Sun May 12 17:13:46 UTC 2024 I: starting to build prodigal/unstable/arm64 on jenkins on '2024-05-12 17:13' Sun May 12 17:13:46 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_19/17902/console.log Sun May 12 17:13:46 UTC 2024 I: Downloading source for unstable/prodigal=1:2.6.3-6 --2024-05-12 17:13:46-- http://deb.debian.org/debian/pool/main/p/prodigal/prodigal_2.6.3-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1992 (1.9K) [text/prs.lines.tag] Saving to: ‘prodigal_2.6.3-6.dsc’ 0K . 100% 213M=0s 2024-05-12 17:13:46 (213 MB/s) - ‘prodigal_2.6.3-6.dsc’ saved [1992/1992] Sun May 12 17:13:46 UTC 2024 I: prodigal_2.6.3-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prodigal Binary: prodigal Architecture: any Version: 1:2.6.3-6 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille Homepage: http://prodigal.ornl.gov/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/prodigal Vcs-Git: https://salsa.debian.org/med-team/prodigal.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: prodigal deb science optional arch=any Checksums-Sha1: 1259e999193cd0c095935baebfb8bcb0233e850f 610934 prodigal_2.6.3.orig.tar.gz 281a30ce91f8775880a5d92d210506e6522921b0 49304 prodigal_2.6.3-6.debian.tar.xz Checksums-Sha256: 89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f 610934 prodigal_2.6.3.orig.tar.gz e47e360e0d4a97a361ed1cb6c294072a9d847f2a28a88e7d406122b4fa9c8583 49304 prodigal_2.6.3-6.debian.tar.xz Files: 5181809fdb740e9a675cfdbb6c038466 610934 prodigal_2.6.3.orig.tar.gz 2da877285635f03bf298eff790734a8e 49304 prodigal_2.6.3-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOPQJ0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGPxQ/9GZ8yzKQncHykka5SpuzYVNHcnzUcJfrt uYbBAAKjEn9UiRdo+Cu3HliWVVIDbS3LFNmbIuND1kXpyt9GQl15/5pD3MnqfsAB nog9dYhKoNo6LqjlLGx/avmlcTuJzH7lVFPPDzanaPFYd6ueTfPdkgYBS+JirleM RgmD4xx4sPltoC9660KaNz0U6BOAhU+sY9/SErhUHezSp0D8e+FKowCqVdpazItb 9uxDTUyksgUgwgi/fYD6fhLYZJRSgbCjxGQoc4eOmIYzvgDMPzF+qBrPUMCvdZpc rX6Oup4wPciBpPKlWDpotMoefdlZqiAK2bKeZOidAvIX8P43kjgx9lmguc6ahKTU hFZOtUT3nYYUm8DTf1PJz3y+2CnIPlsn6YlKGNVmimDXJmBxsdn2sQ25ag9npLMu FvEnN0AliLVB6yk+PO4fU8OUr9codpsRZUEcC7rhxxDnb3Tzne6H01pI87SEovyr CxvzPH8uf/LDhZqFQrUl6D0xPoL/boR2cTuIq4J59CBUmkCRCOyStHO26xCK4D8W vz6kKIvFBrGcGNg8Bte64mJrs4hJPeo46x3KtiGZB/whi6HuMSnduElsX7UCWOkq sT7qRO/W7MbwUXtlubbbcD8AEBnX6rVnGJKCxRRg5aPHNGUstvjinNk55w9LjTf3 7d//QfRp1tQ= =QE7B -----END PGP SIGNATURE----- Sun May 12 17:13:46 UTC 2024 I: Checking whether the package is not for us Sun May 12 17:13:46 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Sun May 12 17:13:46 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Sun May 12 17:20:38 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 05:13:49 -12 2024 I: pbuilder-time-stamp: 1715534029 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [prodigal_2.6.3-6.dsc] I: copying [./prodigal_2.6.3.orig.tar.gz] I: copying [./prodigal_2.6.3-6.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 6 13:16:13 2022 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 ./prodigal_2.6.3-6.dsc: no acceptable signature found dpkg-source: info: extracting prodigal in prodigal-2.6.3 dpkg-source: info: unpacking prodigal_2.6.3.orig.tar.gz dpkg-source: info: unpacking prodigal_2.6.3-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_hardcoded_O3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2219857/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='40bc84b463d34388bcb4ad09480f7693' 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='2219857' 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.SzoFYhH9/pbuilderrc_ReFE --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SzoFYhH9/b1 --logfile b1/build.log prodigal_2.6.3-6.dsc' SUDO_GID='109' 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 codethink02-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2219857/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 ... 19744 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} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{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 18.7 MB of archives. After unpacking 75.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Fetched 18.7 MB in 0s (134 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 ... 19744 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... 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 libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... 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_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+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 (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... 