Wed May 31 09:03:42 UTC 2023 I: starting to build freesasa/bookworm/armhf on jenkins on '2023-05-31 09:03' Wed May 31 09:03:42 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_35/3321/console.log Wed May 31 09:03:42 UTC 2023 I: Downloading source for bookworm/freesasa=2.1.2-1 --2023-05-31 09:03:42-- http://cdn-fastly.deb.debian.org/debian/pool/main/f/freesasa/freesasa_2.1.2-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2016 (2.0K) [text/prs.lines.tag] Saving to: ‘freesasa_2.1.2-1.dsc’ 0K . 100% 137M=0s 2023-05-31 09:03:42 (137 MB/s) - ‘freesasa_2.1.2-1.dsc’ saved [2016/2016] Wed May 31 09:03:42 UTC 2023 I: freesasa_2.1.2-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: freesasa Binary: freesasa Architecture: any Version: 2.1.2-1 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://freesasa.github.io Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debichem-team/freesasa Vcs-Git: https://salsa.debian.org/debichem-team/freesasa.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gemmi-dev, libjson-c-dev, libxml2-dev, pkg-config, tao-pegtl-dev Package-List: freesasa deb science optional arch=any Checksums-Sha1: 5832e4bb0d2101d9e6d360b2c78bf3cb5bab5cfb 3281121 freesasa_2.1.2.orig.tar.gz 72b3fbaf6235a428d9ae74c3951ba07be4ef59e4 3240 freesasa_2.1.2-1.debian.tar.xz Checksums-Sha256: 98c3ebd8877daf1a886ae4b7f124b81dcb771dea7a6a864763f3e32043bfe901 3281121 freesasa_2.1.2.orig.tar.gz e77e4786cff9362014d4093abdf99a39835b56d4988b48a70d5230995c3bcd25 3240 freesasa_2.1.2-1.debian.tar.xz Files: 620ec39bf204863caedfca580d4c79f3 3281121 freesasa_2.1.2.orig.tar.gz f9a1513fb6a6dd417284cc97412bf688 3240 freesasa_2.1.2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmL/IcoSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHY38QAIhcdnom9kIG7TSutJF/IzStwxLZzmIn 2jtcWp6IXKGBRPGTVuGqfbnZdigD1pGlg2dEkFpQmQg7iqkfuPLB/QU6k9Q4JXMf 3g/iLJYkRBxvcECzyFhnMxqpILNu7lrBFFo4QQy8+HZhzkpy0r9d8msr8uZsK8AV wGW2I28CVW3GfDylkuFB3jKSmbOlfSNCIeyEHuOtaBFTDWc4E9NGtED4+KWaJKH8 HNGUAAAVKEGMprhFTYLKxjpXO3KKhr62lJ2ERb3YKBE+Rj+XpbJnU+o754zwKBxe 6SBAecpGZdohBK9qqubi1n0AmjKYzJjPsAazwjg/xiXtR23CdGuVU9KdelfDfP0e LF5jRvUHlZolLGZpAoYERrrQ//yoMBoXfWnuzQbZ2GoJKVgNRuIXKNesavHjOzvJ gLAwSBFRJKtjQUicNxesM6dnr8PseSqJ8R/UltHrUzaTLeVjw7qlf5dnu0CHN0HB b/nlyOiH5Emq2wk0Issth3FNMbhO9RZ2nNYeYlQSh7QPLz4jRl2JMxjm0zwZl98s b6XIxLw/gv3udmiEvoQESaT0hqiBL0pXlKm1i0BUCxvf0aLblrSDxydxxOsj7NqY dZ1sBKYdi+ft6sNtWLY4+Q2sFefF8CFVb20ZwpTBCg3hyzIIEUbDuZ9Hh2kodNDV h5AQGR8Li8PQ =IQhx -----END PGP SIGNATURE----- Wed May 31 09:03:42 UTC 2023 I: Checking whether the package is not for us Wed May 31 09:03:42 UTC 2023 I: Starting 1st build on remote node jtx1c-armhf-rb.debian.net. Wed May 31 09:03:42 UTC 2023 I: Preparing to do remote build '1' on jtx1c-armhf-rb.debian.net. Wed May 31 09:09:26 UTC 2023 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 30 21:03:55 -12 2023 I: pbuilder-time-stamp: 1685523835 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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 [freesasa_2.1.2-1.dsc] I: copying [./freesasa_2.1.2.orig.tar.gz] I: copying [./freesasa_2.1.2-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Aug 18 17:38:18 2022 -12 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./freesasa_2.1.2-1.dsc: no acceptable signature found dpkg-source: info: extracting freesasa in freesasa-2.1.2 dpkg-source: info: unpacking freesasa_2.1.2.orig.tar.gz dpkg-source: info: unpacking freesasa_2.1.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-gnu++-setting.patch dpkg-source: info: applying fix-manpage.patch dpkg-source: info: applying no-lc++.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/19361/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='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='1053c70ac6174f338aa0d6ddbc84d8cb' 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='19361' 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/r-b-build.HVRhG94E/pbuilderrc_X6kk --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HVRhG94E/b1 --logfile b1/build.log freesasa_2.1.2-1.