Running as unit: rb-build-arm64_15-63373.service ==================================================================================== Mon Sep 30 22:32:32 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_15) on jenkins, called using "codethink01-arm64 codethink04-arm64" as arguments. Mon Sep 30 22:32:32 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-hXF50dCo" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Sep 30 22:32:32 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Mon Sep 30 22:32:32 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-TyQBQG' Mon Sep 30 22:32:33 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Mon Sep 30 22:32:33 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-jF9T87' ok, let's check if provean is building anywhere yet… ok, provean is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of provean in unstable on arm64 on jenkins now. 1st build will be done on codethink01-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Mon Sep 30 22:32:52 UTC 2024 I: starting to build provean/unstable/arm64 on jenkins on '2024-09-30 22:32' Mon Sep 30 22:32:52 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/63373/console.log 1727735572 arm64 unstable provean Mon Sep 30 22:32:52 UTC 2024 I: Downloading source for unstable/provean=1.1.5+ds-2 --2024-09-30 22:32:53-- http://deb.debian.org/debian/pool/main/p/provean/provean_1.1.5%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1957 (1.9K) [text/prs.lines.tag] Saving to: ‘provean_1.1.5+ds-2.dsc’ 0K . 100% 294M=0s 2024-09-30 22:32:53 (294 MB/s) - ‘provean_1.1.5+ds-2.dsc’ saved [1957/1957] --2024-09-30 22:32:53-- http://deb.debian.org/debian/pool/main/p/provean/provean_1.1.5%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1957 (1.9K) [text/prs.lines.tag] Saving to: ‘provean_1.1.5+ds-2.dsc’ 0K . 100% 294M=0s 2024-09-30 22:32:53 (294 MB/s) - ‘provean_1.1.5+ds-2.dsc’ saved [1957/1957] Mon Sep 30 22:32:53 UTC 2024 I: provean_1.1.5+ds-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: provean Binary: provean Architecture: any Version: 1.1.5+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Andrius Merkys , Homepage: http://provean.jcvi.org Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/provean Vcs-Git: https://salsa.debian.org/med-team/provean.git Build-Depends: cd-hit, debhelper-compat (= 13), ncbi-blast+ Package-List: provean deb science optional arch=any Checksums-Sha1: 0e8149ee7c3900f801e8631ae66cb572b4d56989 22704 provean_1.1.5+ds.orig.tar.xz b61dc8b28f43ab497912be015187047d0370cee1 2220 provean_1.1.5+ds-2.debian.tar.xz Checksums-Sha256: fb9742e161251eeee034e8982e03c719bf9caa2b388fcb32eaefdf422ab3383b 22704 provean_1.1.5+ds.orig.tar.xz 9c0936ddb101f7f0a46d22c2c912c466cbd7544355300bd47e6f77221a448ed1 2220 provean_1.1.5+ds-2.debian.tar.xz Files: 7ab74c207de71dd63e3187013e1b4129 22704 provean_1.1.5+ds.orig.tar.xz adbe2b01aa22c3b26b26108ce69fcfdb 2220 provean_1.1.5+ds-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmKEw6ARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEMiw/8DJcwRivHUvAn+8uTD1iADH/6Cy5Jqady vVG+17j3b27T2EokNKE/tleUZk4NSA4jmFuXEIjN8jx7qs4ieVgVMxRXshwtNP76 Nk2owDDOxI5cJe/mkfQ90hNCLDKoRCLFi+YEDH3Ndhh0ILdLPK8X2g+XmiGcB3Em MuuCnGx1TifACXgOPEfN9v0xTgN8+87YoqqJH5Jho87tRUoOmWQxT15uFSqXdzFi XfyYB1ZVKC04Ic7ouaj14Q68kkc7nM3yXejUUuQjT1EnO7BSH4JkIUHEBe5khtov PrPjibMEBvjilPYYVkAuTf5D6tFmw+YpRyStKzZSYYQVwvxVSkfzeNkHySekCVyZ rguZCcXUob5LtzdZrhIpSihYeXbPuFLYJwjunWx1LZgiurn4gb+G9jA3fK1ElChS tKoOHksWbgWdXM72x+EJUd+wmpa/wwQY94I4cBbopOXW5U8PdHal9+Cgl3wkzJl5 2F388zBdQbi51l0XFjw0gxD67M/lYgj9PdgUh+dCV3ZxlgqMYNaYvaXZyNvybKVa 91NglnBtj8COFLBEDadAdv0pkOztWQ1juhbcuRsWghOOgjb/eJbjR+TzNDaC7Wcw X8zuk71A5r4ZtyzlW/0O9mE0fri1BN6Gy9m8mRecQqThCpdioM3ZcGpVc74v8jxU MVbDnzlpir0= =ThI/ -----END PGP SIGNATURE----- Mon Sep 30 22:32:53 UTC 2024 I: Checking whether the package is not for us Mon Sep 30 22:32:53 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Mon Sep 30 22:32:53 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Mon Sep 30 22:32:53 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Mon Sep 30 22:32:53 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-CSM3cI' ==================================================================================== Mon Nov 3 04:55:54 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "1 provean unstable /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6 1.1.5+ds-2" as arguments. Mon Nov 3 04:55:54 UTC 2025 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-l4RU8SFP" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 3 04:55:54 UTC 2025 I: Downloading source for unstable/provean=1.1.5+ds-2 Reading package lists... NOTICE: 'provean' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/provean.git Please use: git clone https://salsa.debian.org/med-team/provean.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 26.9 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (dsc) [1957 B] Get:2 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (tar) [22.7 kB] Get:3 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (diff) [2220 B] Fetched 26.9 kB in 0s (411 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'provean' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/provean.git Please use: git clone https://salsa.debian.org/med-team/provean.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 26.9 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (dsc) [1957 B] Get:2 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (tar) [22.7 kB] Get:3 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (diff) [2220 B] Fetched 26.9 kB in 0s (411 kB/s) Download complete and in download only mode ============================================================================= Building provean in unstable on arm64 on codethink01-arm64 now. Date: Mon Nov 3 04:55:54 GMT 2025 Date UTC: Mon Nov 3 04:55:54 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: Sun Nov 2 16:55:55 -12 2025 I: pbuilder-time-stamp: 1762145755 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 [provean_1.1.5+ds-2.dsc] I: copying [./provean_1.1.5+ds.orig.tar.xz] I: copying [./provean_1.1.5+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 18 10:00:00 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 ./provean_1.1.5+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting provean in provean-1.1.5+ds dpkg-source: info: unpacking provean_1.1.5+ds.orig.tar.xz dpkg-source: info: unpacking provean_1.1.5+ds-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/813242/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='3ebe37119f71456b80c5055e12bdd1e2' 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='813242' 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.IM3HwHk6/pbuilderrc_Mbwp --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.IM3HwHk6/b1 --logfile b1/build.log provean_1.1.5+ds-2.