Tue Apr 11 12:10:27 UTC 2023 I: starting to build fastdnaml/bookworm/arm64 on jenkins on '2023-04-11 12:10' Tue Apr 11 12:10:27 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_14/6597/console.log Tue Apr 11 12:10:27 UTC 2023 I: Downloading source for bookworm/fastdnaml=1.2.2-15 --2023-04-11 12:10:27-- http://cdn-fastly.deb.debian.org/debian/pool/main/f/fastdnaml/fastdnaml_1.2.2-15.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2037 (2.0K) [text/prs.lines.tag] Saving to: ‘fastdnaml_1.2.2-15.dsc’ 0K . 100% 195M=0s 2023-04-11 12:10:27 (195 MB/s) - ‘fastdnaml_1.2.2-15.dsc’ saved [2037/2037] Tue Apr 11 12:10:27 UTC 2023 I: fastdnaml_1.2.2-15.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: fastdnaml Binary: fastdnaml Architecture: any Version: 1.2.2-15 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Charles Plessy Homepage: ftp://ftp.bio.indiana.edu/molbio/evolve/fastdnaml/fastDNAml.html Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/fastdnaml Vcs-Git: https://salsa.debian.org/med-team/fastdnaml.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: fastdnaml deb science optional arch=any Checksums-Sha1: 78197cbd760163f65085ac80c36d4286a1f29e34 70005 fastdnaml_1.2.2.orig.tar.gz 69d8758531b599fca477f82d26f963722d045018 7848 fastdnaml_1.2.2-15.debian.tar.xz Checksums-Sha256: 34690ec9a8e2fe1d86bea4a7cb10f7bc47e5e4c30719e1c9451210df4f160180 70005 fastdnaml_1.2.2.orig.tar.gz 63cca554d57e0ce0982b5b45de1955766d0986b6cc17de488fbd982c66b93f3e 7848 fastdnaml_1.2.2-15.debian.tar.xz Files: dd9c737e0f433879500391d0e229f763 70005 fastdnaml_1.2.2.orig.tar.gz 9b78e45a6d97335e6a86c9fa29a30f22 7848 fastdnaml_1.2.2-15.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/LZ6sRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEMXQ/9GI4RhX1doJiz/SVIIYPQAD/vDpQZfI9e Y4ZTlbs8YirEOb0LWxRF2xLm7KsQDGmzTdm2VVhB4d1/wLE83RtAE1P7yEnry7G7 lqWZtgz3P7+Yz8TmPku3k1bG95H92cq3/pjxQkBMEy8NAtpUT3bthsQ6UXt6i/Do Ob+TCDuWvhsr/MrBmgO8iSm7ChfNg467/sw3/eyRawhWrJ7V/g/ACnyJuObXkJRw OxRp+CsSNTOAdoqF5yE1MTLppTkhwZ+cU8pxj45V2/QyP493Q57hEJuJidy0OhJf XOT+r0hIkxhMpdi0ICNr0N+taZ73RzI5nBjXB5r9wgnzBfFPkFQySqfVhfIS8kYZ y3+QLNlud4LsDw0nFRtvUy5XwLnMzAelFQTh+KvoEJCdj8Cs5JGlHgr0DcL/NDgd VDtYfzRd740mtyj5fozmkdN2pwDmO5RrFW/QaeY7sVdah1kGPg4pXjOSydhY2Yyz Qdqn9iARpaDoZIbo7k2nEWLVWluCeZCJ0f9vljRpw+eBybkHkv9HFWvBD3UlNrKX SGRvlbyFOxCRrQC0fKHQLGgcXLBNXTdQmZP8L95XIBGg6XBKkMqvKiohyJ1uzy07 St/o0ljYW9pu2asa8NhGR0/ttU72jU/t/nqgboHrpY1bA2ulQtDp1h+7m3JUass3 Pckq1graS48= =+ve4 -----END PGP SIGNATURE----- Tue Apr 11 12:10:27 UTC 2023 I: Checking whether the package is not for us Tue Apr 11 12:10:27 UTC 2023 I: Starting 1st build on remote node codethink12-arm64.debian.net. Tue Apr 11 12:10:27 UTC 2023 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Tue Apr 11 12:11:09 UTC 2023 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 11 00:10:29 -12 2023 I: pbuilder-time-stamp: 1681215029 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 [fastdnaml_1.2.2-15.dsc] I: copying [./fastdnaml_1.2.2.orig.tar.gz] I: copying [./fastdnaml_1.2.2-15.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 4 22:57:47 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./fastdnaml_1.2.2-15.dsc: no acceptable signature found dpkg-source: info: extracting fastdnaml in fastdnaml-1.2.2 dpkg-source: info: unpacking fastdnaml_1.2.2.orig.tar.gz dpkg-source: info: unpacking fastdnaml_1.2.2-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile.patch dpkg-source: info: applying scripts.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15213/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='15213' 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.TX768qu0/pbuilderrc_UICQ --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.TX768qu0/b1 --logfile b1/build.log fastdnaml_1.2.2-15.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink12-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 8 22:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/15213/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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 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. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.3 MB of archives. After unpacking 74.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Fetched 18.3 MB in 0s (38.7 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 ... 19616 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_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.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 ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.1+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-8) ... 