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux jtx1c 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/19361/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-compat (= 13), gemmi-dev, libjson-c-dev, libxml2-dev, pkg-config, tao-pegtl-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 ... 19324 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 gemmi-dev; however: Package gemmi-dev is not installed. pbuilder-satisfydepends-dummy depends on libjson-c-dev; however: Package libjson-c-dev is not installed. pbuilder-satisfydepends-dummy depends on libxml2-dev; however: Package libxml2-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however: Package tao-pegtl-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} gemmi-dev{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu-dev{a} libicu72{a} libjson-c-dev{a} libjson-c5{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpkgconf3{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libxml2-dev{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tao-pegtl-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 29.7 MB of archives. After unpacking 119 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf gemmi-dev armhf 0.5.7+ds-2+b1 [404 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf icu-devtools armhf 72.1-3 [183 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libicu-dev armhf 72.1-3 [10.1 MB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libjson-c5 armhf 0.16-2 [40.4 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libjson-c-dev armhf 0.16-2 [66.8 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libxml2-dev armhf 2.9.14+dfsg-1.2 [709 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf tao-pegtl-dev all 3.2.7-1 [69.4 kB] Fetched 29.7 MB in 3s (11.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19324 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... 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Processing triggers for libc-bin (2.36-9) ... 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/freesasa-2.1.2/ && 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 > ../freesasa_2.1.2-1_source.changes dpkg-buildpackage: info: source package freesasa dpkg-buildpackage: info: source version 2.1.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:42: warning: The macro `AC_PROG_CC_C99' is obsolete. configure.ac:42: You should run autoupdate. ./lib/autoconf/c.m4:1659: AC_PROG_CC_C99 is expanded from... configure.ac:42: the top level configure.ac:123: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete ./lib/autoconf/programs.m4:716: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:709: AC_PROG_LEX is expanded from... configure.ac:123: the top level configure.ac:16: installing './compile' configure.ac:46: installing './config.guess' configure.ac:46: installing './config.sub' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for ranlib... ranlib checking for sqrt in -lm... yes checking for dlsym in -ldl... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking for inttypes.h... (cached) yes checking for libintl.h... yes checking for malloc.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for dlfcn.h... yes checking for inline... inline checking for size_t... (cached) yes checking for C/C++ restrict keyword... __restrict__ checking for int16_t... yes checking for int32_t... yes checking for int8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for inline... (cached) inline checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for memset... yes checking for mkdir... yes checking for sqrt... yes checking for strchr... yes checking for strdup... yes checking for strerror... yes checking for strncasecmp... yes checking for getopt_long... yes checking for getline... yes checking whether g++ supports C++14 features with -std=gnu++14... yes checking for pthread_create in -lpthread... yes checking for pthread.h... yes checking for xmllint... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for libxml-2.0... yes checking for json_object_get in -ljson-c... yes checking for json-c/json_object.h... yes checking for jsonlint... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating doc/Doxyfile config.status: creating doc/man/freesasa.1 config.status: creating tests/Makefile config.status: creating share/Makefile config.status: creating tests/test-cli config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j3 make[1]: Entering directory '/build/freesasa-2.1.2' make all-recursive make[2]: Entering directory '/build/freesasa-2.1.2' Making all in src make[3]: Entering directory '/build/freesasa-2.1.2/src' g++ -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cc g++ -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cif.o cif.cc gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o classifier.o classifier.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o classifier_protor.o classifier_protor.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o classifier_oons.o classifier_oons.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o classifier_naccess.o classifier_naccess.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o coord.o coord.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o pdb.o pdb.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o log.o log.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o sasa_lr.o sasa_lr.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o sasa_sr.o sasa_sr.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o structure.o structure.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o node.o node.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o freesasa.o freesasa.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o nb.o nb.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o util.o util.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o rsa.o rsa.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o selection.o selection.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o lexer.o lexer.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o parser.o parser.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o json.o json.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o xml.o xml.c gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -c -o example.o example.c rm -f libfreesasa.a ar cru libfreesasa.a classifier.o classifier_protor.o classifier_oons.o classifier_naccess.o coord.o pdb.o log.o sasa_lr.o sasa_sr.o structure.o node.o freesasa.o nb.o util.o rsa.o selection.o lexer.o parser.o json.o xml.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfreesasa.a gcc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wl,-z,now -o example example.o libfreesasa.a -ljson-c -lxml2 -lpthread -ldl -lm In file included from /usr/include/c++/12/vector:70, from /usr/include/tao/pegtl/parse_error.hpp:13, from /usr/include/tao/pegtl/normal.hpp:14, from /usr/include/tao/pegtl/parse.hpp:11, from /usr/include/tao/pegtl.hpp:9, from /usr/include/gemmi/cif.hpp:13, from cif.cc:12: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /usr/include/gemmi/unitcell.hpp:358:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /usr/include/gemmi/unitcell.hpp:360:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /usr/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:284:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:292:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:335:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'void gemmi::impl::read_connectivity(gemmi::cif::Block&, gemmi::Structure&)' at /usr/include/gemmi/mmcif.hpp:240:32: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:503:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:518:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:524:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:535:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::NcsOp; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:629:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:769:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::impl::apply_hd_mixture(gemmi::Residue*, double)' at /usr/include/gemmi/mmcif.hpp:448:24, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /usr/include/gemmi/mmcif.hpp:771:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/freesasa-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o