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 codethink01-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/813242/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: cd-hit, debhelper-compat (= 13), ncbi-blast+ dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 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 cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ 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} cd-hit{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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After unpacking 208 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 cd-hit arm64 4.8.1-4 [506 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 liblmdb0 arm64 0.9.31-1+b1 [43.0 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto7t64 arm64 2.28.8-1 [269 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libmbedx509-1t64 arm64 2.28.8-1 [131 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libmbedtls14t64 arm64 2.28.8-1 [160 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-6 [142 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 ncbi-blast+ arm64 2.16.0+ds-6 [13.8 MB] Fetched 44.8 MB in 1s (78.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 19895 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (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 ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... 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Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 3 04:56:13 UTC 2025. Universal Time is now: Mon Nov 3 04:56:13 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... 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 (1.14.0-1) ... Setting up gettext (0.22.5-2) ... 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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/provean-1.1.5+ds/ && 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 > ../provean_1.1.5+ds-2_source.changes dpkg-buildpackage: info: source package provean dpkg-buildpackage: info: source version 1.1.5+ds-2 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_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am: installing './depcomp' 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 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 for g++... g++ 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 g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for psiblast... /usr/bin/psiblast checking for cd-hit... /usr/bin/cd-hit checking for blastdbcmd... /usr/bin/blastdbcmd 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 scripts/Makefile config.status: creating examples/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make all-recursive make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making all in src make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o provean.o provean.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Common.o Common.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Options.o Options.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o SequenceDB.o SequenceDB.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ScoreMatrix.o ScoreMatrix.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Sequence.o Sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Tables.o Tables.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Variant.o Variant.cpp Sequence.cpp: In member function 'bool Sequence::SetSequenceFromFastaFile(const char*, std::string)': Sequence.cpp:100:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::SetSequencesFromFastaFile(std::string)': SequenceDB.cpp:295:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 295 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::SetOnlySequencesFromFastaFile(std::string)': SequenceDB.cpp:652:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 652 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:737:35: warning: '.help' directive writing 5 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 737 | sprintf(help_filename, "%s.help", output_prefix); | ^~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from SequenceDB.cpp:17: In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:737:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 6 and 65541 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:738:41: warning: '%s' directive writing up to 65535 bytes into a region of size 65530 [-Wformat-overflow=] 738 | sprintf(cdhit_command, "%s -h > %s", | ^~ 739 | p_options_->cdhit_command_.c_str(), 740 | help_filename); | ~~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:738:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 7 or more bytes (assuming 65542) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:776:53: warning: '%s' directive writing up to 65535 bytes into a region of size 65528 [-Wformat-overflow=] 776 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d -bak 1 > %s.log", | ^~ ...... 779 | output_prefix, | ~~~~~~~~~~~~~ SequenceDB.cpp:776:40: note: assuming directive output of 4 bytes 776 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d -bak 1 > %s.log", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp:776:40: note: using the range [-2147483648, 2147483647] for directive argument In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:776:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 55 or more bytes (assuming 131126) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:785:53: warning: '%s' directive writing up to 65535 bytes into a region of size 65528 [-Wformat-overflow=] 785 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d > %s.log", | ^~ ...... 788 | output_prefix, | ~~~~~~~~~~~~~ SequenceDB.cpp:785:40: note: assuming directive output of 4 bytes 785 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d > %s.log", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp:785:40: note: using the range [-2147483648, 2147483647] for directive argument In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:785:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 48 or more bytes (assuming 131119) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:830:38: warning: '.cluster.bak.clstr' directive writing 18 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 830 | sprintf(cluster_filename, "%s.cluster.bak.clstr", output_prefix); | ^~~~~~~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:830:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 19 and 65554 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:804:42: warning: '.log' directive writing 4 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 804 | sprintf(log_filename, "%s.log", output_prefix); | ^~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:804:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 65540 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'void SequenceDB::RunBlast(std::string, std::string, std::string)': SequenceDB.cpp:1552:47: warning: '%s' directive writing up to 65535 bytes into a region of size 65524 [-Wformat-overflow=] 1552 | sprintf(blast_command, "%s -version > %s", p_options_->psiblast_command_.c_str(), blast_help); | ^~ ~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void SequenceDB::RunBlast(std::string, std::string, std::string)' at SequenceDB.cpp:1552:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 13 or more bytes (assuming 65548) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -o provean provean.o Common.o Options.o SequenceDB.o ScoreMatrix.o Sequence.o Tables.o Variant.o make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making all in scripts make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' sed -e 's,\[@\]PSIBLAST\[@\],/usr/bin/psiblast,g' -e 's,\[@\]CDHIT\[@\],/usr/bin/cd-hit,g' -e 's,\[@\]BLASTDB\[@\],,g' -e 's,\[@\]BLASTDBCMD\[@\],/usr/bin/blastdbcmd,g' -e 's,\[@\]VERSION\[@\],1.1.5,g' < ./provean.sh.in > provean.sh chmod +x provean.sh make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making all in examples make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making check in src make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making check in scripts make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making check in examples make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/provean/ make -j12 install DESTDIR=/build/reproducible-path/provean-1.1.5\+ds/debian/provean AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making install in src make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c provean '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making install in scripts make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c provean.sh '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making install in examples make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/data/provean/examples' /usr/bin/install -c -m 644 P04637.fasta P04637.var '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/data/provean/examples' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/doc/provean' /usr/bin/install -c -m 644 README LICENSE '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/doc/provean' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' dh_install rm debian/provean/usr/bin/provean.sh make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'provean' in '../provean_1.1.5+ds-2_arm64.deb'. dpkg-deb: building package 'provean-dbgsym' in '../provean-dbgsym_1.1.5+ds-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../provean_1.1.5+ds-2_arm64.buildinfo dpkg-genchanges --build=binary -O../provean_1.1.5+ds-2_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/813242 and its subdirectories I: Current time: Sun Nov 2 16:56:32 -12 2025 I: pbuilder-time-stamp: 1762145792 Mon Nov 3 04:56:32 UTC 2025 I: Signing ./b1/provean_1.1.5+ds-2_arm64.buildinfo as provean_1.1.5+ds-2_arm64.buildinfo.asc Mon Nov 3 04:56:33 UTC 2025 I: Signed ./b1/provean_1.1.5+ds-2_arm64.buildinfo as ./b1/provean_1.1.5+ds-2_arm64.buildinfo.asc Mon Nov 3 04:56:33 UTC 2025 - build #1 for provean/unstable/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Mon Nov 3 04:56:33 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-l4RU8SFP, removing. /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Sep 30 22:33 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 30 22:32 b2 -rw-r--r-- 1 jenkins jenkins 1957 May 18 2022 provean_1.1.5+ds-2.dsc -rw------- 1 jenkins jenkins 3084 Sep 30 22:32 rbuildlog.pGLVXiL /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b1: total 512 -rw-r--r-- 1 jenkins jenkins 50048 Sep 30 22:33 build.log -rw-r--r-- 1 jenkins jenkins 387652 Sep 30 22:33 provean-dbgsym_1.1.5+ds-2_arm64.deb -rw-r--r-- 1 jenkins jenkins 2220 Sep 30 22:33 provean_1.1.5+ds-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1957 Sep 30 22:33 provean_1.1.5+ds-2.dsc -rw-r--r-- 1 jenkins jenkins 5838 Sep 30 22:33 provean_1.1.5+ds-2_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6720 Sep 30 22:33 provean_1.1.5+ds-2_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1425 Sep 30 22:33 provean_1.1.5+ds-2_arm64.changes -rw-r--r-- 1 jenkins jenkins 45700 Sep 30 22:33 provean_1.1.5+ds-2_arm64.deb -rw-r--r-- 1 jenkins jenkins 1300 Sep 30 22:33 provean_1.1.5+ds-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b2: total 0 Mon Sep 30 22:33:34 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 2 16:55:55 -12 2025 I: pbuilder-time-stamp: 1762145755 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 [provean_1.1.5+ds-2.dsc] I: copying [./provean_1.1.5+ds.orig.tar.xz] I: copying [./provean_1.1.5+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 18 10:00:00 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 ./provean_1.1.5+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting provean in provean-1.1.5+ds dpkg-source: info: unpacking provean_1.1.5+ds.orig.tar.xz dpkg-source: info: unpacking provean_1.1.5+ds-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/813242/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='3ebe37119f71456b80c5055e12bdd1e2' 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='813242' 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.IM3HwHk6/pbuilderrc_Mbwp --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.IM3HwHk6/b1 --logfile b1/build.log provean_1.1.5+ds-2.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 codethink01-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/813242/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: cd-hit, debhelper-compat (= 13), ncbi-blast+ dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 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 cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ 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} cd-hit{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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After unpacking 208 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 cd-hit arm64 4.8.1-4 [506 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 liblmdb0 arm64 0.9.31-1+b1 [43.0 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto7t64 arm64 2.28.8-1 [269 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libmbedx509-1t64 arm64 2.28.8-1 [131 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libmbedtls14t64 arm64 2.28.8-1 [160 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-6 [142 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 ncbi-blast+ arm64 2.16.0+ds-6 [13.8 MB] Fetched 44.8 MB in 1s (78.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 19895 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (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 ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21287 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. 