Tue Apr 30 02:03:36 UTC 2024 I: starting to build ampliconnoise/unstable/amd64 on jenkins on '2024-04-30 02:03' Tue Apr 30 02:03:36 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_14/4978/console.log Tue Apr 30 02:03:36 UTC 2024 I: Downloading source for unstable/ampliconnoise=1.29-11 --2024-04-30 02:03:37-- http://deb.debian.org/debian/pool/main/a/ampliconnoise/ampliconnoise_1.29-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2156 (2.1K) [text/prs.lines.tag] Saving to: ‘ampliconnoise_1.29-11.dsc’ 0K .. 100% 288M=0s 2024-04-30 02:03:37 (288 MB/s) - ‘ampliconnoise_1.29-11.dsc’ saved [2156/2156] Tue Apr 30 02:03:37 UTC 2024 I: ampliconnoise_1.29-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ampliconnoise Binary: ampliconnoise Architecture: any Version: 1.29-11 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille , Pranav Ballaney Homepage: https://github.com/lanzen/ampliconnoise Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/ampliconnoise Vcs-Git: https://salsa.debian.org/med-team/ampliconnoise.git Testsuite: autopkgtest Testsuite-Triggers: openmpi-bin Build-Depends: debhelper-compat (= 13), libgsl-dev, libopenmpi-dev Package-List: ampliconnoise deb science optional arch=any Checksums-Sha1: 743cbd53fa3410dea902f3dc82864041defc3c4b 1403119 ampliconnoise_1.29.orig.tar.gz 1f1f4d9db0993658c7c000285bbd2f82ac1272c3 11372 ampliconnoise_1.29-11.debian.tar.xz Checksums-Sha256: 0bf946806d77ecaf0994ad8ebf9a5e98ad33c809f6def5c9340a16c367918167 1403119 ampliconnoise_1.29.orig.tar.gz 055203de0c1b7519ab79ca6a515a8301d99e02774308b2e43d72189a1aa8f811 11372 ampliconnoise_1.29-11.debian.tar.xz Files: d6723e6f9cc71d7eb6f1a65ba4643aac 1403119 ampliconnoise_1.29.orig.tar.gz 571630989107ec2f6883b0b174cf2e96 11372 ampliconnoise_1.29-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmYXp0URHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFStQ/8C3f2VkfT0aSp4kDFrQKlxB+sdgOQCa6B W6tBTh1juViKZDdjQ77cGXdxeXlqDqJ/1guIjbV8+U0fe9npvSqafFrz44txgdB0 DkQDuHtlUODFlTxlQeultii1DMUcBr9ox4W8yX1OqzokBHf9huuInHBN0MLBujSr bXfSwvWdVAQqtjI2S7NTzrZAJU8RkK7UqEYT2o5FBvPtHfrSmtIggUoen2VV/zKc 1fP67va5cjLoDklvEnIjOr1C/s90rg98UaTuFe3ZOAK+awyaAVJ1jB9XF8oyQh43 T7ncriPd7ecLSEAIAkTGJ3VDFb3a7UXroyURY5eiRV+VfVZRHO0EnvLPwfBbxV24 OryBzW1c9oUd6kQXJ1iJdFN7/tHQ5um0ZsCCPnWIkXcljKGLveclRH72YWW4rS6v baomnM3amhTcdp4vA1qVwwZVYRvDub9XV8AD3TL7bv37VryMerS4CXoLRx8LThZ7 KEUwoCZ5wUj6fxdkLsOLtr0GJsQVo7u5P4t7hCkZY36xujEuV46ZWitusfuP3CMP ZFP6JOd44F1Bd0JFxJMe9E6PJmNTElSw7FwrChbgzvHYGCpF5N6519CoPL+9wb6b CH/hvUNHITCJF+5ZLFzB9omUsYVtYsESpPB6rucyZKlb05WNC6uLFq3CexJB7VnL zJ/3VPbmSSE= =Q5RN -----END PGP SIGNATURE----- Tue Apr 30 02:03:37 UTC 2024 I: Checking whether the package is not for us Tue Apr 30 02:03:37 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Apr 30 02:03:37 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Apr 30 02:04:54 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 1 20:26:38 -12 2025 I: pbuilder-time-stamp: 1748852798 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 [ampliconnoise_1.29-11.dsc] I: copying [./ampliconnoise_1.29.orig.tar.gz] I: copying [./ampliconnoise_1.29-11.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Apr 11 09:03:01 2024 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 ./ampliconnoise_1.29-11.dsc: no acceptable signature found dpkg-source: info: extracting ampliconnoise in ampliconnoise-1.29 dpkg-source: info: unpacking ampliconnoise_1.29.orig.tar.gz dpkg-source: info: unpacking ampliconnoise_1.29-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-path-for-data.patch dpkg-source: info: applying fix-segfault-on-non-fasta-input.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying clang-ftbfs.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying fix_sequence_of_function_definitions.patch dpkg-source: info: applying fix_missing_header.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1590650/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='69fabdffa5a24010a6c29758ece6db8a' 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='1590650' 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.moTVgxqj/pbuilderrc_pvuE --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.moTVgxqj/b1 --logfile b1/build.log ampliconnoise_1.29-11.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 30 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1590650/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: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libgsl-dev, libopenmpi-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19694 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libbsd0{a} libcbor0.10{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2t64{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libucx0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 106 MB of archives. After unpacking 440 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc1-1 [22.3 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 19 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.7p1-4 [965 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14-20240429-1 [836 