Running as unit: rb-build-arm64_9-105863.service; invocation ID: e56f22153ad1480d87e8c80eeca08e3d ==================================================================================== Sat Nov 1 13:16:45 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_9) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Sat Nov 1 13:16:45 UTC 2025 - actually running "reproducible_build.sh" (md5sum bcb6fe1b50cf4e8eedacd0971a9eb63f) as "/tmp/jenkins-script-dZb1LKuv" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Nov 1 13:16:45 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Nov 1 13:16:45 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-DYvVCX' Sat Nov 1 13:16:46 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Nov 1 13:16:46 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-TyKED0' ok, let's check if freesasa is building anywhere yet… ok, freesasa is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of freesasa in forky on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Sat Nov 1 13:16:55 UTC 2025 I: starting to build freesasa/forky/arm64 on jenkins on '2025-11-01 13:16' Sat Nov 1 13:16:55 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_9/105863/console.log 1762003015 arm64 forky freesasa Sat Nov 1 13:16:55 UTC 2025 I: Downloading source for forky/freesasa=2.1.2-4 --2025-11-01 13:16:55-- http://deb.debian.org/debian/pool/main/f/freesasa/freesasa_2.1.2-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2028 (2.0K) [text/prs.lines.tag] Saving to: ‘freesasa_2.1.2-4.dsc’ 0K . 100% 223M=0s 2025-11-01 13:16:55 (223 MB/s) - ‘freesasa_2.1.2-4.dsc’ saved [2028/2028] --2025-11-01 13:16:55-- http://deb.debian.org/debian/pool/main/f/freesasa/freesasa_2.1.2-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2028 (2.0K) [text/prs.lines.tag] Saving to: ‘freesasa_2.1.2-4.dsc’ 0K . 100% 223M=0s 2025-11-01 13:16:55 (223 MB/s) - ‘freesasa_2.1.2-4.dsc’ saved [2028/2028] Sat Nov 1 13:16:55 UTC 2025 I: freesasa_2.1.2-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: freesasa Binary: freesasa Architecture: any Version: 2.1.2-4 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://freesasa.github.io Standards-Version: 4.6.2 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, zlib1g-dev Package-List: freesasa deb science optional arch=any Checksums-Sha1: 5832e4bb0d2101d9e6d360b2c78bf3cb5bab5cfb 3281121 freesasa_2.1.2.orig.tar.gz 1230bc21930313cc6f8a6c49e3da1a424758e343 3380 freesasa_2.1.2-4.debian.tar.xz Checksums-Sha256: 98c3ebd8877daf1a886ae4b7f124b81dcb771dea7a6a864763f3e32043bfe901 3281121 freesasa_2.1.2.orig.tar.gz 11d1172147e756a68dc54275fcfcd644cc3b475722c28c2c805e60f2db66fd85 3380 freesasa_2.1.2-4.debian.tar.xz Files: 620ec39bf204863caedfca580d4c79f3 3281121 freesasa_2.1.2.orig.tar.gz 1cb27a3800bd0e3f671b1704e3715838 3380 freesasa_2.1.2-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmTTcQoSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHuMIP/jKSs2N6c7uDlKp2weVtQwTuWXiSEi2T YM95s4encmHoDIBIVuHNDk2EXVG81V4tZ/O0iSZYbIjwTYti7jU4OEqSm5UUli8g PMoluztxJeXg6AS8aFfTBOxJLx53fRA/T57p3KuUOqqpAT2Kxrq11Hi4oK/4dU/k BUTrI6/mMmK01VE9o2pRdFlIN0aYGLmtT2enUWcb5f+iYFMX2o+cvDMHX7aXeYFD ch/O7fAxWjeOdH11JyZH7H9SUtcrhTSSDJC4i/Tw+vo7CGPiVj+YPkX8zWZXwX3v KWW0mnCTMibUy/buxZ7SDwCf3Gi7DPch4yayZq1O+QH2qhK9zaQE+cErC6OP+DH2 ni7clCFv7qz64dwQ3iC9K/PBvOZ/HSug09s1G311T7YYPjdd+eTovmOfSf/V3OwN Dtn220y1vKfiDfzPnaBj1DgX5iDZZwrpwFROC49OAKQNplbSyzY5qnCpY/Xv2uZ9 edMpOLu9ddb72sQmsubW8msf9jGSggwJ1N5WGbO8ULpGIgZK/tgZl9gt88mHZMMt L/9U+74ipFP7v/Kwb9Cn+y393hIc0FR9DFZt+5/xHqTrtoykHNhboRdy1pHz6IfM 1T6WiCEVmlVKcqMZJ36Sey6NSjTLjjQdvoWRTxbKSJJT14RcCeg1iVjYD+jxWHc0 tT5snolJadl9 =MAAk -----END PGP SIGNATURE----- Sat Nov 1 13:16:55 UTC 2025 I: Checking whether the package is not for us Sat Nov 1 13:16:56 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sat Nov 1 13:16:56 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sat Nov 1 13:16:56 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Nov 1 13:16:56 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-4Hr7RE' ==================================================================================== Sat Nov 1 13:16:56 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 freesasa forky /srv/reproducible-results/rbuild-debian/r-b-build.D1rpkrRS 2.1.2-4" as arguments. Sat Nov 1 13:16:56 UTC 2025 - actually running "reproducible_build.sh" (md5sum bcb6fe1b50cf4e8eedacd0971a9eb63f) as "/tmp/jenkins-script-KNWTknmb" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Nov 1 13:16:56 UTC 2025 I: Downloading source for forky/freesasa=2.1.2-4 Reading package lists... NOTICE: 'freesasa' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/freesasa.git Please use: git clone https://salsa.debian.org/debichem-team/freesasa.