Tue Sep 1 17:20:30 UTC 2020 I: starting to build dssp/buster/armhf on jenkins on '2020-09-01 17:20' Tue Sep 1 17:20:30 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_15/8098/console.log Tue Sep 1 17:20:30 UTC 2020 I: Downloading source for buster/dssp=3.0.0-3 --2020-09-01 17:20:31-- http://deb.debian.org/debian/pool/main/d/dssp/dssp_3.0.0-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2109 (2.1K) Saving to: ‘dssp_3.0.0-3.dsc’ 0K .. 100% 215M=0s 2020-09-01 17:20:31 (215 MB/s) - ‘dssp_3.0.0-3.dsc’ saved [2109/2109] Tue Sep 1 17:20:31 UTC 2020 I: dssp_3.0.0-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: dssp Binary: dssp Architecture: any Version: 3.0.0-3 Maintainer: Debian Med Packaging Team Uploaders: Maarten L. Hekkelman , Laszlo Kajan , Andreas Tille Homepage: http://www.cmbi.ru.nl/dssp.html Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/dssp Vcs-Git: https://salsa.debian.org/med-team/dssp.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-system-dev, libboost-thread-dev Package-List: dssp deb science optional arch=any Checksums-Sha1: 4b35bc8e7d9f62262b00b918d5b194fbdd65ffaa 47974 dssp_3.0.0.orig.tar.gz efaf3bc6d47258d9eea0a389aa1f07d0b115fe2e 62124 dssp_3.0.0-3.debian.tar.xz Checksums-Sha256: 25d39a2107767b622a59dd9fa790112c1516564b8518fc6ac0fab081d5ac3ab0 47974 dssp_3.0.0.orig.tar.gz 52782766c11d82e410637538d0b801d6a0def5cc38e3af3c10e149b15c9f40aa 62124 dssp_3.0.0-3.debian.tar.xz Files: e34b0d67622a702661fad441f22a65b0 47974 dssp_3.0.0.orig.tar.gz a2df58196f5112ac3174d4faa02ad701 62124 dssp_3.0.0-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlvVjdYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG8ng//TneHxrpIaIVrQ/bhDoIogpdI7tYBqHrs RH5xwUBx/y41VeTf9QkUdYtiG6EFwC93vcSCTy72MmMebsW4JuRR3FRfiXFnK7fc DOMMwquM6l6Hv53JOohFO784qypV+cQBM6vRCPEMeC14LIJQB2LONJuR+n10tvd4 xR9TiciZdIZr4ZiHq+6G2qanG0hyq3A1DSD0Lj+6mvfIZnRozLNwzea5hTrM9Km2 BF0Km+JLCySeEuzmYVNYns2xTiooZsvRK9bE2kM6DKFg7oDlY3aiyZzSI665bWfJ VnuFFy2RA5oGHVTShgA3jZGYYOB/w0hcUWhDI82r/lSqP3E6Oy0McALNX0LYpeT+ xpeRlXT2Q0fBJGvw+8HcJiN2S62QfIWO8jSbrRqiu42W3IxyHxRclNzP1Pz0P62Z k/2ILx8E34uBbz4Ox781rrfcYKKV2PGxSIarlPSfyudABCxuUyU3m2cBevucJjb5 8Tt+L2liRYJ+msbUq+huDZ0IAPhin5+jS1y/qat2hFAVxkrz/CnDv1jZxnWZuj2Q 1ROljx5sjEBZ4keNbz3AJttHjzTPHLakaTts193N0q9bWyjo/Gic8YOkWvitWMbz g3mgXwbooqoKlsesqbsRlrumtj3tzi9rXHBaK19/HmMFvq+MVJuetg/S/iFmzv9o 3vbLcXSI0ME= =d4sn -----END PGP SIGNATURE----- Tue Sep 1 17:20:31 UTC 2020 I: Checking whether the package is not for us Tue Sep 1 17:20:31 UTC 2020 I: Starting 1st build on remote node ff2b-armhf-rb.debian.net. Tue Sep 1 17:20:31 UTC 2020 I: Preparing to do remote build '1' on ff2b-armhf-rb.debian.net. Tue Sep 1 17:24:02 UTC 2020 I: Deleting $TMPDIR on ff2b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 1 05:20:37 -12 2020 I: pbuilder-time-stamp: 1598980837 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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 [dssp_3.0.0-3.dsc] I: copying [./dssp_3.0.0.orig.tar.gz] I: copying [./dssp_3.0.0-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Oct 27 22:22:14 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./dssp_3.0.0-3.dsc dpkg-source: info: extracting dssp in dssp-3.0.0 dpkg-source: info: unpacking dssp_3.0.0.orig.tar.gz dpkg-source: info: unpacking dssp_3.0.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile dpkg-source: info: applying hardening.patch dpkg-source: info: applying boost1.65.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10076/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='22109f2f0f424288990d54363ffe6b61' 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='10076' 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.sWBqJ15zaP/pbuilderrc_DrJR --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.sWBqJ15zaP/b1 --logfile b1/build.log dssp_3.0.0-3.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux ff2b 4.19.0-10-armmp-lpae #1 SMP Debian 4.19.132-1 (2020-07-24) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 30 20:26 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/10076/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-system-dev, libboost-thread-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 ... 