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libgfortran-13-dev amd64 13.2.0-24 [847 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-24 [10.7 MB] Get: 45 http://deb.debian.org/debian unstable/main amd64 gfortran-13 amd64 13.2.0-24 [12.2 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-11 [23.7 MB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 54 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [181 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [107 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [61.1 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-8.1+b3 [305 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.10.0-1+b1 [250 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 50.0-2+b1 [642 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13 [2427 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 4.1.6-13 [169 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.2-3 [3940 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13 [226 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 4.1.6-13 [972 kB] Fetched 106 MB in 1s (109 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. 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Preparing to unpack .../100-libopenmpi-dev_4.1.6-13_amd64.deb ... Unpacking libopenmpi-dev:amd64 (4.1.6-13) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libpciaccess0:amd64 (0.17-3+b1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libcbor0.10:amd64 (0.10.2-1.2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libcom-err2:amd64 (1.47.1~rc1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... 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Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.14.0-1+b2) ... Setting up libgfortran-13-dev:amd64 (13.2.0-24) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libtool (2.4.7-7) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... 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Setting up libopenmpi3t64:amd64 (4.1.6-13) ... Setting up openmpi-bin (4.1.6-13) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.6-13) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Processing triggers for libc-bin (2.37-19) ... 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/ampliconnoise-1.29/ && 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 > ../ampliconnoise_1.29-11_source.changes dpkg-buildpackage: info: source package ampliconnoise dpkg-buildpackage: info: source version 1.29-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j42 clean make[1]: Entering directory '/build/reproducible-path/ampliconnoise-1.29' (cd FCluster && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/FCluster' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *o FCluster make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/FCluster' (cd FastaUnique && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/FastaUnique' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o FastaUnique make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/FastaUnique' (cd NDist && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/NDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o NDist make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/NDist' (cd PyroDist && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PyroDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o PyroDist make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PyroDist' (cd PyroNoise && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoise' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o PyroNoise make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoise' (cd PyroNoiseM && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoiseM' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o PyroNoiseM make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoiseM' (cd PyroNoiseA && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoiseA' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o PyroNoiseA make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoiseA' (cd SeqDist && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/SeqDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o SeqDist make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/SeqDist' (cd SeqNoise && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/SeqNoise' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o SeqNoise make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/SeqNoise' (cd SplitClusterEven && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/SplitClusterEven' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o SplitClusterEven make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/SplitClusterEven' (cd SplitClusterClust && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/SplitClusterClust' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o SplitClusterClust make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/SplitClusterClust' (cd Perseus && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/Perseus' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o Perseus