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Preparing to unpack .../32-libmbedcrypto7t64_2.28.8-1_arm64.deb ... Unpacking libmbedcrypto7t64:arm64 (2.28.8-1) ... Selecting previously unselected package libmbedx509-1t64:arm64. Preparing to unpack .../33-libmbedx509-1t64_2.28.8-1_arm64.deb ... Unpacking libmbedx509-1t64:arm64 (2.28.8-1) ... Selecting previously unselected package libmbedtls14t64:arm64. Preparing to unpack .../34-libmbedtls14t64_2.28.8-1_arm64.deb ... Unpacking libmbedtls14t64:arm64 (2.28.8-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../35-libnghttp2-14_1.63.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.63.0-1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../36-libuv1t64_1.48.0-6_arm64.deb ... Unpacking libuv1t64:arm64 (1.48.0-6) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../37-ncbi-data_6.1.20170106+dfsg2-4_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-4) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../38-ncbi-blast+_2.16.0+ds-6_arm64.deb ... Unpacking ncbi-blast+ (2.16.0+ds-6) ... Setting up cd-hit (4.8.1-4) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up liblmdb0:arm64 (0.9.31-1+b1) ... Setting up ncbi-data (6.1.20170106+dfsg2-4) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmbedcrypto7t64:arm64 (2.28.8-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libuv1t64:arm64 (1.48.0-6) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libnghttp2-14:arm64 (1.63.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 3 04:56:13 UTC 2025. Universal Time is now: Mon Nov 3 04:56:13 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... 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 (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libmbedx509-1t64:arm64 (2.28.8-1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libmbedtls14t64:arm64 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:arm64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up ncbi-blast+ (2.16.0+ds-6) ... Processing triggers for libc-bin (2.40-3) ... 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/provean-1.1.5+ds/ && 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 > ../provean_1.1.5+ds-2_source.changes dpkg-buildpackage: info: source package provean dpkg-buildpackage: info: source version 1.1.5+ds-2 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_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am: installing './depcomp' 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 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 for g++... g++ 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 g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for psiblast... /usr/bin/psiblast checking for cd-hit... /usr/bin/cd-hit checking for blastdbcmd... /usr/bin/blastdbcmd 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 scripts/Makefile config.status: creating examples/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make all-recursive make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making all in src make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o provean.o provean.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Common.o Common.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Options.o Options.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o SequenceDB.o SequenceDB.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ScoreMatrix.o ScoreMatrix.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Sequence.o Sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Tables.o Tables.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Variant.o Variant.cpp Sequence.cpp: In member function 'bool Sequence::SetSequenceFromFastaFile(const char*, std::string)': Sequence.cpp:100:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::SetSequencesFromFastaFile(std::string)': SequenceDB.cpp:295:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 295 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::SetOnlySequencesFromFastaFile(std::string)': SequenceDB.cpp:652:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 652 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:737:35: warning: '.help' directive writing 5 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 737 | sprintf(help_filename, "%s.help", output_prefix); | ^~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from SequenceDB.cpp:17: In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:737:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 6 and 65541 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:738:41: warning: '%s' directive writing up to 65535 bytes into a region of size 65530 [-Wformat-overflow=] 738 | sprintf(cdhit_command, "%s -h > %s", | ^~ 739 | p_options_->cdhit_command_.c_str(), 740 | help_filename); | ~~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:738:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 7 or more bytes (assuming 65542) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:776:53: warning: '%s' directive writing up to 65535 bytes into a region of size 65528 [-Wformat-overflow=] 776 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d -bak 1 > %s.log", | ^~ ...... 779 | output_prefix, | ~~~~~~~~~~~~~ SequenceDB.cpp:776:40: note: assuming directive output of 4 bytes 776 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d -bak 1 > %s.log", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp:776:40: note: using the range [-2147483648, 2147483647] for directive argument In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:776:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 55 or more bytes (assuming 131126) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:785:53: warning: '%s' directive writing up to 65535 bytes into a region of size 65528 [-Wformat-overflow=] 785 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d > %s.log", | ^~ ...... 788 | output_prefix, | ~~~~~~~~~~~~~ SequenceDB.cpp:785:40: note: assuming directive output of 4 bytes 785 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d > %s.log", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp:785:40: note: using the range [-2147483648, 2147483647] for directive argument In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:785:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 48 or more bytes (assuming 131119) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:830:38: warning: '.cluster.bak.clstr' directive writing 18 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 830 | sprintf(cluster_filename, "%s.cluster.bak.clstr", output_prefix); | ^~~~~~~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:830:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 19 and 65554 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:804:42: warning: '.log' directive writing 4 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 804 | sprintf(log_filename, "%s.log", output_prefix); | ^~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:804:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 65540 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'void SequenceDB::RunBlast(std::string, std::string, std::string)': SequenceDB.cpp:1552:47: warning: '%s' directive writing up