Wl,-z,relro -Wl,-z,now src/po_tree.c: In function 'fetch_matrix': src/po_tree.c:330:2: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 330 | fscanf (datei, "%d\n", viecher); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/po_tree.c:341:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 341 | fscanf (datei, "%s ",(*pnamen)[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/po_tree.c:345:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 345 | fscanf (datei, "%s \n",(*pnamen)[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/po_tree.c:378:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 378 | fscanf (datei, "%c ",&(matrix[i][*ccs])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/po_tree.c:381:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 381 | fscanf (datei, "%c \n",&(matrix[(*viecher)-1][*ccs])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - test max_of_diag() : 1 - test generate_random_vector() : 1 - test get_new_x() : 1 - test makeOrthogonal() : 1 - test normalize() : 1 - test getY() : 1 - test splitGroups() : 1 All test passed. ......OK dynamic linking was successful for proteinortho_clustering! [100%] Everything is compiled with no errors. make[1]: Leaving directory '/build/proteinortho-6.0.28+dfsg' dh_auto_test make -j8 test make[1]: Entering directory '/build/proteinortho-6.0.28+dfsg' [TEST] Clean up all test files... [TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped) [1/12] -p=blastp test: [TEST] Clean up all test files... passed [2/12] -p=blastp+ synteny (PoFF) test: tput: unknown terminal "unknown" tput: unknown terminal "unknown" tput: unknown terminal "unknown" tput: unknown terminal "unknown" passed [3/12] -p=diamond test: passed [4/12] -p=diamond (--moresensitive) test (subparaBlast): passed [5/12] -p=lastp (lastal) test: lastal missing, skipping... [6/12] -p=topaz test: topaz missing, skipping... [7/12] -p=usearch test: usearch missing, skipping... [8/12] -p=ublast test: usearch missing, skipping... [9/12] -p=rapsearch test: rapsearch missing, skipping... [10/12] -p=blatp (blat) test: blat missing, skipping... [11/12] -p=mmseqsp (mmseqs) test: mmseqs missing, skipping... [12/12] -p=autoblast (automatically detect blastp,blastn,...) test: blastall missing, skipping... [TEST] 2. -step=3 tests (proteinortho_clustering) [1/2] various test functions of proteinortho_clustering (if this fails, try make clean first): passed [2/2] Compare results of 'with lapack' and 'without lapack': passed [TEST] All tests passed make[1]: Leaving directory '/build/proteinortho-6.0.28+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/proteinortho-6.0.28+dfsg' mkdir -p /build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin make -j8 install DESTDIR=/build/proteinortho-6.0.28\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/proteinortho-6.0.28\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/build/proteinortho-6.0.28+dfsg' INSTALLING everything to /build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl' 'proteinortho' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho' 'src/BUILD/Linux_aarch64/proteinortho_extract_from_graph.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_aarch64/proteinortho_formatUsearch.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_aarch64/proteinortho_compareProteinorthoGraphs.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_aarch64/proteinortho_do_mcl.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_aarch64/proteinortho2html.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_aarch64/proteinortho2xml.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_aarch64/proteinortho_clustering' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_aarch64/proteinortho_singletons.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_aarch64/proteinortho_ffadj_mcs.py' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_aarch64/proteinortho2tree.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_aarch64/proteinortho_history.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_aarch64/proteinortho_cleanupblastgraph' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_aarch64/proteinortho_graphMinusRemovegraph' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_aarch64/proteinortho_treeBuilderCore' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_treeBuilderCore' 'src/BUILD/Linux_aarch64/proteinortho_grab_proteins.