make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/Perseus' (cd PerseusD && make clean) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PerseusD' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -rf *.o PerseusD make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PerseusD' (cd bin && rm -rf *) make[1]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/ampliconnoise-1.29' dh_clean rm -f *.o rm -f *.1 make[1]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j42 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/ampliconnoise-1.29' (cd FCluster && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/FCluster' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c FCluster.c FCluster.c:223:1: warning: return type defaults to 'int' [-Wimplicit-int] 223 | UpdateMinCacheForRow(struct t_Min* asMin,int i,float** aafDistMatrix) | ^~~~~~~~~~~~~~~~~~~~ FCluster.c:244:1: warning: return type defaults to 'int' [-Wimplicit-int] 244 | UpdateMinCacheForMarkedRows(struct t_Min* asMin,float** aafDistMatrix,int nN) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ linking... cc -Wl,-z,relro -Wl,-z,now -o FCluster FCluster.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/FCluster' (cd FastaUnique && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/FastaUnique' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c FastaUnique.c linking... cc -Wl,-z,relro -Wl,-z,now -o FastaUnique FastaUnique.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/FastaUnique' (cd NDist && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/NDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c NDist.c linking... mpicc -Wl,-z,relro -Wl,-z,now -o NDist NDist.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/NDist' (cd PyroDist && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PyroDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c PyroDist.c linking... mpicc -Wl,-z,relro -Wl,-z,now -o PyroDist PyroDist.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PyroDist' (cd PyroNoise && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoise' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c PyroNoise.c PyroNoise.c: In function 'writeCentroids': PyroNoise.c:2073:21: warning: too many arguments for format [-Wformat-extra-args] 2073 | fprintf(stderr, "Can't open szCenFile for writing\n",szCenFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ linking... mpicc -Wl,-z,relro -Wl,-z,now -o PyroNoise PyroNoise.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoise' (cd SeqDist && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/SeqDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c SeqDist.c linking... mpicc -Wl,-z,relro -Wl,-z,now -o SeqDist SeqDist.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/SeqDist' (cd PyroNoiseM && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoiseM' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c PyroNoiseM.c PyroNoiseM.c: In function 'writeCentroids': PyroNoiseM.c:2139:21: warning: too many arguments for format [-Wformat-extra-args] 2139 | fprintf(stderr, "Can't open szCenFile for writing\n",szCenFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ linking... mpicc -Wl,-z,relro -Wl,-z,now -o PyroNoiseM PyroNoiseM.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoiseM' (cd PyroNoiseA && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoiseA' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -O3 -c PyroNoiseA.c linking... mpicc -o PyroNoiseA PyroNoiseA.o -lm -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PyroNoiseA' (cd SeqNoise && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/SeqNoise' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c SeqNoise.c SeqNoise.c: In function 'main': SeqNoise.c:121:25: warning: too many arguments for format [-Wformat-extra-args] 121 | if(bVerbose){printf("%d: Broadcast distance matrix\n", rank, nSize, nPacket); fflush(stdout);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ linking... mpicc -Wl,-z,relro -Wl,-z,now -o SeqNoise SeqNoise.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/SeqNoise' (cd SplitClusterEven && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/SplitClusterEven' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c SplitClusterEven.c SplitClusterEven.c: In function 'readMapFile': SplitClusterEven.c:681:19: warning: too many arguments for format [-Wformat-extra-args] 681 | fprintf(stderr, "Failed to open map file\n", szMapFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ SplitClusterEven.c: In function 'main': SplitClusterEven.c:89:28: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 89 | sprintf(szTreeFile,"%s/%s%s",szDir,szDir,TREE_SUFFIX); | ^~ ~~~~~ SplitClusterEven.c:89:5: note: 'sprintf' output between 7 and 2053 bytes into a destination of size 1024 89 | sprintf(szTreeFile,"%s/%s%s",szDir,szDir,TREE_SUFFIX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SplitClusterEven.c:90:27: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 90 | sprintf(szDatFile,"%s/%s%s",szDir,szDir,DAT_SUFFIX); | ^~ ~~~~~ SplitClusterEven.c:90:5: note: 'sprintf' output between 6 and 2052 bytes into a