to 65535 bytes into a region of size 65524 [-Wformat-overflow=] 1552 | sprintf(blast_command, "%s -version > %s", p_options_->psiblast_command_.c_str(), blast_help); | ^~ ~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void SequenceDB::RunBlast(std::string, std::string, std::string)' at SequenceDB.cpp:1552:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 13 or more bytes (assuming 65548) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -o provean provean.o Common.o Options.o SequenceDB.o ScoreMatrix.o Sequence.o Tables.o Variant.o make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making all in scripts make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' sed -e 's,\[@\]PSIBLAST\[@\],/usr/bin/psiblast,g' -e 's,\[@\]CDHIT\[@\],/usr/bin/cd-hit,g' -e 's,\[@\]BLASTDB\[@\],,g' -e 's,\[@\]BLASTDBCMD\[@\],/usr/bin/blastdbcmd,g' -e 's,\[@\]VERSION\[@\],1.1.5,g' < ./provean.sh.in > provean.sh chmod +x provean.sh make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making all in examples make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making check in src make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making check in scripts make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making check in examples make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/provean/ make -j12 install DESTDIR=/build/reproducible-path/provean-1.1.5\+ds/debian/provean AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making install in src make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c provean '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making install in scripts make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c provean.sh '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making install in examples make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/data/provean/examples' /usr/bin/install -c -m 644 P04637.fasta P04637.var '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/data/provean/examples' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/doc/provean' /usr/bin/install -c -m 644 README LICENSE '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/doc/provean' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' dh_install rm debian/provean/usr/bin/provean.sh make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'provean' in '../provean_1.1.5+ds-2_arm64.deb'. dpkg-deb: building package 'provean-dbgsym' in '../provean-dbgsym_1.1.5+ds-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../provean_1.1.5+ds-2_arm64.buildinfo dpkg-genchanges --build=binary -O../provean_1.1.5+ds-2_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/813242 and its subdirectories I: Current time: Sun Nov 2 16:56:32 -12 2025 I: pbuilder-time-stamp: 1762145792 Mon Sep 30 22:33:35 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Mon Sep 30 22:33:35 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Mon Sep 30 22:33:35 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Mon Sep 30 22:33:35 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-N8WNwj' ==================================================================================== Mon Sep 30 22:33:37 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 provean unstable /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6 1.1.5+ds-2" as arguments. Mon Sep 30 22:33:37 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-XMOanrc3" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Sep 30 22:33:37 UTC 2024 I: Downloading source for unstable/provean=1.1.5+ds-2 Reading package lists... NOTICE: 'provean' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/provean.git Please use: git clone https://salsa.debian.org/med-team/provean.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 26.9 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (dsc) [1957 B] Get:2 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (tar) [22.7 kB] Get:3 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (diff) [2220 B] Fetched 26.9 kB in 0s (1535 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'provean' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/provean.git Please use: git clone https://salsa.debian.org/med-team/provean.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 26.9 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (dsc) [1957 B] Get:2 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (tar) [22.7 kB] Get:3 http://deb.debian.org/debian unstable/main provean 1.1.5+ds-2 (diff) [2220 B] Fetched 26.9 kB in 0s (1535 kB/s) Download complete and in download only mode ============================================================================= Re-Building provean in unstable on arm64 on codethink04-arm64 now. Date: Mon Sep 30 23:33:37 BST 2024 Date UTC: Mon Sep 30 22:33:37 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/pbuilderrc_af0R + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' provean = debian-installer -o provean = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' provean = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/pbuilderrc_af0R --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b2 --logfile b2/build.log provean_1.1.5+ds-2.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 1 12:33:37 +14 2024 I: pbuilder-time-stamp: 1727735617 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 [provean_1.1.5+ds-2.dsc] I: copying [./provean_1.1.5+ds.orig.tar.xz] I: copying [./provean_1.1.5+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 18 10:00:00 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 ./provean_1.1.5+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting provean in provean-1.1.5+ds dpkg-source: info: unpacking provean_1.1.5+ds.orig.tar.xz dpkg-source: info: unpacking provean_1.1.5+ds-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 30 22:33 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=82088f32b4044994b037e81da9ad3d39 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1572698 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/pbuilderrc_af0R --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b2 --logfile b2/build.log provean_1.1.5+ds-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1572698/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: cd-hit, debhelper-compat (= 13), ncbi-blast+ dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 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 cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ 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} cd-hit{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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After unpacking 208 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 cd-hit arm64 4.8.1-4 [506 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 liblmdb0 arm64 0.9.31-1+b1 [43.0 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto7t64 arm64 2.28.8-1 [269 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libmbedx509-1t64 