18932 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-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-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-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} bsdmainutils{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} libarchive-zip-perl{a} libboost-atomic1.67-dev{a} libboost-atomic1.67.0{a} libboost-chrono1.67-dev{a} libboost-chrono1.67.0{a} libboost-date-time1.67-dev{a} libboost-date-time1.67.0{a} libboost-filesystem-dev{a} libboost-filesystem1.67-dev{a} libboost-filesystem1.67.0{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-program-options-dev{a} libboost-program-options1.67-dev{a} libboost-program-options1.67.0{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-system-dev{a} libboost-system1.67-dev{a} libboost-thread-dev{a} libboost-thread1.67-dev{a} libboost-thread1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu-dev{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 41.0 MB of archives. After unpacking 279 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main armhf icu-devtools armhf 63.1-6+deb10u1 [168 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libboost-atomic1.67.0 armhf 1.67.0-13+deb10u1 [226 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libboost-atomic1.67-dev armhf 1.67.0-13+deb10u1 [225 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libboost-chrono1.67.0 armhf 1.67.0-13+deb10u1 [231 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libboost-chrono1.67-dev armhf 1.67.0-13+deb10u1 [234 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libboost-date-time1.67.0 armhf 1.67.0-13+deb10u1 [236 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libboost-serialization1.67.0 armhf 1.67.0-13+deb10u1 [303 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libboost-serialization1.67-dev armhf 1.67.0-13+deb10u1 [370 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libboost-date-time1.67-dev armhf 1.67.0-13+deb10u1 [248 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libboost-filesystem1.67.0 armhf 1.67.0-13+deb10u1 [255 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libboost-system1.67-dev armhf 1.67.0-13+deb10u1 [232 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libboost-filesystem1.67-dev armhf 1.67.0-13+deb10u1 [262 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libboost-filesystem-dev armhf 1.67.0.1 [3684 B] Get: 48 http://deb.debian.org/debian buster/main armhf libboost-regex1.67.0 armhf 1.67.0-13+deb10u1 [438 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libicu-dev armhf 63.1-6+deb10u1 [8940 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libboost-regex1.67-dev armhf 1.67.0-13+deb10u1 [538 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libboost-iostreams1.67-dev armhf 1.67.0-13+deb10u1 [254 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libboost-iostreams-dev armhf 1.67.0.1 [3632 B] Get: 53 http://deb.debian.org/debian buster/main armhf libboost-program-options1.67.0 armhf 1.67.0-13+deb10u1 [336 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libboost-program-options1.67-dev armhf 1.67.0-13+deb10u1 [385 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libboost-program-options-dev armhf 1.67.0.1 [3656 B] Get: 56 http://deb.debian.org/debian buster/main armhf libboost-system-dev armhf 1.67.0.1 [3788 B] Get: 57 http://deb.debian.org/debian buster/main armhf libboost-thread1.67.0 armhf 1.67.0-13+deb10u1 [261 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libboost-thread1.67-dev armhf 1.67.0-13+deb10u1 [270 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libboost-thread-dev armhf 1.67.0.1 [3672 B] Fetched 41.0 MB in 5s (8563 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. 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Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/dssp-3.0.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package dssp dpkg-buildpackage: info: source version 3.0.