Sun Jun 4 18:49:39 UTC 2023 I: starting to build ampliconnoise/bookworm/armhf on jenkins on '2023-06-04 18:49' Sun Jun 4 18:49:39 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_11/1776/console.log Sun Jun 4 18:49:39 UTC 2023 I: Downloading source for bookworm/ampliconnoise=1.29-10 --2023-06-04 18:49:40-- http://cdn-fastly.deb.debian.org/debian/pool/main/a/ampliconnoise/ampliconnoise_1.29-10.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2156 (2.1K) [text/prs.lines.tag] Saving to: ‘ampliconnoise_1.29-10.dsc’ 0K .. 100% 90.2M=0s 2023-06-04 18:49:40 (90.2 MB/s) - ‘ampliconnoise_1.29-10.dsc’ saved [2156/2156] Sun Jun 4 18:49:40 UTC 2023 I: ampliconnoise_1.29-10.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: ampliconnoise Binary: ampliconnoise Architecture: any Version: 1.29-10 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille , Pranav Ballaney Homepage: https://github.com/lanzen/ampliconnoise Standards-Version: 4.6.0 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 7a46a23a59e4b96bec1e5823528c987ba7b1f981 10652 ampliconnoise_1.29-10.debian.tar.xz Checksums-Sha256: 0bf946806d77ecaf0994ad8ebf9a5e98ad33c809f6def5c9340a16c367918167 1403119 ampliconnoise_1.29.orig.tar.gz e8d621804f8fdde0b12ef05a160a8ac490b0c944dad94a21f79dd23d82ffffec 10652 ampliconnoise_1.29-10.debian.tar.xz Files: d6723e6f9cc71d7eb6f1a65ba4643aac 1403119 ampliconnoise_1.29.orig.tar.gz eca56f7fb6fbea9704744485d09a885f 10652 ampliconnoise_1.29-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFgslsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFNhw//VWLEcyX9XV5VX+jGqJvg+Efat8YG3r+l rCdL9MfPD3CjCeoifNucT/rVcfJr6GFC7bOdJNlw94VH95UoFKv7eB8GU+Nrdnho zMigimCAuUooseksP9L41uCKrcj6AXf5+3xy5PMRy9O/J05kQKqzS53k6kH5TJQ1 iGCPrMYoQVgAHtVOjJ2se1KWICayeedBi3/BfOzOg7Dl2TE2v7Pz6yOaN82ufKJX dB4qYRGU999gnZW4UM+KT5PKzmsz1+/BnUbwOJbi8Y1Lmay3ln1Q4hUxlwboFWDQ nYki3KtVefD0gNFrst25OCyoV54+ivXtHUb2IlS8noEMGlJ5eJkfwIE6DnTUhRVw Q0v4rZByViXnwG+T0vrL+FPIPxsqEmkkHPv0s6CJC/Zh4fChOzmWSeUZv5uXLZ9I ZuLLAemsiAXt1P/datKL/Z3aDJI/KpbHp7SccLpMUPCY5+KaMqTNPQmyn+OtNqGv ogKTpKXttiwu8NEjYree9csQrRzxCBUes+dc6k5if708CimVCaGAAVahii26K3X8 h6zTcc7hllwVsHKrdCmvOcdWYAJLinRn0lsSDyfheqvaTokuQ35PGVnJDU/lPWbE WsQ3bGXzxduz81zc+paaeksH103hWCc7DAztPIIfqX8PRBm52p4puQL2z4ypYvcp 8/ZpROwcSjo= =bcyr -----END PGP SIGNATURE----- Sun Jun 4 18:49:40 UTC 2023 I: Checking whether the package is not for us Sun Jun 4 18:49:40 UTC 2023 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net. Sun Jun 4 18:49:40 UTC 2023 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net. Sun Jun 4 18:59:54 UTC 2023 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 4 06:49:47 -12 2023 I: pbuilder-time-stamp: 1685904587 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ampliconnoise_1.29-10.dsc] I: copying [./ampliconnoise_1.29.orig.tar.gz] I: copying [./ampliconnoise_1.29-10.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Oct 8 09:04:27 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ampliconnoise_1.29-10.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_1.29-10.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/32257/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='b0a132adb07343049d2c9e6395beaf75' 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='32257' 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.zetasRRS/pbuilderrc_QM67 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zetasRRS/b1 --logfile b1/build.log ampliconnoise_1.29-10.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32b 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/32257/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: armhf 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 ... 19324 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-12{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcbor0.8{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{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} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2{a} librdmacm1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{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 libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 82 newly installed, 0 to remove and 0 not upgraded. Need to get 39.5 MB of archives. After unpacking 139 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf libedit2 armhf 3.1-20221030-2 [77.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libcbor0.8 armhf 0.8.0-2+b1 [23.1 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libfido2-1 armhf 1.12.0-2+b1 [69.3 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf openssh-client armhf 1:9.2p1-2 [893 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 26 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 28 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libgfortran-12-dev armhf 12.2.0-14 [298 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf gfortran-12 armhf 12.2.0-14 [7633 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libnl-3-200 armhf 3.7.0-0.2+b1 [55.8 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-200 armhf 3.7.0-0.2+b1 [156 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libibverbs1 armhf 44.0-2 [53.6 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf ibverbs-providers armhf 44.0-2 [28.4 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libevent-2.1-7 armhf 2.1.12-stable-8 [161 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-8 [120 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-8 [97.5 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-8 [53.2 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-8 [58.3 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libevent-dev armhf 2.1.12-stable-8 [290 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf librdmacm1 armhf 44.0-2 [60.6 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libfabric1 armhf 1.17.0-3 [385 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libgslcblas0 armhf 2.7.1+dfsg-5 [80.1 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libgsl27 armhf 2.7.1+dfsg-5 [766 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libgsl-dev armhf 2.7.1+dfsg-5 [976 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libhwloc15 armhf 2.9.0-1 [127 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libnuma1 armhf 2.0.16-1 [17.8 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libnuma-dev