arm64 2.28.8-1 [131 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libmbedtls14t64 arm64 2.28.8-1 [160 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-6 [142 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 ncbi-blast+ arm64 2.16.0+ds-6 [13.8 MB] Fetched 44.8 MB in 0s (188 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 19895 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (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 ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/provean-1.1.5+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../provean_1.1.5+ds-2_source.changes dpkg-buildpackage: info: source package provean dpkg-buildpackage: info: source version 1.1.5+ds-2 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_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am: installing './depcomp' 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 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 for g++... g++ 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 g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for psiblast... /usr/bin/psiblast checking for cd-hit... /usr/bin/cd-hit checking for blastdbcmd... /usr/bin/blastdbcmd 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 scripts/Makefile config.status: creating examples/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make all-recursive make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making all in src make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o provean.o provean.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Common.o Common.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Options.o Options.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o SequenceDB.o SequenceDB.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ScoreMatrix.o ScoreMatrix.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Sequence.o Sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Tables.o Tables.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Variant.o Variant.cpp Sequence.cpp: In member function 'bool Sequence::SetSequenceFromFastaFile(const char*, std::string)': Sequence.cpp:100:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::SetSequencesFromFastaFile(std::string)': SequenceDB.cpp:295:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 295 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::SetOnlySequencesFromFastaFile(std::string)': SequenceDB.cpp:652:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 652 | fgets(buf, sizeof(buf), fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:737:35: warning: '.help' directive writing 5 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 737 | sprintf(help_filename, "%s.help", output_prefix); | ^~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from SequenceDB.cpp:17: In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:737:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 6 and 65541 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:738:41: warning: '%s' directive writing up to 65535 bytes into a region of size 65530 [-Wformat-overflow=] 738 | sprintf(cdhit_command, "%s -h > %s", | ^~ 739 | p_options_->cdhit_command_.c_str(), 740 | help_filename); | ~~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:738:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 7 or more bytes (assuming 65542) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:776:53: warning: '%s' directive writing up to 65535 bytes into a region of size 65528 [-Wformat-overflow=] 776 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d -bak 1 > %s.log", | ^~ ...... 779 | output_prefix, | ~~~~~~~~~~~~~ SequenceDB.cpp:776:40: note: assuming directive output of 4 bytes 776 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d -bak 1 > %s.log", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp:776:40: note: using the range [-2147483648, 2147483647] for directive argument In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:776:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 55 or more bytes (assuming 131126) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:785:53: warning: '%s' directive writing up to 65535 bytes into a region of size 65528 [-Wformat-overflow=] 785 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d > %s.log", | ^~ ...... 788 | output_prefix, | ~~~~~~~~~~~~~ SequenceDB.cpp:785:40: note: assuming directive output of 4 bytes 785 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d > %s.log", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SequenceDB.cpp:785:40: note: using the range [-2147483648, 2147483647] for directive argument In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:785:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 48 or more bytes (assuming 131119) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:830:38: warning: '.cluster.bak.clstr' directive writing 18 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 830 | sprintf(cluster_filename, "%s.cluster.bak.clstr", output_prefix); | ^~~~~~~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:830:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 19 and 65554 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)': SequenceDB.cpp:804:42: warning: '.log' directive writing 4 bytes into a region of size between 1 and 65536 [-Wformat-overflow=] 804 | sprintf(log_filename, "%s.log", output_prefix); | ^~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:804:10: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 65540 bytes into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SequenceDB.cpp: In member function 'void SequenceDB::RunBlast(std::string, std::string, std::string)': SequenceDB.cpp:1552:47: warning: '%s' directive writing up to 65535 bytes into a region of size 65524 [-Wformat-overflow=] 1552 | sprintf(blast_command, "%s -version > %s", p_options_->psiblast_command_.c_str(), blast_help); | ^~ ~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void SequenceDB::RunBlast(std::string, std::string, std::string)' at SequenceDB.cpp:1552:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 13 or more bytes (assuming 65548) into a destination of size 65536 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/provean-1.1.