Tue Nov 16 01:33:57 UTC 2021 I: starting to build proteinortho/bullseye/amd64 on jenkins on '2021-11-16 01:33' Tue Nov 16 01:33:57 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_18/48614/console.log Tue Nov 16 01:33:57 UTC 2021 I: Downloading source for bullseye/proteinortho=6.0.28+dfsg-1 --2021-11-16 01:34:02-- 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% 136M=0s 2021-11-16 01:34:02 (136 MB/s) - ‘proteinortho_6.0.28+dfsg-1.dsc’ saved [2184/2184] Tue Nov 16 01:34:02 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----- Tue Nov 16 01:34:02 UTC 2021 I: Checking whether the package is not for us Tue Nov 16 01:34:02 UTC 2021 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Nov 16 01:34:02 UTC 2021 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Nov 16 01:35:50 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 18 19:57:06 -12 2022 I: pbuilder-time-stamp: 1671436626 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.AaJkrpkb/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/3500021/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=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='589dc794502f472e8e33a253f56fdc16' 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='3500021' 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.4aojdMbXz3/pbuilderrc_Eymh --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4aojdMbXz3/b1 --logfile b1/build.log proteinortho_6.0.28+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) 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 Nov 23 06:04 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/3500021/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), 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 ... 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 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 48.7 MB of archives. After unpacking 208 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 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 diamond-aligner amd64 2.0.7-1 [1412 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libblas-dev amd64 3.9.0-3 [161 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 liblapack-dev amd64 3.9.0-3 [4247 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Fetched 48.7 MB in 1s (82.2 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 .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... 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Processing triggers for libc-bin (2.31-13+deb11u2) ... 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 amd64 debian/rules clean dh clean dh_auto_clean make -j16 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 -j16 "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_x86_64/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_x86_64/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_x86_64/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_x86_64/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 -j16 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) [TEST] Clean up all test files... [1/12] -p=blastp test: 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 -j16 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_x86_64/proteinortho_extract_from_graph.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_x86_64/proteinortho2html.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_x86_64/proteinortho_clustering' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_x86_64/proteinortho_history.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_x86_64/proteinortho_treeBuilderCore' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_treeBuilderCore' 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' -> '/build/proteinortho-6.0.28+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_x86_64/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_amd64.deb'. dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.0.28+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../proteinortho_6.0.28+dfsg-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/3500021 and its subdirectories I: Current time: Sun Dec 18 19:58:52 -12 2022 I: pbuilder-time-stamp: 1671436732 Tue Nov 16 01:35:51 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Tue Nov 16 01:35:51 UTC 2021 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Tue Nov 16 01:36:59 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Tue Nov 16 01:36:59 UTC 2021 I: proteinortho_6.0.28+dfsg-1_amd64.changes: Format: 1.8 Date: Mon, 01 Feb 2021 15:55:28 +0530 Source: proteinortho Binary: proteinortho proteinortho-dbgsym Architecture: amd64 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: f856dcf24a1e0bfd0cbd37b585f56ecccd362528 924260 proteinortho-dbgsym_6.0.28+dfsg-1_amd64.deb f53617415853bfde8ba1979913d5f2b6cb73115d 5973 proteinortho_6.0.28+dfsg-1_amd64.buildinfo efa253410c6dc1ae96a5b88b03cae9463547073c 210904 proteinortho_6.0.28+dfsg-1_amd64.deb Checksums-Sha256: 395f68174b88d8057006d5746f82e14ea3d1eee71bf36e19875013b92c3b62d1 924260 proteinortho-dbgsym_6.0.28+dfsg-1_amd64.deb 3f9d403921c97411e0a25abfcc8004f09b68af2b73950647bbcdc314a096ca75 5973 proteinortho_6.0.28+dfsg-1_amd64.buildinfo e2778c57361e2d0d57d9116509d24dad9734eeb133ddc577f2d54c675f056051 210904 proteinortho_6.0.28+dfsg-1_amd64.deb Files: e6e8555d35e971cd94e7fc5f348bff67 924260 debug optional proteinortho-dbgsym_6.0.28+dfsg-1_amd64.deb 2d32abf6a7966d3eca7ee1546ed48300 5973 science optional proteinortho_6.0.28+dfsg-1_amd64.buildinfo d38f5b7d4b0ce9a6046bcf41b5d522f0 210904 science optional proteinortho_6.0.28+dfsg-1_amd64.deb Tue Nov 16 01:37:06 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.4aojdMbXz3/proteinortho_6.0.28+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.4aojdMbXz3/proteinortho_6.0.28+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.4aojdMbXz3/proteinortho_6.0.28+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.4aojdMbXz3/b1/proteinortho_6.0.28+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.4aojdMbXz3/b2/proteinortho_6.0.28+dfsg-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: 1.151s) 1.151s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.039s) 0.039s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Nov 16 01:39:30 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Tue Nov 16 01:39:30 UTC 2021 I: proteinortho from bullseye built successfully and reproducibly on amd64. Tue Nov 16 01:39:33 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Nov 16 01:39:33 UTC 2021 I: Submitting 8.0K b1/proteinortho_6.0.28+dfsg-1_amd64.buildinfo.asc Tue Nov 16 01:39:34 UTC 2021 I: Submitting 8.0K b2/proteinortho_6.0.28+dfsg-1_amd64.buildinfo.asc Tue Nov 16 01:39:35 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Nov 16 01:39:35 UTC 2021 I: Done submitting .buildinfo files. Tue Nov 16 01:39:35 UTC 2021 I: Removing signed proteinortho_6.0.28+dfsg-1_amd64.buildinfo.asc files: removed './b1/proteinortho_6.0.28+dfsg-1_amd64.buildinfo.asc' removed './b2/proteinortho_6.0.28+dfsg-1_amd64.buildinfo.asc'