Thu Oct 28 20:57:26 UTC 2021 I: starting to build skesa/bullseye/amd64 on jenkins on '2021-10-28 20:57' Thu Oct 28 20:57:26 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_3/24597/console.log Thu Oct 28 20:57:26 UTC 2021 I: Downloading source for bullseye/skesa=2.4.0-1 --2021-10-28 20:57:26-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/skesa/skesa_2.4.0-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2088 (2.0K) Saving to: ‘skesa_2.4.0-1.dsc’ 0K .. 100% 157M=0s 2021-10-28 20:57:27 (157 MB/s) - ‘skesa_2.4.0-1.dsc’ saved [2088/2088] Thu Oct 28 20:57:27 UTC 2021 I: skesa_2.4.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: skesa Binary: skesa Architecture: any Version: 2.4.0-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/ncbi/SKESA Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/skesa Vcs-Git: https://salsa.debian.org/med-team/skesa.git Build-Depends: debhelper-compat (= 12), libboost-dev, libboost-chrono-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-regex-dev, libboost-system-dev, libboost-timer-dev, libncbi-vdb-dev, libngs-sdk-dev Package-List: skesa deb science optional arch=any Checksums-Sha1: 5f77c432dbc512571a176f3f77fcc1c1cb691b30 138729 skesa_2.4.0.orig.tar.gz 9b27c1d83ed2a8fd405438b672b588598bc311e2 15840 skesa_2.4.0-1.debian.tar.xz Checksums-Sha256: c07b56dfa394c013e519d5a246b7dee03db41d8ac912ab9ca02cf4d20bf13b15 138729 skesa_2.4.0.orig.tar.gz 042b114710af0365799b7e52d5cb62a7f32e81e02eb1f2b7dee67a19ecfbc7f8 15840 skesa_2.4.0-1.debian.tar.xz Files: 0846b4a906285d34e7e45d08b37ba18f 138729 skesa_2.4.0.orig.tar.gz b80581889df25f0c025ec75c28200f36 15840 skesa_2.4.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl7D1IITHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0VG+D/9YpHfpKaBQTxJl/Bijl7S86MWjH2V5 /OLJG3DvBCoVzzPiPox6QKGmxYuwYGI2E2L/QJdrEnWb863tCbr4OD+VKBp1qRbU T0TOEeGQfMNkDYNXSK66ynLIH7k2xLi0LVFiOl4z9nSfDlhQG10BeYpm1cxJCupg bwj+2lY5lwh6cRBfU5j85Y3T3TLOm/nxMoxOyAj5hFjb7ZDSk3XV6RP/JwjYlCyJ dO9G4AtWLzUGIdph5AoX/Xmvevbtbnk9Au4L7dJ3o0pQ7DPS/8Eog5Vj4pvBQcIA ii8vB96IFRtrrfsehA0eskngiVcn6hVqxFLU37+smI6by75OC+Gq2GjLtKRVfkyV Nc5bIadKWQuvKIwrtLY+PLS6oLrYYqxN0SUeCp443DqGyEwGoX7bEcY3sWD4VlQT ei+MEgsKuDMA2Pbc3z+izOSUC62xv2WLvvcSOrXAcdz+5l2URfG6whtMIG8Pvz+H tspHs50mNg96+cwh4rsp8Ra5va4tgdGDXhyKf+WNnt9HVbxt0w9yUC3xajQ/mq8S uCd35eZ+XB3YUI1dREEqJ4+1NH6QgS6umvVjI+c9qvtoo9xiIbH1P3bX4FEawz6y lLWM9l1sEMFrnpG7vqja1DEe2GNuQBVk2ZhjVh1f5XXTOkI0Kigm45iJXIf1/vsA xL2X3WAV1+iqag== =a4CZ -----END PGP SIGNATURE----- Thu Oct 28 20:57:27 UTC 2021 I: Checking whether the package is not for us Thu Oct 28 20:57:27 UTC 2021 I: Starting 1st build on remote node ionos1-amd64.debian.net. Thu Oct 28 20:57:27 UTC 2021 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Thu Oct 28 21:02:37 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 28 08:57:28 -12 2021 I: pbuilder-time-stamp: 1635454648 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 [skesa_2.4.0-1.dsc] I: copying [./skesa_2.4.0.orig.tar.gz] I: copying [./skesa_2.4.0-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.EyXv_Gno/trustedkeys.kbx': General error gpgv: Signature made Tue May 19 00:43:46 2020 -12 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./skesa_2.4.0-1.dsc dpkg-source: info: extracting skesa in skesa-2.4.0 dpkg-source: info: unpacking skesa_2.4.0.orig.tar.gz dpkg-source: info: unpacking skesa_2.4.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_ngs-sdk.patch dpkg-source: info: applying hardening.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1798019/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=' ' INVOCATION_ID='1732a31fa7c4474cac5addbf50330b56' 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='1798019' 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.qib6oXZeMX/pbuilderrc_cNVJ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.qib6oXZeMX/b1 --logfile b1/build.log skesa_2.4.0-1.