destination of size 1024 90 | sprintf(szDatFile,"%s/%s%s",szDir,szDir,DAT_SUFFIX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SplitClusterEven.c:91:28: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 91 | sprintf(szListFile,"%s/%s%s",szDir,szDir,LIST_SUFFIX); | ^~ ~~~~~ SplitClusterEven.c:91:5: note: 'sprintf' output between 7 and 2053 bytes into a destination of size 1024 91 | sprintf(szListFile,"%s/%s%s",szDir,szDir,LIST_SUFFIX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SplitClusterEven.c:142:30: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 142 | sprintf(szTreeFile,"%s/%s%s",szDir,szDir,TREE_SUFFIX); | ^~ ~~~~~ SplitClusterEven.c:142:7: note: 'sprintf' output between 7 and 2053 bytes into a destination of size 1024 142 | sprintf(szTreeFile,"%s/%s%s",szDir,szDir,TREE_SUFFIX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SplitClusterEven.c:143:29: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 143 | sprintf(szDatFile,"%s/%s%s",szDir,szDir,DAT_SUFFIX); | ^~ ~~~~~ SplitClusterEven.c:143:7: note: 'sprintf' output between 6 and 2052 bytes into a destination of size 1024 143 | sprintf(szDatFile,"%s/%s%s",szDir,szDir,DAT_SUFFIX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SplitClusterEven.c:144:30: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 144 | sprintf(szListFile,"%s/%s%s",szDir,szDir,LIST_SUFFIX); | ^~ ~~~~~ SplitClusterEven.c:144:7: note: 'sprintf' output between 7 and 2053 bytes into a destination of size 1024 144 | sprintf(szListFile,"%s/%s%s",szDir,szDir,LIST_SUFFIX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ linking... cc -Wl,-z,relro -Wl,-z,now -o SplitClusterEven SplitClusterEven.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/SplitClusterEven' (cd SplitClusterClust && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/SplitClusterClust' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c SplitClusterClust.c SplitClusterClust.c: In function 'readMapFile': SplitClusterClust.c:316:19: warning: too many arguments for format [-Wformat-extra-args] 316 | fprintf(stderr, "Failed to open map file\n", szMapFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ SplitClusterClust.c: In function 'main': SplitClusterClust.c:52:29: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 52 | sprintf(szDatFile,"%s/%s%s",szDir,szDir,DAT_SUFFIX); | ^~ ~~~~~ SplitClusterClust.c:52:7: note: 'sprintf' output between 6 and 2052 bytes into a destination of size 1024 52 | sprintf(szDatFile,"%s/%s%s",szDir,szDir,DAT_SUFFIX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SplitClusterClust.c:88:29: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 88 | sprintf(szDatFile,"%s/%s%s",szDir,szDir,DAT_SUFFIX); | ^~ ~~~~~ SplitClusterClust.c:88:7: note: 'sprintf' output between 6 and 2052 bytes into a destination of size 1024 88 | sprintf(szDatFile,"%s/%s%s",szDir,szDir,DAT_SUFFIX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ linking... gcc -Wl,-z,relro -Wl,-z,now -o SplitClusterClust SplitClusterClust.o -lm make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/SplitClusterClust' (cd Perseus && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/Perseus' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c Perseus.c Perseus.c: In function 'calcLoonIndex': Perseus.c:1638:34: warning: '%s' directive writing up to 65535 bytes into a region of size 65524 [-Wformat-overflow=] 1638 | sprintf(szCommand,"mafft-linsi %s > %s 2> %s",szTempFasta,szTempAlign, TEMP_ERROR_FILE); | ^~ ~~~~~~~~~~~ Perseus.c:1638:3: note: 'sprintf' output between 28 and 131098 bytes into a destination of size 65536 1638 | sprintf(szCommand,"mafft-linsi %s > %s 2> %s",szTempFasta,szTempAlign, TEMP_ERROR_FILE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ linking... cc -Wl,-z,relro -Wl,-z,now -o Perseus Perseus.o -lm -lgsl -lgslcblas make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/Perseus' (cd PerseusD && CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29/PerseusD' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ampliconnoise-1.29=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c PerseusD.c PerseusD.c: In function 'calcLoonIndex': PerseusD.c:1649:34: warning: '%s' directive writing up to 65535 bytes into a region of size 65524 [-Wformat-overflow=] 1649 | sprintf(szCommand,"mafft-linsi %s > %s 2> %s",szTempFasta,szTempAlign, TEMP_ERROR_FILE); | ^~ ~~~~~~~~~~~ PerseusD.c:1649:3: note: 'sprintf' output between 28 and 131098 bytes into a destination of size 65536 1649 | sprintf(szCommand,"mafft-linsi %s > %s 2> %s",szTempFasta,szTempAlign, TEMP_ERROR_FILE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ linking... cc -Wl,-z,relro -Wl,-z,now -o PerseusD PerseusD.o -lm -lgsl -lgslcblas make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29/PerseusD' make[1]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/ampliconnoise-1.29' make install make[2]: Entering directory '/build/reproducible-path/ampliconnoise-1.29' cp FCluster/FCluster bin cp FastaUnique/FastaUnique bin cp NDist/NDist bin cp PyroDist/PyroDist bin cp PyroNoise/PyroNoise bin cp PyroNoiseM/PyroNoiseM