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/fastdnaml-1.2.2/ && 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 > ../fastdnaml_1.2.2-15_source.changes dpkg-buildpackage: info: source package fastdnaml dpkg-buildpackage: info: source version 1.2.2-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j8 clean make[1]: Entering directory '/build/fastdnaml-1.2.2' (cd source; rm -f *.o fastDNAml) rm -rf tests rm -f checkpoint.* make[1]: Leaving directory '/build/fastdnaml-1.2.2' debian/rules override_dh_clean make[1]: Entering directory '/build/fastdnaml-1.2.2' dh_clean rm -fr source/fastDNAml make[1]: Leaving directory '/build/fastdnaml-1.2.2' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastdnaml-1.2.2' cd source && cc -g -O2 -ffile-prefix-map=/build/fastdnaml-1.2.2=. -fstack-protector-strong -Wformat -Werror=format-security fastDNAml.c -o fastDNAml -lm -Wl,-z,relro -Wl,-z,now In file included from fastDNAml.c:207: fastDNAml.h:222:10: warning: conflicting types for built-in function 'malloc'; expected 'void *(long unsigned int)' [-Wbuiltin-declaration-mismatch] 222 | char *malloc(); | ^~~~~~ fastDNAml.h:1:1: note: 'malloc' is declared in header '' +++ |+#include 1 | /* fastDNAml.h */ fastDNAml.c: In function 'freeTopol': fastDNAml.h:228:28: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:342:5: note: in expansion of macro 'Free' 342 | Free(tpl->links); | ^~~~ fastDNAml.c:208:1: note: include '' or provide a declaration of 'free' 207 | #include "fastDNAml.h" /* Requires version 1.2 */ +++ |+#include 208 | fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:342:5: note: in expansion of macro 'Free' 342 | Free(tpl->links); | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:342:5: note: in expansion of macro 'Free' 342 | Free(tpl->links); | ^~~~ fastDNAml.c: In function 'freeTreeNode': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:1533:23: note: in expansion of macro 'Free' 1533 | if (p->x->lv) Free(p->x->lv); | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:1533:23: note: in expansion of macro 'Free' 1533 | if (p->x->lv) Free(p->x->lv); | ^~~~ fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:1534:9: note: in expansion of macro 'Free' 1534 | Free(p->x); | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:1534:9: note: in expansion of macro 'Free' 1534 | Free(p->x); | ^~~~ fastDNAml.c: In function 'freeTree': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:1560:5: note: in expansion of macro 'Free' 1560 | Free(tr->nodep[1]); /* Free the actual nodes */ | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:1560:5: note: in expansion of macro 'Free' 1560 | Free(tr->nodep[1]); /* Free the actual nodes */ | ^~~~ fastDNAml.c: In function 'setupxarray': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:2028:9: note: in expansion of macro 'Free' 2028 | Free(x); | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:2028:9: note: in expansion of macro 'Free' 2028 | Free(x); | ^~~~ fastDNAml.c: In function 'makenewz': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:2604:5: note: in expansion of macro 'Free' 2604 | Free(abi); | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:2604:5: note: in expansion of macro 'Free' 2604 | Free(abi); | ^~~~ fastDNAml.c: In function 'readKeyValue': fastDNAml.c:2886:15: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration] 2886 | string += strlen(key); | ^~~~~~ fastDNAml.c:208:1: note: include '' or provide a declaration of 'strlen' 207 | #include "fastDNAml.h" /* Requires version 1.2 */ +++ |+#include 208 | fastDNAml.c:2886:15: warning: incompatible implicit declaration of built-in function 'strlen' [-Wbuiltin-declaration-mismatch] 2886 | string += strlen(key); | ^~~~~~ fastDNAml.c:2886:15: note: include '' or provide a declaration of 'strlen' fastDNAml.c: In function 'fopen_pid': fastDNAml.c:3231:47: warning: implicit declaration of function 'getpid' [-Wimplicit-function-declaration] 3231 | (void) sprintf(name_pid, "%s.