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://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 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 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 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 07:09 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 07:09 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 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 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 08:25 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 Oct 20 23:41 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 07:09 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 07:09 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 07:09 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/1798019/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 (= 12), libboost-dev, libboost-chrono-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-regex-dev, libboost-system-dev, libboost-timer-dev, libncbi-vdb-dev, libngs-sdk-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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-chrono-dev; however: Package libboost-chrono-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-timer-dev; however: Package libboost-timer-dev is not installed. pbuilder-satisfydepends-dummy depends on libncbi-vdb-dev; however: Package libncbi-vdb-dev is not installed. pbuilder-satisfydepends-dummy depends on libngs-sdk-dev; however: Package libngs-sdk-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} icu-devtools{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libboost-chrono-dev{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-timer-dev{a} libboost-timer1.74-dev{a} libboost-timer1.74.0{a} libboost1.74-dev{a} libbz2-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhdf5-103-1{a} libicu-dev{a} libicu67{a} libkdf5-2{a} libkdf5-dev{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto3{a} libmbedtls-dev{a} libmbedtls12{a} libmbedx509-0{a} libncbi-vdb-dev{a} libncbi-vdb2{a} libncbi-wvdb-dev{a} libncbi-wvdb2{a} libngs-sdk-dev{a} libngs-sdk2{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 70 newly installed, 0 to remove and 0 not upgraded. Need to get 49.4 MB of archives. After unpacking 328 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 icu-devtools amd64 67.1-7 [201 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libaec-dev amd64 1.0.4-1 [18.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libboost-chrono1.74.0 amd64 1.74.0-9 [252 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libboost-chrono1.74-dev amd64 1.74.0-9 [260 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libboost-chrono-dev amd64 1.74.0.3 [4960 B] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74.0 amd64 1.74.0-9 [516 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libicu-dev amd64 67.1-7 [9597 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74-dev amd64 1.74.0-9 [588 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams1.74-dev amd64 1.74.0-9 [273 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74.0 amd64 1.74.0-9 [356 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74-dev amd64 1.74.0-9 [386 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libboost-regex-dev amd64 1.74.0.3 [4600 B] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libboost-system1.74.0 amd64 1.74.0-9 [241 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libboost-system1.74-dev amd64 1.74.0-9 [243 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libboost-system-dev amd64 1.74.0.3 [4468 B] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libboost-timer1.74.0 amd64 1.74.0-9 [250 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libboost-timer1.74-dev amd64 1.74.0-9 [254 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libboost-timer-dev amd64 1.74.0.3 [4456 B] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libmbedtls-dev amd64 2.16.9-0.1 [515 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libkdf5-2 amd64 2.10.9+dfsg-2 [20.8 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libkdf5-dev amd64 2.10.9+dfsg-2 [20.4 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libncbi-vdb2 amd64 2.10.9+dfsg-2 [1266 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libncbi-wvdb2 amd64 2.10.9+dfsg-2 [1159 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libncbi-wvdb-dev amd64 2.10.9+dfsg-2 [1295 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libncbi-vdb-dev amd64 2.10.9+dfsg-2 [1717 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk2 amd64 2.10.9-1 [59.2 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk-dev amd64 2.10.9-1 [104 kB] Fetched 49.4 MB in 1s (57.8 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 ... 