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -o provean provean.o Common.o Options.o SequenceDB.o ScoreMatrix.o Sequence.o Tables.o Variant.o make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making all in scripts make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' sed -e 's,\[@\]PSIBLAST\[@\],/usr/bin/psiblast,g' -e 's,\[@\]CDHIT\[@\],/usr/bin/cd-hit,g' -e 's,\[@\]BLASTDB\[@\],,g' -e 's,\[@\]BLASTDBCMD\[@\],/usr/bin/blastdbcmd,g' -e 's,\[@\]VERSION\[@\],1.1.5,g' < ./provean.sh.in > provean.sh chmod +x provean.sh make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making all in examples make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making check in src make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making check in scripts make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making check in examples make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/provean/ make -j12 install DESTDIR=/build/reproducible-path/provean-1.1.5\+ds/debian/provean AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' Making install in src make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' /usr/bin/install -c provean '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making install in scripts make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' /usr/bin/install -c provean.sh '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' Making install in examples make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/data/provean/examples' /usr/bin/install -c -m 644 P04637.fasta P04637.var '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/data/provean/examples' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/examples' make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/doc/provean' /usr/bin/install -c -m 644 README LICENSE '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/share/doc/provean' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/provean-1.1.5+ds' dh_install rm debian/provean/usr/bin/provean.sh make[1]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'provean' in '../provean_1.1.5+ds-2_arm64.deb'. dpkg-deb: building package 'provean-dbgsym' in '../provean-dbgsym_1.1.5+ds-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../provean_1.1.5+ds-2_arm64.buildinfo dpkg-genchanges --build=binary -O../provean_1.1.5+ds-2_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: user script /srv/workspace/pbuilder/1572698/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/B01_cleanup finished 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/1572698 and its subdirectories I: Current time: Tue Oct 1 12:34:20 +14 2024 I: pbuilder-time-stamp: 1727735660 + false + set +x Mon Sep 30 22:34:20 UTC 2024 I: Signing ./b2/provean_1.1.5+ds-2_arm64.buildinfo as provean_1.1.5+ds-2_arm64.buildinfo.asc Mon Sep 30 22:34:20 UTC 2024 I: Signed ./b2/provean_1.1.5+ds-2_arm64.buildinfo as ./b2/provean_1.1.5+ds-2_arm64.buildinfo.asc Mon Sep 30 22:34:20 UTC 2024 - build #2 for provean/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Mon Sep 30 22:34:20 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-XMOanrc3, removing. /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6: total 72 drwxr-xr-x 2 jenkins jenkins 4096 Sep 30 22:33 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 30 22:34 b2 -rw-r--r-- 1 jenkins jenkins 1957 May 18 2022 provean_1.1.5+ds-2.dsc -rw------- 1 jenkins jenkins 53433 Sep 30 22:33 rbuildlog.pGLVXiL /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b1: total 520 -rw-r--r-- 1 jenkins jenkins 50048 Sep 30 22:33 build.log -rw-r--r-- 1 jenkins jenkins 387652 Sep 30 22:33 provean-dbgsym_1.1.5+ds-2_arm64.deb -rw-r--r-- 1 jenkins jenkins 2220 Sep 30 22:33 provean_1.1.5+ds-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1957 Sep 30 22:33 provean_1.1.5+ds-2.dsc -rw-r--r-- 1 jenkins jenkins 5838 Sep 30 22:33 provean_1.1.5+ds-2_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6720 Sep 30 22:33 provean_1.1.5+ds-2_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1425 Sep 30 22:33 provean_1.1.5+ds-2_arm64.changes -rw-r--r-- 1 jenkins jenkins 45700 Sep 30 22:33 provean_1.1.5+ds-2_arm64.deb -rw-r--r-- 1 jenkins jenkins 1300 Sep 30 22:33 provean_1.1.5+ds-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b2: total 512 -rw-r--r-- 1 jenkins jenkins 51996 Sep 30 22:34 build.log -rw-r--r-- 1 jenkins jenkins 387652 Sep 30 22:34 provean-dbgsym_1.1.5+ds-2_arm64.deb -rw-r--r-- 1 jenkins jenkins 2220 Sep 30 22:34 provean_1.1.5+ds-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1957 Sep 30 22:34 provean_1.1.5+ds-2.dsc -rw-r--r-- 1 jenkins jenkins 5838 Sep 30 22:34 provean_1.1.5+ds-2_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6720 Sep 30 22:34 provean_1.1.5+ds-2_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1425 Sep 30 22:34 provean_1.1.5+ds-2_arm64.changes -rw-r--r-- 1 jenkins jenkins 45700 Sep 30 22:34 provean_1.1.5+ds-2_arm64.deb -rw-r--r-- 1 jenkins jenkins 1300 Sep 30 22:34 provean_1.1.5+ds-2_source.changes Mon Sep 30 22:34:21 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Mon Sep 30 22:34:22 UTC 2024 I: provean_1.1.5+ds-2_arm64.changes: Format: 1.8 Date: Wed, 18 May 2022 11:57:03 +0200 Source: provean Binary: provean provean-dbgsym Architecture: arm64 Version: 1.1.5+ds-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: provean - Protein Variation Effect Analyzer Changes: provean (1.1.5+ds-2) unstable; urgency=medium . * Team upload. * Source-only upload * Standards-Version: 4.6.1 (routine-update) * Add salsa-ci file (routine-update) Checksums-Sha1: 8ff466358b2d34d024e5a41776949697998fd383 387652 provean-dbgsym_1.1.5+ds-2_arm64.deb 864af78581929c3725ff71134f40a9a656ee6836 5838 provean_1.1.5+ds-2_arm64.buildinfo cccb642878b2819b9d694a95e810bb98d294a9b6 45700 provean_1.1.5+ds-2_arm64.deb Checksums-Sha256: dfe6e57453126ba7385aac422330adc2ef517f469265188532b626cb2d5011a1 387652 provean-dbgsym_1.1.5+ds-2_arm64.deb 94754e72c88d14deea937dd9a7d24abf286b505f78e47f002b8a90fc4385078a 5838 provean_1.1.5+ds-2_arm64.buildinfo 45a6ba5cbf9f3940c804b78d7f41cc97af5a89ce62e8066a2482c8073f409d43 45700 provean_1.1.5+ds-2_arm64.deb Files: a9181d47fb046629b5e5d57031198874 387652 debug optional provean-dbgsym_1.1.5+ds-2_arm64.deb b2d0df5ea87e42a2c17a98d14a47e806 5838 science optional provean_1.1.5+ds-2_arm64.buildinfo 853e131ff4a418072639bd57d7123518 45700 science optional provean_1.1.5+ds-2_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/provean_1.1.5+ds-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/provean_1.1.5+ds-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/provean_1.1.5+ds-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/provean_1.1.5+ds-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/provean_1.1.5+ds-2_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/provean_1.1.5+ds-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-09-30 22:33:34.596361998 +0000 +++ b2/build.log 2024-09-30 22:34:21.322373751 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Nov 2 16:55:55 -12 2025 -I: pbuilder-time-stamp: 1762145755 +I: Current time: Tue Oct 1 12:33:37 +14 2024 +I: pbuilder-time-stamp: 1727735617 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: unpacking provean_1.1.5+ds-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/813242/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 30 22:33 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1572698/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='3ebe37119f71456b80c5055e12bdd1e2' - 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='813242' - PS1='# ' - PS2='> ' + INVOCATION_ID=82088f32b4044994b037e81da9ad3d39 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1572698 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.IM3HwHk6/pbuilderrc_Mbwp --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.IM3HwHk6/b1 --logfile b1/build.log provean_1.1.5+ds-2.