%d", filenm, getpid()); | ^~~~~~ fastDNAml.c: In function 'treeOut': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:3683:5: note: in expansion of macro 'Free' 3683 | Free(treestr); | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:3683:5: note: in expansion of macro 'Free' 3683 | Free(treestr); | ^~~~ fastDNAml.c: In function 'cmpBestTrees': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:4535:5: note: in expansion of macro 'Free' 4535 | Free(log_f0); | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:4535:5: note: in expansion of macro 'Free' 4535 | Free(log_f0); | ^~~~ fastDNAml.c: In function 'makeDenovoTree': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:4765:5: note: in expansion of macro 'Free' 4765 | Free(enterorder); | ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^~~~ fastDNAml.c:4765:5: note: in expansion of macro 'Free' 4765 | Free(enterorder); | ^~~~ fastDNAml.c: At top level: fastDNAml.c:4775:3: warning: return type defaults to 'int' [-Wimplicit-int] 4775 | main () | ^~~~ make[1]: Leaving directory '/build/fastdnaml-1.2.2' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/fastdnaml-1.2.2' # do nothing make[1]: Leaving directory '/build/fastdnaml-1.2.2' debian/rules override_dh_install make[1]: Entering directory '/build/fastdnaml-1.2.2' dh_install cp -a docs/fastDNAml_doc_1.2.txt `pwd`/debian/`dh_listpackages`/usr/share/`dh_listpackages`/fastdnaml_help # the scripts have to be executable thus mentioning these in debian/install is not enough cp -a scripts/* `pwd`/debian/`dh_listpackages`/usr/lib/`dh_listpackages`/bin chmod 755 `pwd`/debian/`dh_listpackages`/usr/lib/`dh_listpackages`/bin/* make[1]: Leaving directory '/build/fastdnaml-1.2.2' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_installmenu 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'fastdnaml-dbgsym' in '../fastdnaml-dbgsym_1.2.2-15_arm64.deb'. dpkg-deb: building package 'fastdnaml' in '../fastdnaml_1.2.2-15_arm64.deb'. dpkg-genbuildinfo --build=binary -O../fastdnaml_1.2.2-15_arm64.buildinfo dpkg-genchanges --build=binary -O../fastdnaml_1.2.2-15_arm64.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: not including original 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/15213 and its subdirectories I: Current time: Tue Apr 11 00:11:07 -12 2023 I: pbuilder-time-stamp: 1681215067 Tue Apr 11 12:11:09 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink11-arm64.debian.net. Tue Apr 11 12:11:09 UTC 2023 I: Preparing to do remote build '2' on codethink11-arm64.debian.net. Tue Apr 11 12:11:53 UTC 2023 I: Deleting $TMPDIR on codethink11-arm64.debian.net. Tue Apr 11 12:11:54 UTC 2023 I: fastdnaml_1.2.2-15_arm64.changes: Format: 1.8 Date: Sat, 05 Dec 2020 11:52:15 +0100 Source: fastdnaml Binary: fastdnaml fastdnaml-dbgsym Architecture: arm64 Version: 1.2.2-15 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fastdnaml - Tool for construction of phylogenetic trees of DNA sequences Changes: fastdnaml (1.2.2-15) unstable; urgency=medium . * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) Checksums-Sha1: e0282051a70fbf4cadc97a64e3e44448f2bacd2e 68448 fastdnaml-dbgsym_1.2.2-15_arm64.deb 29db6125f7c9cd01c1f00bc26038706abed7d9a8 5140 fastdnaml_1.2.2-15_arm64.buildinfo 6627b274f60b2ebd6c7222491cf7438852bf4d9b 56832 fastdnaml_1.2.2-15_arm64.deb Checksums-Sha256: 53da441c6e9f6356bcf408fd79b55a7c700db6378ff703c4d943e7d0bde41ab2 68448 fastdnaml-dbgsym_1.2.2-15_arm64.deb 12a7e7bf9afef3c502da3ada6bde0d922b503791f9d4023a886f68d9ab9989a7 5140 fastdnaml_1.2.2-15_arm64.buildinfo 97eee9820486f28d23292732ed7fd9009298f7191c7f4f53495af2d216d2bf30 56832 fastdnaml_1.2.2-15_arm64.deb Files: 3093bdfd5f2deffee1438748676d5f83 68448 debug optional fastdnaml-dbgsym_1.2.2-15_arm64.deb e2c11396aad42740396f3832671f639f 5140 science optional fastdnaml_1.2.2-15_arm64.buildinfo 4fec8a0d90b217545c4917952eff3e48 56832 science optional fastdnaml_1.2.2-15_arm64.deb Tue Apr 11 12:11:55 UTC 2023 I: diffoscope 240 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.TX768qu0/fastdnaml_1.2.2-15.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TX768qu0/fastdnaml_1.2.2-15.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TX768qu0/fastdnaml_1.2.2-15.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TX768qu0/b1/fastdnaml_1.2.2-15_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.TX768qu0/b2/fastdnaml_1.2.2-15_arm64.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: 0.320s) 0.320s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.018s) 0.018s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Tue Apr 11 12:11:56 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 11 12:11:56 UTC 2023 I: fastdnaml from bookworm built successfully and reproducibly on arm64. Tue Apr 11 12:11:57 UTC 2023 I: Submitting .buildinfo files to external archives: Tue Apr 11 12:11:57 UTC 2023 I: Submitting 8.0K b1/fastdnaml_1.2.2-15_arm64.buildinfo.asc Tue Apr 11 12:11:58 UTC 2023 I: Submitting 8.0K b2/fastdnaml_1.2.2-15_arm64.buildinfo.asc Tue Apr 11 12:11:59 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 11 12:11:59 UTC 2023 I: Done submitting .buildinfo files. Tue Apr 11 12:11:59 UTC 2023 I: Removing signed fastdnaml_1.2.2-15_arm64.buildinfo.asc files: removed './b1/fastdnaml_1.2.2-15_arm64.buildinfo.asc' removed './b2/fastdnaml_1.2.2-15_arm64.buildinfo.asc'