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Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0-9) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libboost-chrono1.74-dev:amd64 (1.74.0-9) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up libngs-sdk2:amd64 (2.10.9-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libaec0:amd64 (1.0.4-1) ... Setting up libboost-program-options1.74-dev:amd64 (1.74.0-9) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libboost-program-options-dev:amd64 (1.74.0.3) ... Setting up libboost-system1.74-dev:amd64 (1.74.0-9) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libboost-regex1.74.0:amd64 (1.74.0-9) ... Setting up autopoint (0.21-4) ... Setting up icu-devtools (67.1-7) ... Setting up libngs-sdk-dev:amd64 (2.10.9-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libboost-timer1.74.0:amd64 (1.74.0-9) ... Setting up libicu-dev:amd64 (67.1-7) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up libsz2:amd64 (1.0.4-1) ... Setting up libbz2-dev:amd64 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libboost-chrono-dev:amd64 (1.74.0.3) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libboost-system-dev:amd64 (1.74.0.3) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libaec-dev:amd64 (1.0.4-1) ... Setting up m4 (1.4.18-5) ... Setting up libmbedtls-dev:amd64 (2.16.9-0.1) ... Setting up libncbi-vdb2 (2.10.9+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libncbi-wvdb2 (2.10.9+dfsg-2) ... Setting up libboost-timer1.74-dev:amd64 (1.74.0-9) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Setting up dwz (0.13+20210201-1) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0-9) ... Setting up groff-base (1.22.4-6) ... Setting up libncbi-wvdb-dev (2.10.9+dfsg-2) ... Setting up libboost-regex-dev:amd64 (1.74.0.3) ... Setting up libboost-timer-dev:amd64 (1.74.0.3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libkdf5-2 (2.10.9+dfsg-2) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-iostreams1.74-dev:amd64 (1.74.0-9) ... Setting up dh-autoreconf (20) ... Setting up libkdf5-dev (2.10.9+dfsg-2) ... Setting up debhelper (13.3.4) ... Setting up libboost-iostreams-dev:amd64 (1.74.0.3) ... Setting up libncbi-vdb-dev (2.10.9+dfsg-2) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/skesa-2.4.0/ && 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 > ../skesa_2.4.0-1_source.changes dpkg-buildpackage: info: source package skesa dpkg-buildpackage: info: source version 2.4.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_auto_clean make -j15 clean make[1]: Entering directory '/build/skesa-2.4.0' rm -f skesa gfa_connector kmercounter *.o /build/skesa-2.4.0/NGS/ngs.done make[1]: Leaving directory '/build/skesa-2.4.0' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/skesa-2.4.0' c++ -std=c++11 -fdiagnostics-color=never -c -o skesa.o skesa.cpp -g -O2 -fdebug-prefix-map=/build/skesa-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -msse4.2 -I /build/skesa-2.4.0/NGS/ngs_out/include -I /build/skesa-2.4.0/NGS/vdb_out/include c++ -std=c++11 -fdiagnostics-color=never -c -o glb_align.o glb_align.cpp -g -O2 -fdebug-prefix-map=/build/skesa-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -msse4.2 -I /build/skesa-2.4.0/NGS/ngs_out/include -I /build/skesa-2.4.0/NGS/vdb_out/include c++ -std=c++11 -fdiagnostics-color=never -c -o gfa_connector.o gfa_connector.cpp -g -O2 -fdebug-prefix-map=/build/skesa-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -msse4.2 -I /build/skesa-2.4.0/NGS/ngs_out/include -I /build/skesa-2.4.0/NGS/vdb_out/include c++ -std=c++11 -fdiagnostics-color=never -c -o kmercounter.o kmercounter.cpp -g -O2 -fdebug-prefix-map=/build/skesa-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -msse4.2 -I /build/skesa-2.4.0/NGS/ngs_out/include -I /build/skesa-2.4.0/NGS/vdb_out/include c++ -std=c++11 -fdiagnostics-color=never -o