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3287 kB of source archives. Get:1 http://deb.debian.org/debian forky/main freesasa 2.1.2-4 (dsc) [2028 B] Get:2 http://deb.debian.org/debian forky/main freesasa 2.1.2-4 (tar) [3281 kB] Get:3 http://deb.debian.org/debian forky/main freesasa 2.1.2-4 (diff) [3380 B] Fetched 3287 kB in 0s (30.3 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'freesasa' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/freesasa.git Please use: git clone https://salsa.debian.org/debichem-team/freesasa.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3287 kB of source archives. Get:1 http://deb.debian.org/debian forky/main freesasa 2.1.2-4 (dsc) [2028 B] Get:2 http://deb.debian.org/debian forky/main freesasa 2.1.2-4 (tar) [3281 kB] Get:3 http://deb.debian.org/debian forky/main freesasa 2.1.2-4 (diff) [3380 B] Fetched 3287 kB in 0s (30.3 MB/s) Download complete and in download only mode ============================================================================= Building freesasa in forky on arm64 on codethink04-arm64 now. Date: Sat Nov 1 13:16:57 GMT 2025 Date UTC: Sat Nov 1 13:16:57 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 1 01:16:57 -12 2025 I: pbuilder-time-stamp: 1762003017 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_2.1.2-4.dsc] I: copying [./freesasa_2.1.2.orig.tar.gz] I: copying [./freesasa_2.1.2-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./freesasa_2.1.2-4.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_2.1.2-4.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2769492/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='5ce431521c3546bca47239a6c86ad705' 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='2769492' 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.D1rpkrRS/pbuilderrc_DSkQ --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.D1rpkrRS/b1 --logfile b1/build.log freesasa_2.1.2-4.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2769492/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gemmi-dev, libjson-c-dev, libxml2-dev, pkg-config, tao-pegtl-dev, zlib1g-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 ... 19971 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. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libjson-c-dev{a} libjson-c5{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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} zlib1g-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, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 14.4 MB of archives. After unpacking 57.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-7 [540 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 gemmi-dev arm64 0.7.1+ds-2 [1104 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 libjson-c5 arm64 0.18+ds-1.1 [44.8 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libjson-c-dev arm64 0.18+ds-1.1 [74.5 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 liblzma-dev arm64 5.8.1-2 [344 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libxml2-dev arm64 2.14.6+dfsg-0.1 [732 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Fetched 14.4 MB in 0s (34.5 MB/s) Preconfiguring packages ... 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 ... 19971 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.2-4_arm64.deb ... Unpacking bsdextrautils (2.41.2-4) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.18.1-2_all.deb ... Unpacking automake (1:1.18.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-7_all.deb ... Unpacking libtool (2.5.4-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... 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Processing triggers for libc-bin (2.41-12) ... 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/reproducible-path/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_2.1.2-4_source.changes dpkg-buildpackage: info: source package freesasa dpkg-buildpackage: info: source version 2.1.2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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.m4:1662: 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.m4:743: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:736: 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=aarch64-linux-gnu --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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/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 xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar 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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/freesasa-2.1.2' dh_auto_build -- freesasa_LDADD='libfreesasa.a ${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2' make -j12 freesasa_LDADD="libfreesasa.a \${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2" make[2]: Entering directory '/build/reproducible-path/freesasa-2.1.2' make all-recursive make[3]: Entering directory '/build/reproducible-path/freesasa-2.1.2' Making all in src make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -c -o example.o example.c xml.c: In function 'freesasa_write_xml': xml.c:612:5: warning: 'content' is deprecated [-Wdeprecated-declarations] 612 | fprintf(output, "%s", (const char *)buf->content); | ^~~~~~~ In file included from /usr/include/libxml2/libxml/parser.h:16, from /usr/include/libxml2/libxml/tree.h:17, from xml.c:6: /usr/include/libxml2/libxml/tree.h:103:14: note: declared here 103 | xmlChar *content XML_DEPRECATED_MEMBER; | ^~~~~~~ rm -f libfreesasa.a ar cr 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 ranlib libfreesasa.a gcc -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wl,-z,now -o example example.o libfreesasa.a -ljson-c -lxml2 -lpthread -ldl -lm cif.cc: In function 'std::vector freesasa_cif_structure_array(FILE*, int*, const freesasa_classifier*, int)': cif.cc:294:51: error: 'const __gnu_cxx::__alloc_traits, gemmi::Model>::value_type' {aka 'const struct gemmi::Model'} has no member named 'name' 294 | __func__, models[i].name.c_str()); | ^~~~ cif.cc:300:85: error: 'const __gnu_cxx::__alloc_traits, gemmi::Model>::value_type' {aka 'const struct gemmi::Model'} has no member named 'name' 300 | freesasa_structure *structure = structure_from_chain(doc, models[i].name, chain_name, classifier, options); | ^~~~ cif.cc:321:53: error: 'const __gnu_cxx::__alloc_traits, gemmi::Model>::value_type' {aka 'const struct gemmi::Model'} has no member named 'name' 321 | structure_from_model(doc, models[i].name, classifier, options)); | ^~~~ cif.cc: In function 'int reset_freesasa_tables(gemmi::cif::Block&)': cif.cc:715:23: error: 'struct gemmi::cif::Table' has no member named 'convert_pair_to_loop' 715 | table.convert_pair_to_loop(); | ^~~~~~~~~~~~~~~~~~~~ make[4]: *** [Makefile:582: cif.o] Error 1 make[4]: Leaving directory '/build/reproducible-path/freesasa-2.1.2/src' make[3]: *** [Makefile:397: all-recursive] Error 1 make[3]: Leaving directory '/build/reproducible-path/freesasa-2.1.2' make[2]: *** [Makefile:336: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/freesasa-2.1.2' dh_auto_build: error: make -j12 freesasa_LDADD="libfreesasa.a \${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2" returned exit code 2 make[1]: *** [debian/rules:11: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/freesasa-2.1.2' make: *** [debian/rules:7: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/2769492 and its subdirectories Starting cleanup. All cleanup done. Sat Nov 1 13:17:22 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-KNWTknmb, removing. /srv/reproducible-results/rbuild-debian/r-b-build.D1rpkrRS: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 13:17 b1 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 13:16 b2 -rw-rw-r-- 1 jenkins jenkins 2028 Aug 9 2023 freesasa_2.1.2-4.dsc -rw------- 1 jenkins jenkins 3139 Nov 1 13:16 rbuildlog.nZi0tL8 /srv/reproducible-results/rbuild-debian/r-b-build.D1rpkrRS/b1: total 40 -rw-r--r-- 1 jenkins jenkins 37478 Nov 1 13:17 build.log /srv/reproducible-results/rbuild-debian/r-b-build.D1rpkrRS/b2: total 0 Sat Nov 1 13:17:23 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 1 01:16:57 -12 2025 I: pbuilder-time-stamp: 1762003017 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_2.1.2-4.dsc] I: copying [./freesasa_2.1.2.orig.tar.gz] I: copying [./freesasa_2.1.2-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./freesasa_2.1.2-4.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_2.1.2-4.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2769492/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='5ce431521c3546bca47239a6c86ad705' 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='2769492' 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.D1rpkrRS/pbuilderrc_DSkQ --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.D1rpkrRS/b1 --logfile b1/build.log freesasa_2.1.2-4.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2769492/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gemmi-dev, libjson-c-dev, libxml2-dev, pkg-config, tao-pegtl-dev, zlib1g-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 ... 19971 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. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libjson-c-dev{a} libjson-c5{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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} zlib1g-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, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 14.4 MB of archives. After unpacking 57.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-7 [540 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 gemmi-dev arm64 0.7.1+ds-2 [1104 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 libjson-c5 arm64 0.18+ds-1.1 [44.8 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libjson-c-dev arm64 0.18+ds-1.1 [74.5 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 liblzma-dev arm64 5.8.1-2 [344 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libxml2-dev arm64 2.14.6+dfsg-0.1 [732 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Fetched 14.4 MB in 0s (34.5 MB/s) Preconfiguring packages ... 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 ... 