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 groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-11) ... 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/prodigal-2.6.3/ && 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 > ../prodigal_2.6.3-6_source.changes dpkg-buildpackage: info: source package prodigal dpkg-buildpackage: info: source version 1:2.6.3-6 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 -j12 distclean make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' rm -f bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o rm -f prodigal make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' dh_clean rm -f prodigal.1 make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o bitmap.o bitmap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o dprog.o dprog.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o gene.o gene.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o main.o main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o metagenomic.o metagenomic.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o node.o node.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o sequence.o sequence.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o training.o training.c gene.c: In function 'record_gene_data': gene.c:303:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 303 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 305 | sd_spacer[nod[ndx].rbs[1]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:298:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 298 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 | sd_spacer[nod[ndx].rbs[0]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:309:12: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 309 | else sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%dbp", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 | genes[i].gene_data, qt, nod[ndx].mot.spacer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:307:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 307 | sprintf(genes[i].gene_data, "%srbs_motif=None;rbs_spacer=None", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 308 | genes[i].gene_data); | ~~~~~~~~~~~~~~~~~~~ gene.c:290:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 290 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 292 | sd_spacer[nod[ndx].rbs[1]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:286:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 286 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | sd_spacer[nod[ndx].rbs[0]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:312:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 312 | sprintf(genes[i].gene_data, "%s;gc_cont=%.3f", genes[i].gene_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 313 | nod[ndx].gc_cont); | ~~~~~~~~~~~~~~~~~ gene.c:322:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 322 | sprintf(genes[i].score_data, "%stscore=%.2f;", genes[i].score_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 323 | nod[ndx].tscore); | ~~~~~~~~~~~~~~~~ gene.c: In function 'print_genes': gene.c:347:26: warning: 'model="' directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 347 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~ gene.c:347:5: note: 'sprintf' output 10 or more bytes (assuming 10009) into a destination of size 10000 347 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:347:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gene.c:343:26: warning: 'model="Ab initio";' directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 343 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~ gene.c:343:5: note: 'sprintf' output between 19 and 10018 bytes into a destination of size 10000 343 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:343:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gene.c:349:24: warning: 'gc_cont=' directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~ gene.c:349:21: note: assuming directive output of 4 bytes 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:349:3: note: 'sprintf' output between 37 and 10366 bytes into a destination of size 10000 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 350 | tinf->gc*100.0, tinf->trans_table, tinf->uses_sd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:349:3: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c: In function 'write_start_file': node.c:1426:26: warning: 'model="' directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1426 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~ node.c:1426:5: note: 'sprintf' output 10 or more bytes (assuming 10009) into a destination of size 10000 