kmercounter kmercounter.o glb_align.o -L /build/skesa-2.4.0/NGS/vdb_out/lib64 -lncbi-ngs-c++ -lncbi-vdb -L /build/skesa-2.4.0/NGS/ngs_out/lib64 -lngs-c++ -Wl,-Bstatic -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -Wl,-Bdynamic -lrt -ldl -lm -lpthread -lz c++ -std=c++11 -fdiagnostics-color=never -o gfa_connector gfa_connector.o glb_align.o -L /build/skesa-2.4.0/NGS/vdb_out/lib64 -lncbi-ngs-c++ -lncbi-vdb -L /build/skesa-2.4.0/NGS/ngs_out/lib64 -lngs-c++ -Wl,-Bstatic -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -Wl,-Bdynamic -lrt -ldl -lm -lpthread -lz c++ -std=c++11 -fdiagnostics-color=never -o skesa skesa.o glb_align.o -L /build/skesa-2.4.0/NGS/vdb_out/lib64 -lncbi-ngs-c++ -lncbi-vdb -L /build/skesa-2.4.0/NGS/ngs_out/lib64 -lngs-c++ -Wl,-Bstatic -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -Wl,-Bdynamic -lrt -ldl -lm -lpthread -lz -Wl,-z,relro make[1]: Leaving directory '/build/skesa-2.4.0' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'skesa' in '../skesa_2.4.0-1_amd64.deb'. dpkg-deb: building package 'skesa-dbgsym' in '../skesa-dbgsym_2.4.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../skesa_2.4.0-1_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/1798019 and its subdirectories I: Current time: Thu Oct 28 09:02:37 -12 2021 I: pbuilder-time-stamp: 1635454957 Thu Oct 28 21:02:37 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Oct 28 21:02:37 UTC 2021 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Oct 28 21:17:30 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Thu Oct 28 21:17:31 UTC 2021 I: skesa_2.4.0-1_amd64.changes: Format: 1.8 Date: Sun, 17 May 2020 20:14:52 +0200 Source: skesa Binary: skesa skesa-dbgsym Architecture: amd64 Version: 2.4.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: skesa - strategic Kmer extension for scrupulous assemblies Changes: skesa (2.4.0-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.5.0 (routine-update) * Created https://github.com/ncbi/SKESA/pull/28 to hopefully avoid the hardening patch. Checksums-Sha1: 303f109b996293612aa2272ef69441117f4d2abf 13864248 skesa-dbgsym_2.4.0-1_amd64.deb 6ec5f43e9a8c6c85d6fdd63fbb32f792b4fb7eb6 6333 skesa_2.4.0-1_amd64.buildinfo 3b0c0c420668ccb28be2f94e74889454192e6aed 664228 skesa_2.4.0-1_amd64.deb Checksums-Sha256: f5034743c1d3d2ec4084dadb5ec972508df1a60980d69b81c939abb72afb7c9e 13864248 skesa-dbgsym_2.4.0-1_amd64.deb 73c390c7cb62bf34d95d12b798dd842236541076899f4d011ad3c4c47332c581 6333 skesa_2.4.0-1_amd64.buildinfo 0da2a976e77e2f7233408c0e9bc1775b6eec267093b000132b9d758be4912023 664228 skesa_2.4.0-1_amd64.deb Files: 2fc818318f0cd8443954b06b98dd12e8 13864248 debug optional skesa-dbgsym_2.4.0-1_amd64.deb c812d24c10fef10461bcbf216a8c33aa 6333 science optional skesa_2.4.0-1_amd64.buildinfo aa84e3573017b6c78e50f8b9cb8b28be 664228 science optional skesa_2.4.0-1_amd64.deb Thu Oct 28 21:17:38 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.qib6oXZeMX/skesa_2.4.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.qib6oXZeMX/skesa_2.4.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.qib6oXZeMX/skesa_2.4.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.qib6oXZeMX/b1/skesa_2.4.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.qib6oXZeMX/b2/skesa_2.4.0-1_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: 7.936s) 7.936s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 1.443s) 1.443s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Oct 28 21:18:10 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Thu Oct 28 21:18:10 UTC 2021 I: skesa from bullseye built successfully and reproducibly on amd64. Thu Oct 28 21:18:13 UTC 2021 I: Submitting .buildinfo files to external archives: Thu Oct 28 21:18:13 UTC 2021 I: Submitting 8.0K b1/skesa_2.4.0-1_amd64.buildinfo.asc Thu Oct 28 21:18:15 UTC 2021 I: Submitting 8.0K b2/skesa_2.4.0-1_amd64.buildinfo.asc Thu Oct 28 21:18:16 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Oct 28 21:18:16 UTC 2021 I: Done submitting .buildinfo files. Thu Oct 28 21:18:16 UTC 2021 I: Removing signed skesa_2.4.0-1_amd64.buildinfo.asc files: removed './b1/skesa_2.4.0-1_amd64.buildinfo.asc' removed './b2/skesa_2.4.0-1_amd64.buildinfo.asc'