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_aarch64/proteinortho_summary.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl' Everything installed successfully to /build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin. If needed you can add /build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin'. make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/proteinortho-6.0.28+dfsg' make[1]: Leaving directory '/build/proteinortho-6.0.28+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/proteinortho-6.0.28+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/proteinortho-6.0.28+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/proteinortho-6.0.28+dfsg' dh_fixperms find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \; make[1]: Leaving directory '/build/proteinortho-6.0.28+dfsg' 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 'proteinortho' in '../proteinortho_6.0.28+dfsg-1_arm64.deb'. dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.0.28+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../proteinortho_6.0.28+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/3029 and its subdirectories I: Current time: Sat Aug 21 02:57:26 -12 2021 I: pbuilder-time-stamp: 1629557846 Sat Aug 21 14:57:28 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink13-arm64.debian.net. Sat Aug 21 14:57:28 UTC 2021 I: Preparing to do remote build '2' on codethink13-arm64.debian.net. Sat Aug 21 14:59:42 UTC 2021 I: Deleting $TMPDIR on codethink13-arm64.debian.net. Sat Aug 21 14:59:43 UTC 2021 I: proteinortho_6.0.28+dfsg-1_arm64.changes: Format: 1.8 Date: Mon, 01 Feb 2021 15:55:28 +0530 Source: proteinortho Binary: proteinortho proteinortho-dbgsym Architecture: arm64 Version: 6.0.28+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: proteinortho - Detection of (Co-)orthologs in large-scale protein analysis Changes: proteinortho (6.0.28+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 97ef7fcd9f0a4240798bccd3adde3ec796f3bc1c 903568 proteinortho-dbgsym_6.0.28+dfsg-1_arm64.deb d2c5bbc0e5f1497c48f6d09a43e4cef93ef1183a 5789 proteinortho_6.0.28+dfsg-1_arm64.buildinfo e0d08333c054ac6a504990050b337845ea5836dc 202224 proteinortho_6.0.28+dfsg-1_arm64.deb Checksums-Sha256: 9624d25c38578c2ef8fd53ce03a1128d86039be244e7896c511f0d27d51911a8 903568 proteinortho-dbgsym_6.0.28+dfsg-1_arm64.deb 6a598402c7cf7bdad528b7dac15b811757044fc6d2552efd215b32b87de9b496 5789 proteinortho_6.0.28+dfsg-1_arm64.buildinfo ccb76b6e0d11f71729f5ac322d65125aed7f78945c5bae733a079f3a26a930f8 202224 proteinortho_6.0.28+dfsg-1_arm64.deb Files: 10c74428154be7b7c3060270f801eb1d 903568 debug optional proteinortho-dbgsym_6.0.28+dfsg-1_arm64.deb 08dd7885d7af187a3e94cf545126ad8f 5789 science optional proteinortho_6.0.28+dfsg-1_arm64.buildinfo fbfd543878a06e954fe66881308a8337 202224 science optional proteinortho_6.0.28+dfsg-1_arm64.deb Sat Aug 21 14:59:44 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.KPm7iKMdny/proteinortho_6.0.28+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.KPm7iKMdny/proteinortho_6.0.28+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.KPm7iKMdny/proteinortho_6.0.28+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.KPm7iKMdny/b1/proteinortho_6.0.28+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.KPm7iKMdny/b2/proteinortho_6.0.28+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.251s) 0.251s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.026s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sat Aug 21 14:59:45 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sat Aug 21 14:59:45 UTC 2021 I: proteinortho from bullseye built successfully and reproducibly on arm64. Sat Aug 21 14:59:46 UTC 2021 I: Submitting .buildinfo files to external archives: Sat Aug 21 14:59:46 UTC 2021 I: Submitting 8.0K b1/proteinortho_6.0.28+dfsg-1_arm64.buildinfo.asc Sat Aug 21 14:59:47 UTC 2021 I: Submitting 8.0K b2/proteinortho_6.0.28+dfsg-1_arm64.buildinfo.asc Sat Aug 21 14:59:47 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Aug 21 14:59:47 UTC 2021 I: Done submitting .buildinfo files. Sat Aug 21 14:59:47 UTC 2021 I: Removing signed proteinortho_6.0.28+dfsg-1_arm64.buildinfo.asc files: removed './b1/proteinortho_6.0.28+dfsg-1_arm64.buildinfo.asc' removed './b2/proteinortho_6.0.28+dfsg-1_arm64.buildinfo.asc'