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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/pbuilderrc_af0R --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b2 --logfile b2/build.log provean_1.1.5+ds-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/813242/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -171,7 +203,7 @@ Get: 58 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-6 [142 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 ncbi-blast+ arm64 2.16.0+ds-6 [13.8 MB] -Fetched 44.8 MB in 1s (78.6 MB/s) +Fetched 44.8 MB in 0s (188 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 19895 files and directories currently installed.) @@ -391,8 +423,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Nov 3 04:56:13 UTC 2025. -Universal Time is now: Mon Nov 3 04:56:13 UTC 2025. +Local time is now: Mon Sep 30 22:33:57 UTC 2024. +Universal Time is now: Mon Sep 30 22:33:57 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -440,7 +472,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/provean-1.1.5+ds/ && 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 > ../provean_1.1.5+ds-2_source.changes +I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/provean-1.1.5+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../provean_1.1.5+ds-2_source.changes dpkg-buildpackage: info: source package provean dpkg-buildpackage: info: source version 1.1.5+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -675,16 +711,16 @@ Making install in src make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/src' - /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' /usr/bin/install -c provean '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/src' Making install in scripts make[2]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[3]: Entering directory '/build/reproducible-path/provean-1.1.5+ds/scripts' - /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' /usr/bin/install -c provean.sh '/build/reproducible-path/provean-1.1.5+ds/debian/provean/usr/bin' make[3]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' make[2]: Leaving directory '/build/reproducible-path/provean-1.1.5+ds/scripts' @@ -739,12 +775,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1572698/tmp/hooks/B01_cleanup finished 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/813242 and its subdirectories -I: Current time: Sun Nov 2 16:56:32 -12 2025 -I: pbuilder-time-stamp: 1762145792 +I: removing directory /srv/workspace/pbuilder/1572698 and its subdirectories +I: Current time: Tue Oct 1 12:34:20 +14 2024 +I: pbuilder-time-stamp: 1727735660 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/provean_1.1.5+ds-2.diff: 69.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/provean_1.1.5+ds-2.diff.gz b2/build.log: 81.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 81.9% -- replaced with stdout Mon Sep 30 22:34:23 UTC 2024 I: diffoscope 278 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_provean_unstable_arm64_1727735663 + touch /var/log/reproducible-builds/diffoscope_stamp_provean_unstable_arm64_1727735663 + RESULT=0 + systemd-run '--description=diffoscope on provean/1.1.5+ds-2 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_15-63373 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6 --run-session -c jenkins-reproducible-unstable-diffoscope-f5eb6097-43b6-471c-bde6-8ad958d09364 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/dbd-tmp-Bv42SJt ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/provean_1.1.5+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/provean_1.1.5+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/provean_1.1.5+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b1/provean_1.1.5+ds-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b2/provean_1.1.5+ds-2_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_15-63373.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/provean_1.1.5+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/provean_1.1.5+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/provean_1.1.5+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b1/provean_1.1.5+ds-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.IM3HwHk6/b2/provean_1.1.5+ds-2_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: 0.394s) 0.394s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.021s) 0.021s 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: 719ms CPU time consumed: 720ms _ __ _ __ _____ _____ __ _ _ __ | '_ \| '__/ _ \ \ / / _ \/ _` | '_ \ | |_) | | | (_) \ V / __/ (_| | | | | | .__/|_| \___/ \_/ \___|\__,_|_| |_| |_| Mon Sep 30 22:34:24 UTC 2024 I: diffoscope 278 found no differences in the changes files, and a .buildinfo file also exists. Mon Sep 30 22:34:24 UTC 2024 I: provean from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-30 22:34:24] INFO: Starting at 2024-09-30 22:34:24.984765 [2024-09-30 22:34:25] INFO: Generating the pages of 1 package(s) [2024-09-30 22:34:25] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/provean didn't produce a buildlog, even though it has been built. [2024-09-30 22:34:25] INFO: Finished at 2024-09-30 22:34:25.194802, took: 0:00:00.210042 Mon Sep 30 22:34:25 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/provean.html Mon Sep 30 22:34:25 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Sep 30 22:34:25 UTC 2024 I: Submitting 8.0K b1/provean_1.1.5+ds-2_arm64.buildinfo.asc https://buildinfo.debian.net/864af78581929c3725ff71134f40a9a656ee6836/provean_1.1.5+ds-2_arm64 Mon Sep 30 22:34:26 UTC 2024 I: Submitting 8.0K b2/provean_1.1.5+ds-2_arm64.buildinfo.asc https://buildinfo.debian.net/e4ab3bec2d98e611851f8529adab7746f9dff6ca/provean_1.1.5+ds-2_arm64 Mon Sep 30 22:34:27 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Sep 30 22:34:27 UTC 2024 I: Done submitting .buildinfo files. Mon Sep 30 22:34:27 UTC 2024 I: Removing signed provean_1.1.5+ds-2_arm64.buildinfo.asc files: removed './b1/provean_1.1.5+ds-2_arm64.buildinfo.asc' removed './b2/provean_1.1.5+ds-2_arm64.buildinfo.asc' 1727735667 arm64 unstable provean Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/provean_1.1.5+ds-2.rbuild.log: 79.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/provean_1.1.5+ds-2.rbuild.log.gz [2024-09-30 22:34:27] INFO: Starting at 2024-09-30 22:34:27.511284 [2024-09-30 22:34:27] INFO: Generating the pages of 1 package(s) [2024-09-30 22:34:27] INFO: Finished at 2024-09-30 22:34:27.718922, took: 0:00:00.207645 All cleanup done. Mon Sep 30 22:34:27 UTC 2024 - total duration: 0h 1m 52s. Mon Sep 30 22:34:27 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-hXF50dCo, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1min 55.505s CPU time consumed: 7.553s