19971 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.2-4_arm64.deb ... Unpacking bsdextrautils (2.41.2-4) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.18.1-2_all.deb ... Unpacking automake (1:1.18.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-7_all.deb ... Unpacking libtool (2.5.4-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.193-3_arm64.deb ... Unpacking libelf1t64:arm64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_arm64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../24-libxml2-16_2.14.6+dfsg-0.1_arm64.deb ... Unpacking libxml2-16:arm64 (2.14.6+dfsg-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.28_all.deb ... Unpacking debhelper (13.28) ... Selecting previously unselected package tao-pegtl-dev. Preparing to unpack .../29-tao-pegtl-dev_3.2.7-1_all.deb ... Unpacking tao-pegtl-dev (3.2.7-1) ... Selecting previously unselected package gemmi-dev. Preparing to unpack .../30-gemmi-dev_0.7.1+ds-2_arm64.deb ... Unpacking gemmi-dev (0.7.1+ds-2) ... Selecting previously unselected package libjson-c5:arm64. Preparing to unpack .../31-libjson-c5_0.18+ds-1.1_arm64.deb ... Unpacking libjson-c5:arm64 (0.18+ds-1.1) ... Selecting previously unselected package libjson-c-dev:arm64. Preparing to unpack .../32-libjson-c-dev_0.18+ds-1.1_arm64.deb ... Unpacking libjson-c-dev:arm64 (0.18+ds-1.1) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../33-liblzma-dev_5.8.1-2_arm64.deb ... Unpacking liblzma-dev:arm64 (5.8.1-2) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../34-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../35-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libxml2-dev:arm64. Preparing to unpack .../36-libxml2-dev_2.14.6+dfsg-0.1_arm64.deb ... Unpacking libxml2-dev:arm64 (2.14.6+dfsg-0.1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../37-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../38-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package pkg-config:arm64. Preparing to unpack .../39-pkg-config_1.8.1-4_arm64.deb ... Unpacking pkg-config:arm64 (1.8.1-4) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.6+dfsg-0.1) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3.1) ... Setting up liblzma-dev:arm64 (5.8.1-2) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up libjson-c5:arm64 (0.18+ds-1.1) ... Setting up tao-pegtl-dev (3.2.7-1) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up libjson-c-dev:arm64 (0.18+ds-1.1) ... Setting up gemmi-dev (0.7.1+ds-2) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libxml2-dev:arm64 (2.14.6+dfsg-0.1) ... Setting up pkg-config:arm64 (1.8.1-4) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.28) ... Processing triggers for libc-bin (2.41-12) ... 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/reproducible-path/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_2.1.2-4_source.changes dpkg-buildpackage: info: source package freesasa dpkg-buildpackage: info: source version 2.1.2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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.m4:1662: 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.m4:743: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:736: 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=aarch64-linux-gnu --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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/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 xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar 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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/freesasa-2.1.2' dh_auto_build -- freesasa_LDADD='libfreesasa.a ${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2' make -j12 freesasa_LDADD="libfreesasa.a \${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2" make[2]: Entering directory '/build/reproducible-path/freesasa-2.1.2' make all-recursive make[3]: Entering directory '/build/reproducible-path/freesasa-2.1.2' Making all in src make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -c -o example.o example.c xml.c: In function 'freesasa_write_xml': xml.c:612:5: warning: 'content' is deprecated [-Wdeprecated-declarations] 612 | fprintf(output, "%s", (const char *)buf->content); | ^~~~~~~ In file included from /usr/include/libxml2/libxml/parser.h:16, from /usr/include/libxml2/libxml/tree.h:17, from xml.c:6: /usr/include/libxml2/libxml/tree.h:103:14: note: declared here 103 | xmlChar *content XML_DEPRECATED_MEMBER; | ^~~~~~~ rm -f libfreesasa.a ar cr 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 ranlib libfreesasa.a gcc -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/freesasa-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wl,-z,now -o example example.o libfreesasa.a -ljson-c -lxml2 -lpthread -ldl -lm cif.cc: In function 'std::vector freesasa_cif_structure_array(FILE*, int*, const freesasa_classifier*, int)': cif.cc:294:51: error: 'const __gnu_cxx::__alloc_traits, gemmi::Model>::value_type' {aka 