1426 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1426:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c:1422:26: warning: 'model="Ab initio";' directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1422 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~ node.c:1422:5: note: 'sprintf' output between 19 and 10018 bytes into a destination of size 10000 1422 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1422:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c:1428:24: warning: 'gc_cont=' directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~ node.c:1428:21: note: assuming directive output of 4 bytes 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1428:3: note: 'sprintf' output between 37 and 10366 bytes into a destination of size 10000 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1429 | tinf->gc*100.0, tinf->trans_table, tinf->uses_sd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1428:3: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -o prodigal bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o -lm -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' echo "Do not try to install to /usr/local" Do not try to install to /usr/local make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'prodigal' in '../prodigal_2.6.3-6_arm64.deb'. dpkg-deb: building package 'prodigal-dbgsym' in '../prodigal-dbgsym_2.6.3-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../prodigal_2.6.3-6_arm64.buildinfo dpkg-genchanges --build=binary -O../prodigal_2.6.3-6_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/2219857 and its subdirectories I: Current time: Sun May 12 05:20:37 -12 2024 I: pbuilder-time-stamp: 1715534437 Sun May 12 17:20:39 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sun May 12 17:20:39 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sun May 12 17:29:13 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sun May 12 17:29:14 UTC 2024 I: prodigal_2.6.3-6_arm64.changes: Format: 1.8 Date: Tue, 06 Dec 2022 14:00:03 +0100 Source: prodigal Binary: prodigal prodigal-dbgsym Architecture: arm64 Version: 1:2.6.3-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: prodigal - Microbial (bacterial and archaeal) gene finding program Changes: prodigal (1:2.6.3-6) unstable; urgency=medium . * Fix watch file * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: 87441b8325968853adb884837058134efec53778 95456 prodigal-dbgsym_2.6.3-6_arm64.deb 751eb0f7b1bb2354cbde19edf9e7b26499085883 5079 prodigal_2.6.3-6_arm64.buildinfo c5531db99da3617e4828f360ab8eb1365e8a93d5 630368 prodigal_2.6.3-6_arm64.deb Checksums-Sha256: 544cdb06b7a0bdc866a684d6560aadb0861d356c554934512bbc273811b81838 95456 prodigal-dbgsym_2.6.3-6_arm64.deb 6e605dbe2b391d2d66dfe237777d201ef62e621b3c120db5f5d3b476002139d4 5079 prodigal_2.6.3-6_arm64.buildinfo d943c685fd4f04037cbad47fbe21faf5195be3acace61c09622792efcfa0b0c0 630368 prodigal_2.6.3-6_arm64.deb Files: f7bfc216cad028d6b7a4c96f95fe5784 95456 debug optional prodigal-dbgsym_2.6.3-6_arm64.deb 245c083f034a028abd7c7db2d52d6322 5079 science optional prodigal_2.6.3-6_arm64.buildinfo 66c8dab24f3f7ee6e3955f4e400f4f82 630368 science optional prodigal_2.6.3-6_arm64.deb Sun May 12 17:29:15 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_19-17902.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.SzoFYhH9/prodigal_2.6.3-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.SzoFYhH9/prodigal_2.6.3-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.SzoFYhH9/prodigal_2.6.3-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.SzoFYhH9/b1/prodigal_2.6.3-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.SzoFYhH9/b2/prodigal_2.6.3-6_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: 0.385s) 0.385s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.024s) 0.024s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 764ms CPU time consumed: 749ms Sun May 12 17:29:16 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Sun May 12 17:29:16 UTC 2024 I: prodigal from unstable built successfully and reproducibly on arm64. Sun May 12 17:29:18 UTC 2024 I: Submitting .buildinfo files to external archives: Sun May 12 17:29:18 UTC 2024 I: Submitting 8.0K b1/prodigal_2.6.3-6_arm64.buildinfo.asc Sun May 12 17:29:19 UTC 2024 I: Submitting 8.0K b2/prodigal_2.6.3-6_arm64.buildinfo.asc Sun May 12 17:29:20 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 12 17:29:20 UTC 2024 I: Done submitting .buildinfo files. Sun May 12 17:29:20 UTC 2024 I: Removing signed prodigal_2.6.3-6_arm64.buildinfo.asc files: removed './b1/prodigal_2.6.3-6_arm64.buildinfo.asc' removed './b2/prodigal_2.6.3-6_arm64.buildinfo.asc'