bin cp PyroNoiseA/PyroNoiseA bin cp SeqDist/SeqDist bin cp SeqNoise/SeqNoise bin cp SplitClusterEven/SplitClusterEven bin cp SplitClusterClust/SplitClusterClust bin cp Perseus/Perseus bin cp PerseusD/PerseusD bin make[2]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29' dh_install bin/* /usr/bin dh_install Data/* /usr/share/ampliconnoise/Data/ dh_install Scripts/* /usr/share/ampliconnoise/Scripts/ make[1]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/ampliconnoise-1.29' debian/ampliconnoise.pod pod2man -c AmpliconNoise Documentation debian/ampliconnoise.pod > ampliconnoise.1 dh_installman ampliconnoise.1 ( for f in bin/* ; do \ ln -s ampliconnoise.1 debian/ampliconnoise/usr/share/man/man1/`basename "$f"`.1 ; \ done ) make[1]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29' dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/ampliconnoise-1.29' # Use xz compression for data file to shrink size even more find debian -name C005.dat -exec xz \{\} \; dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/ampliconnoise-1.29' dh_fixperms dh_missing dh_dwz -a dwz: debian/ampliconnoise/usr/bin/PyroNoiseA: .debug_info section not present dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package ampliconnoise: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package ampliconnoise: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'ampliconnoise' in '../ampliconnoise_1.29-11_amd64.deb'. dpkg-deb: building package 'ampliconnoise-dbgsym' in '../ampliconnoise-dbgsym_1.29-11_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ampliconnoise_1.29-11_amd64.buildinfo dpkg-genchanges --build=binary -O../ampliconnoise_1.29-11_amd64.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/1590650 and its subdirectories I: Current time: Sun Jun 1 20:27:53 -12 2025 I: pbuilder-time-stamp: 1748852873 Tue Apr 30 02:04:55 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue Apr 30 02:04:55 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue Apr 30 02:12:53 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue Apr 30 02:12:54 UTC 2024 I: ampliconnoise_1.29-11_amd64.changes: Format: 1.8 Date: Thu, 11 Apr 2024 09:56:08 +0200 Source: ampliconnoise Binary: ampliconnoise ampliconnoise-dbgsym Architecture: amd64 Version: 1.29-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: ampliconnoise - removal of noise from 454 sequenced PCR amplicons Closes: 1066300 Changes: ampliconnoise (1.29-11) unstable; urgency=medium . * Fix the sequence of function definitions to make sure UpdateMinCacheForRow() is known before its first usage Closes: #1066300 * Adjust DEP3 headers and add Forwarded: No (orphaned upstream) * Add missing header file * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: dac63e8a401656e80ac9e1a9f466c87a6f9d59fb 328804 ampliconnoise-dbgsym_1.29-11_amd64.deb e11aae6df0396cb7b9011fde678e2c1837808997 7637 ampliconnoise_1.29-11_amd64.buildinfo 869326b1f8160481811822a2cafb08e22e9bf1aa 1112688 ampliconnoise_1.29-11_amd64.deb Checksums-Sha256: 459d27d0ca93d99aca9db4133492159222f53993023be0257dcf6ece6f2f6531 328804 ampliconnoise-dbgsym_1.29-11_amd64.deb 6eb0a3a1281f1988a1e96251fdb35b181d8d6e05f1d899d47f4ac1ba1066b811 7637 ampliconnoise_1.29-11_amd64.buildinfo 514fa660b867612783eed06d99537fbde6bad7bd38582211ab4f91ba3cfb389b 1112688 ampliconnoise_1.29-11_amd64.deb Files: 057b0a0d9c7d435719220c0a13c1b397 328804 debug optional ampliconnoise-dbgsym_1.29-11_amd64.deb 607d84772e981048c05abe4e6925accb 7637 science optional ampliconnoise_1.29-11_amd64.buildinfo d39912c68bb59a74a1f0c38105554c68 1112688 science optional ampliconnoise_1.29-11_amd64.deb Tue Apr 30 02:12:55 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_14-4978.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.moTVgxqj/ampliconnoise_1.29-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.moTVgxqj/ampliconnoise_1.29-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.moTVgxqj/ampliconnoise_1.29-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.moTVgxqj/b1/ampliconnoise_1.29-11_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.moTVgxqj/b2/ampliconnoise_1.29-11_amd64.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: 0.371s) 0.371s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.030s) 0.030s 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: 704ms CPU time consumed: 705ms Tue Apr 30 02:12:56 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 30 02:12:56 UTC 2024 I: ampliconnoise from unstable built successfully and reproducibly on amd64. Tue Apr 30 02:12:57 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 30 02:12:57 UTC 2024 I: Submitting 12K b1/ampliconnoise_1.29-11_amd64.buildinfo.asc Tue Apr 30 02:12:58 UTC 2024 I: Submitting 12K b2/ampliconnoise_1.29-11_amd64.buildinfo.asc Tue Apr 30 02:12:59 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 30 02:12:59 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 30 02:12:59 UTC 2024 I: Removing signed ampliconnoise_1.29-11_amd64.buildinfo.asc files: removed './b1/ampliconnoise_1.29-11_amd64.buildinfo.asc' removed './b2/ampliconnoise_1.29-11_amd64.buildinfo.asc'