'const struct gemmi::Model'} has no member named 'name' 294 | __func__, models[i].name.c_str()); | ^~~~ cif.cc:300:85: error: 'const __gnu_cxx::__alloc_traits, gemmi::Model>::value_type' {aka 'const struct gemmi::Model'} has no member named 'name' 300 | freesasa_structure *structure = structure_from_chain(doc, models[i].name, chain_name, classifier, options); | ^~~~ cif.cc:321:53: error: 'const __gnu_cxx::__alloc_traits, gemmi::Model>::value_type' {aka 'const struct gemmi::Model'} has no member named 'name' 321 | structure_from_model(doc, models[i].name, classifier, options)); | ^~~~ cif.cc: In function 'int reset_freesasa_tables(gemmi::cif::Block&)': cif.cc:715:23: error: 'struct gemmi::cif::Table' has no member named 'convert_pair_to_loop' 715 | table.convert_pair_to_loop(); | ^~~~~~~~~~~~~~~~~~~~ make[4]: *** [Makefile:582: cif.o] Error 1 make[4]: Leaving directory '/build/reproducible-path/freesasa-2.1.2/src' make[3]: *** [Makefile:397: all-recursive] Error 1 make[3]: Leaving directory '/build/reproducible-path/freesasa-2.1.2' make[2]: *** [Makefile:336: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/freesasa-2.1.2' dh_auto_build: error: make -j12 freesasa_LDADD="libfreesasa.a \${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2" returned exit code 2 make[1]: *** [debian/rules:11: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/freesasa-2.1.2' make: *** [debian/rules:7: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/2769492 and its subdirectories freesasa failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/arm64/freesasa_2.1.2-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/arm64/freesasa_2.1.2-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/freesasa_2.1.2-4.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/freesasa_2.1.2-4.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/forky/arm64/freesasa_2.1.2-4_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/freesasa_2.1.2-4.diff.gz' Sat Nov 1 13:17:23 UTC 2025 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 79.8% -- replaced with stdout Sat Nov 1 13:17:23 UTC 2025 I: https://tests.reproducible-builds.org/debian/forky/arm64/freesasa : reproducible ➤ FTBFS INSERT 0 1 INSERT 0 1 DELETE 1 [2025-11-01 13:17:24] INFO: Starting at 2025-11-01 13:17:24.239613 [2025-11-01 13:17:24] INFO: Generating the pages of 1 package(s) [2025-11-01 13:17:24] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/freesasa_2.1.2-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/freesasa_2.1.2-4.diff.gz is missing [2025-11-01 13:17:24] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/freesasa_2.1.2-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/freesasa_2.1.2-4.diff.gz is missing [2025-11-01 13:17:24] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/freesasa_2.1.2-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/freesasa_2.1.2-4.diff.gz is missing [2025-11-01 13:17:24] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/freesasa didn't produce a buildlog, even though it has been built. [2025-11-01 13:17:24] INFO: Finished at 2025-11-01 13:17:24.468986, took: 0:00:00.229378 Sat Nov 1 13:17:24 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/forky/arm64/freesasa.html [2025-11-01 13:17:24] INFO: Starting at 2025-11-01 13:17:24.807367 [2025-11-01 13:17:24] INFO: Scheduling packages in arm64/forky [2025-11-01 13:17:24] INFO: jenkins scheduled in forky/arm64, reason: 'reproducible ➤ FTBFS': freesasa [2025-11-01 13:17:25] INFO: Finished at 2025-11-01 13:17:25.251730, took: 0:00:00.444369 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/arm64/freesasa_2.1.2-4.rbuild.log: 77.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/arm64/freesasa_2.1.2-4.rbuild.log.gz [2025-11-01 13:17:25] INFO: Starting at 2025-11-01 13:17:25.552942 [2025-11-01 13:17:25] INFO: Generating the pages of 1 package(s) [2025-11-01 13:17:25] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/freesasa_2.1.2-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/freesasa_2.1.2-4.diff.gz is missing [2025-11-01 13:17:25] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/freesasa_2.1.2-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/freesasa_2.1.2-4.diff.gz is missing [2025-11-01 13:17:25] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/freesasa_2.1.2-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/freesasa_2.1.2-4.diff.gz is missing [2025-11-01 13:17:25] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/freesasa_2.1.2-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/freesasa_2.1.2-4.diff.gz is missing [2025-11-01 13:17:25] INFO: Finished at 2025-11-01 13:17:25.723502, took: 0:00:00.170563 All cleanup done. Sat Nov 1 13:17:25 UTC 2025 - total duration: 0h 0m 38s. Sat Nov 1 13:17:25 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-dZb1LKuv, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 40.118s CPU time consumed: 2.963s Memory peak: 58.1M (swap: 0B)