freesasa main.o cif.o libfreesasa.a -ljson-c -lxml2 -lpthread -ldl -lm make[3]: Leaving directory '/build/freesasa-2.1.2/src' Making all in doc make[3]: Entering directory '/build/freesasa-2.1.2/doc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/freesasa-2.1.2/doc' Making all in tests make[3]: Entering directory '/build/freesasa-2.1.2/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/freesasa-2.1.2/tests' Making all in share make[3]: Entering directory '/build/freesasa-2.1.2/share' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/freesasa-2.1.2/share' make[3]: Entering directory '/build/freesasa-2.1.2' make[3]: Leaving directory '/build/freesasa-2.1.2' make[2]: Leaving directory '/build/freesasa-2.1.2' make[1]: Leaving directory '/build/freesasa-2.1.2' dh_auto_test make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 make[1]: Entering directory '/build/freesasa-2.1.2' Making check in src make[2]: Entering directory '/build/freesasa-2.1.2/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/freesasa-2.1.2/src' Making check in doc make[2]: Entering directory '/build/freesasa-2.1.2/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/freesasa-2.1.2/doc' Making check in tests make[2]: Entering directory '/build/freesasa-2.1.2/tests' make make[3]: Entering directory '/build/freesasa-2.1.2/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/freesasa-2.1.2/tests' make check-TESTS make[3]: Entering directory '/build/freesasa-2.1.2/tests' make[4]: Entering directory '/build/freesasa-2.1.2/tests' PASS: test-cli ============================================================================ Testsuite summary for FreeSASA 2.1.2 ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/freesasa-2.1.2/tests' make[3]: Leaving directory '/build/freesasa-2.1.2/tests' make[2]: Leaving directory '/build/freesasa-2.1.2/tests' Making check in share make[2]: Entering directory '/build/freesasa-2.1.2/share' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/freesasa-2.1.2/share' make[2]: Entering directory '/build/freesasa-2.1.2' make[2]: Leaving directory '/build/freesasa-2.1.2' make[1]: Leaving directory '/build/freesasa-2.1.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/freesasa/ make -j3 install DESTDIR=/build/freesasa-2.1.2/debian/freesasa AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/freesasa-2.1.2' Making install in src make[2]: Entering directory '/build/freesasa-2.1.2/src' make[3]: Entering directory '/build/freesasa-2.1.2/src' /bin/mkdir -p '/build/freesasa-2.1.2/debian/freesasa/usr/bin' /bin/mkdir -p '/build/freesasa-2.1.2/debian/freesasa/usr/lib/arm-linux-gnueabihf' /usr/bin/install -c -m 644 libfreesasa.a '/build/freesasa-2.1.2/debian/freesasa/usr/lib/arm-linux-gnueabihf' /bin/mkdir -p '/build/freesasa-2.1.2/debian/freesasa/usr/include' /usr/bin/install -c freesasa '/build/freesasa-2.1.2/debian/freesasa/usr/bin' ( cd '/build/freesasa-2.1.2/debian/freesasa/usr/lib/arm-linux-gnueabihf' && ranlib libfreesasa.a ) /usr/bin/install -c -m 644 freesasa.h '/build/freesasa-2.1.2/debian/freesasa/usr/include' make[3]: Leaving directory '/build/freesasa-2.1.2/src' make[2]: Leaving directory '/build/freesasa-2.1.2/src' Making install in doc make[2]: Entering directory '/build/freesasa-2.1.2/doc' make[3]: Entering directory '/build/freesasa-2.1.2/doc' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/freesasa-2.1.2/debian/freesasa/usr/share/man/man1' /usr/bin/install -c -m 644 man/freesasa.1 '/build/freesasa-2.1.2/debian/freesasa/usr/share/man/man1' make[3]: Leaving directory '/build/freesasa-2.1.2/doc' make[2]: Leaving directory '/build/freesasa-2.1.2/doc' Making install in tests make[2]: Entering directory '/build/freesasa-2.1.2/tests' make[3]: Entering directory '/build/freesasa-2.1.2/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/freesasa-2.1.2/tests' make[2]: Leaving directory '/build/freesasa-2.1.2/tests' Making install in share make[2]: Entering directory '/build/freesasa-2.1.2/share' make[3]: Entering directory '/build/freesasa-2.1.2/share' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/freesasa-2.1.2/debian/freesasa/usr/share/freesasa' /usr/bin/install -c -m 644 dssp.config naccess.config oons.config protor.config '/build/freesasa-2.1.2/debian/freesasa/usr/share/freesasa' make[3]: Leaving directory '/build/freesasa-2.1.2/share' make[2]: Leaving directory '/build/freesasa-2.1.2/share' make[2]: Entering directory '/build/freesasa-2.1.2' make[3]: Entering directory '/build/freesasa-2.1.2' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/freesasa-2.1.2' make[2]: Leaving directory '/build/freesasa-2.1.2' make[1]: Leaving directory '/build/freesasa-2.1.2' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/freesasa/usr/bin/freesasa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'freesasa' in '../freesasa_2.1.2-1_armhf.deb'. dpkg-deb: building package 'freesasa-dbgsym' in '../freesasa-dbgsym_2.1.2-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../freesasa_2.1.2-1_armhf.buildinfo dpkg-genchanges --build=binary -O../freesasa_2.1.2-1_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) 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/19361 and its subdirectories I: Current time: Tue May 30 21:08:58 -12 2023 I: pbuilder-time-stamp: 1685524138 Wed May 31 09:09:30 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt32c-armhf-rb.debian.net. Wed May 31 09:09:30 UTC 2023 I: Preparing to do remote build '2' on virt32c-armhf-rb.debian.net. Wed May 31 09:13:49 UTC 2023 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net. Wed May 31 09:13:52 UTC 2023 I: freesasa_2.1.2-1_armhf.changes: Format: 1.8 Date: Fri, 19 Aug 2022 01:29:44 -0400 Source: freesasa Binary: freesasa freesasa-dbgsym Architecture: armhf Version: 2.1.2-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: freesasa - Solvent Accessible Surface Area of biomolecules Changes: freesasa (2.1.2-1) unstable; urgency=medium . * New upstream version 2.1.2 Checksums-Sha1: 96e014361c2e3a44858d89fd0fa6af39c1e4fef1 1939328 freesasa-dbgsym_2.1.2-1_armhf.deb b8f4d0f91518a57a0abd5cb5bee2ff2a44f00422 5254 freesasa_2.1.2-1_armhf.buildinfo 4a8e6ac6922cf7a88887b05bb76e530ea61cc76b 437920 freesasa_2.1.2-1_armhf.deb Checksums-Sha256: 3817621c84306c18f48c19671cf53b5ba644ed81bac60aa75892b6bf483cc041 1939328 freesasa-dbgsym_2.1.2-1_armhf.deb cf5a718989dd067472e3eac911c931c930c61820c7b6b1b371a68e082c04deff 5254 freesasa_2.1.2-1_armhf.buildinfo 83d27f6cd90cd44b6a4b607a24cf2a521abfe953d346f93f698c21d29c9874b1 437920 freesasa_2.1.2-1_armhf.deb Files: f94ce155f08f4d0f2bf4d619effd09d7 1939328 debug optional freesasa-dbgsym_2.1.2-1_armhf.deb a0c92444faa6f22c50c54c48c9082dcf 5254 science optional freesasa_2.1.2-1_armhf.buildinfo 271ea393ed54c96dfcb4b7c58dbd7d3e 437920 science optional freesasa_2.1.2-1_armhf.deb Wed May 31 09:13:53 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.HVRhG94E/freesasa_2.1.2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.HVRhG94E/freesasa_2.1.2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.HVRhG94E/freesasa_2.1.2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.HVRhG94E/b1/freesasa_2.1.2-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.HVRhG94E/b2/freesasa_2.1.2-1_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: 0.428s) 0.428s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.049s) 0.049s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Wed May 31 09:13:54 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Wed May 31 09:13:54 UTC 2023 I: freesasa from bookworm built successfully and reproducibly on armhf. Wed May 31 09:13:55 UTC 2023 I: Submitting .buildinfo files to external archives: Wed May 31 09:13:55 UTC 2023 I: Submitting 8.0K b1/freesasa_2.1.2-1_armhf.buildinfo.asc Wed May 31 09:13:56 UTC 2023 I: Submitting 8.0K b2/freesasa_2.1.2-1_armhf.buildinfo.asc Wed May 31 09:13:56 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 31 09:13:56 UTC 2023 I: Done submitting .buildinfo files. Wed May 31 09:13:56 UTC 2023 I: Removing signed freesasa_2.1.2-1_armhf.buildinfo.asc files: removed './b1/freesasa_2.1.2-1_armhf.buildinfo.asc' removed './b2/freesasa_2.1.2-1_armhf.buildinfo.asc'