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_auto_clean make -j3 clean make[1]: Entering directory '/build/dssp-3.0.0' rm -rf obj/* mkdssp make[1]: Leaving directory '/build/dssp-3.0.0' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/dssp-3.0.0' mkdir -p obj g++ -MD -c -o obj/mkdssp.o src/mkdssp.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/dssp-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/dssp.o src/dssp.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/dssp-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/primitives-3d.o src/primitives-3d.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/dssp-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/structure.o src/structure.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/dssp-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG In file included from src/structure.cpp:9: src/structure.h: In constructor 'MResidue::MResidue(int32, char, MResidue*)': src/structure.h:283:17: warning: 'MResidue::mRadius' will be initialized after [-Wreorder] double mRadius; ^~~~~~~ src/structure.h:274:33: warning: 'MAtom MResidue::mH' [-Wreorder] MAtom mC, mN, mCA, mO, mH; ^~ src/structure.cpp:440:1: warning: when initialized here [-Wreorder] MResidue::MResidue(int32 inNumber, char inTypeCode, MResidue* inPrevious) ^~~~~~~~ In file included from src/structure.cpp:9: src/structure.h: In constructor 'MProtein::MProtein(const string&, MChain*)': src/structure.h:430:40: warning: 'MProtein::mNrOfHBondsInAntiparallelBridges' will be initialized after [-Wreorder] uint32 mNrOfHBondsInParallelBridges, mNrOfHBondsInAntiparallelBridges; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/structure.h:424:17: warning: 'uint32 MProtein::mResidueCount' [-Wreorder] uint32 mResidueCount, mChainBreaks; ^~~~~~~~~~~~~ src/structure.cpp:1031:1: warning: when initialized here [-Wreorder] MProtein::MProtein(const std::string& inID, MChain* inChain) ^~~~~~~~ g++ -MD -c -o obj/utils.o src/utils.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/dssp-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/mas.o src/mas.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/dssp-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/iocif.o src/iocif.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/dssp-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from src/align-2d.h:14, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = MAccumulator::candidate; _Compare = __gnu_cxx::__ops::_Iter_less_val]': /usr/include/c++/8/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __push_heap(_RandomAccessIterator __first, ^~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MPoint&}; _Tp = MPoint; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MPoint; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void MProtein::GetPoints(std::vector&) const': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void MResidue::GetPoints(std::vector&) const': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void MProtein::GetCAlphaLocations(const string&, std::vector&) const': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MAtom&}; _Tp = MAtom; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MAccumulator::candidate&}; _Tp = MAccumulator::candidate; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In member function 'void MAccumulator::operator()(const MPoint&, const MPoint&, double, double)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'double MResidue::CalculateSurface(const MAtom&, double, const std::vector&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'double MResidue::CalculateSurface(const MAtom&, double, const std::vector&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'MResidue::MResidue(int32, MResidue*, const std::vector&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void MProtein::ReadPDB(std::istream&, bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void MProtein::ReadmmCIF(std::istream&, bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -o mkdssp obj/mkdssp.o obj/dssp.o obj/primitives-3d.o obj/structure.o obj/utils.o obj/mas.o obj/iocif.o -Wl,-z,relro -lboost_thread -lboost_program_options -lboost_iostreams -lboost_system -g -pthread -Wl,-z,relro make[1]: Leaving directory '/build/dssp-3.0.0' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j3 install DESTDIR=/build/dssp-3.0.0/debian/dssp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/dssp-3.0.0' install -d /build/dssp-3.0.0/debian/dssp/usr/bin /build/dssp-3.0.0/debian/dssp/usr/share/man/man1 install -m 755 mkdssp /build/dssp-3.0.0/debian/dssp/usr/bin/mkdssp install doc/mkdssp.1 /build/dssp-3.0.0/debian/dssp/usr/share/man/man1/mkdssp.1 make[1]: Leaving directory '/build/dssp-3.0.0' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/dssp/usr/bin/mkdssp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/dssp/usr/bin/mkdssp was not linked against libboost_iostreams.so.1.67.0 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'dssp' in '../dssp_3.0.0-3_armhf.deb'. dpkg-deb: building package 'dssp-dbgsym' in '../dssp-dbgsym_3.0.0-3_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../dssp_3.0.0-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/10076 and its subdirectories I: Current time: Tue Sep 1 05:23:48 -12 2020 I: pbuilder-time-stamp: 1598981028 Tue Sep 1 17:24:05 UTC 2020 I: 1st build successful. Starting 2nd build on remote node opi2c-armhf-rb.debian.net. Tue Sep 1 17:24:05 UTC 2020 I: Preparing to do remote build '2' on opi2c-armhf-rb.debian.net. Tue Sep 1 17:37:36 UTC 2020 I: Deleting $TMPDIR on opi2c-armhf-rb.debian.net. Tue Sep 1 17:37:39 UTC 2020 I: dssp_3.0.0-3_armhf.changes: Format: 1.8 Date: Sun, 28 Oct 2018 11:18:40 +0100 Source: dssp Binary: dssp dssp-dbgsym Architecture: armhf Version: 3.0.0-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: dssp - protein secondary structure assignment based on 3D structure Changes: dssp (3.0.0-3) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Secure URI in copyright format * Remove trailing whitespace in debian/copyright Checksums-Sha1: b4de5a2a7a92db8f8cdc2a6833649e339602d63e 2716944 dssp-dbgsym_3.0.0-3_armhf.deb cc5db321b84863f8962ef36ecc1f475f0442efc0 5771 dssp_3.0.0-3_armhf.buildinfo 1b01c8adc3324ed02cc8291632c5bc57e5602996 222672 dssp_3.0.0-3_armhf.deb Checksums-Sha256: 36c619ea2806a1b34e0a70fc01fd7e46afba214c8812997b04f0fcbac5a32dfe 2716944 dssp-dbgsym_3.0.0-3_armhf.deb 268e04e80d9418a94599b17e7d5fb2cb4c698f5a69f21318b26dae609391c8c4 5771 dssp_3.0.0-3_armhf.buildinfo 6809b7ddd5ba361db995420a882dcbacd3e9834ca956d179a2b03981f33a78c5 222672 dssp_3.0.0-3_armhf.deb Files: ece845c77063014417f5ff53ab18f53d 2716944 debug optional dssp-dbgsym_3.0.0-3_armhf.deb 0de71f85783702990a2758a4b380b73e 5771 science optional dssp_3.0.0-3_armhf.buildinfo bd830c2f61a814a31034be5a2b8ea245 222672 science optional dssp_3.0.0-3_armhf.deb Tue Sep 1 17:37:49 UTC 2020 I: diffoscope 158 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.sWBqJ15zaP/dssp_3.0.0-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.sWBqJ15zaP/dssp_3.0.0-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.sWBqJ15zaP/dssp_3.0.0-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.sWBqJ15zaP/b1/dssp_3.0.0-3_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.sWBqJ15zaP/b2/dssp_3.0.0-3_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.213s) 0.213s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.045s) 0.045s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Sep 1 17:38:33 UTC 2020 I: diffoscope 158 found no differences in the changes files, and a .buildinfo file also exists. Tue Sep 1 17:38:33 UTC 2020 I: dssp from buster built successfully and reproducibly on armhf. Tue Sep 1 17:38:34 UTC 2020 I: Submitting .buildinfo files to external archives: Tue Sep 1 17:38:34 UTC 2020 I: Submitting 8.0K b1/dssp_3.0.0-3_armhf.buildinfo.asc Tue Sep 1 17:38:36 UTC 2020 I: Submitting 8.0K b2/dssp_3.0.0-3_armhf.buildinfo.asc Tue Sep 1 17:38:38 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Sep 1 17:38:38 UTC 2020 I: Done submitting .buildinfo files. Tue Sep 1 17:38:38 UTC 2020 I: Removing signed dssp_3.0.0-3_armhf.buildinfo.asc files: removed './b1/dssp_3.0.0-3_armhf.buildinfo.asc' removed './b2/dssp_3.0.0-3_armhf.buildinfo.asc'