armhf 2.0.16-1 [33.0 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libltdl7 armhf 2.4.7-5 [390 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libltdl-dev armhf 2.4.7-5 [162 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libhwloc-dev armhf 2.9.0-1 [214 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libpciaccess0 armhf 0.17-2 [48.7 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libxnvctrl0 armhf 525.85.05-1 [12.2 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.1 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libhwloc-plugins armhf 2.9.0-1 [15.9 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libnl-3-dev armhf 3.7.0-0.2+b1 [98.4 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-dev armhf 3.7.0-0.2+b1 [183 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libibverbs-dev armhf 44.0-2 [195 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libmunge2 armhf 0.5.15-2 [15.7 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libpmix2 armhf 4.2.2-1+b1 [553 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libopenmpi3 armhf 4.1.4-3+b1 [1849 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf openmpi-common all 4.1.4-3 [167 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libpmix-dev armhf 4.2.2-1+b1 [864 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf openmpi-bin armhf 4.1.4-3+b1 [194 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libopenmpi-dev armhf 4.1.4-3+b1 [920 kB] Fetched 39.5 MB in 15s (2697 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19324 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.44-3_armhf.deb ... 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Selecting previously unselected package libmunge2. Preparing to unpack .../74-libmunge2_0.5.15-2_armhf.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libpmix2:armhf. Preparing to unpack .../75-libpmix2_4.2.2-1+b1_armhf.deb ... Unpacking libpmix2:armhf (4.2.2-1+b1) ... Selecting previously unselected package libopenmpi3:armhf. Preparing to unpack .../76-libopenmpi3_4.1.4-3+b1_armhf.deb ... Unpacking libopenmpi3:armhf (4.1.4-3+b1) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../77-openmpi-common_4.1.4-3_all.deb ... Unpacking openmpi-common (4.1.4-3) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../78-zlib1g-dev_1%3a1.2.13.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpmix-dev:armhf. Preparing to unpack .../79-libpmix-dev_4.2.2-1+b1_armhf.deb ... Unpacking libpmix-dev:armhf (4.2.2-1+b1) ... 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Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libhwloc15:armhf (2.9.0-1) ... Setting up libevent-core-2.1-7:armhf (2.1.12-stable-8) ... Setting up libevent-2.1-7:armhf (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up libltdl7:armhf (2.4.7-5) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up libnuma1:armhf (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:armhf (2.3.1-1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libnl-3-200:armhf (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:armhf (1.12.0-2+b1) ... Setting up libbsd0:armhf (0.11.7-2) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-8) ... 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:armhf (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-8) ... Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libgsl-dev (2.7.1+dfsg-5) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:armhf (3.1-20221030-2) ... Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ... Setting up libgfortran-12-dev:armhf (12.2.0-14) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:armhf (2.0.16-1) ... Setting up libnl-route-3-200:armhf (3.7.0-0.2+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:armhf (2.4.7-5) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:armhf (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libx11-6:armhf (2:1.8.4-2) ... Setting up libhwloc-dev:armhf (2.9.0-1) ... Setting up libibverbs1:armhf (44.0-2) ... Setting up ibverbs-providers:armhf (44.0-2) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:armhf (525.85.05-1) ... Setting up libnl-route-3-dev:armhf (3.7.0-0.2+b1) ... Setting up librdmacm1:armhf (44.0-2) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:armhf (44.0-2) ... Setting up libhwloc-plugins:armhf (2.9.0-1) ... Setting up libfabric1:armhf (1.17.0-3) ... Setting up libpmix2:armhf (4.2.2-1+b1) ... Setting up libopenmpi3:armhf (4.1.4-3+b1) ... Setting up libpmix-dev:armhf (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... 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:armhf (4.1.4-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Processing triggers for libc-bin (2.36-9) ... 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/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_1.29-10_source.changes dpkg-buildpackage: info: source package ampliconnoise dpkg-buildpackage: info: source version 1.29-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j3 clean make[1]: Entering directory '/build/ampliconnoise-1.29' (cd FCluster && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/FCluster' (cd FastaUnique && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/FastaUnique' (cd NDist && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/NDist' (cd PyroDist && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/PyroDist' (cd PyroNoise && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/PyroNoise' (cd PyroNoiseM && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/PyroNoiseM' (cd PyroNoiseA && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/PyroNoiseA' (cd SeqDist && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/SeqDist' (cd SeqNoise && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/SeqNoise' (cd SplitClusterEven && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/SplitClusterEven' (cd SplitClusterClust && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/SplitClusterClust' (cd Perseus && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/Perseus' (cd PerseusD && make clean) make[2]: Entering directory '/build/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/ampliconnoise-1.29/PerseusD' (cd bin && rm -rf *) make[1]: Leaving directory '/build/ampliconnoise-1.29' debian/rules override_dh_clean make[1]: Entering directory '/build/ampliconnoise-1.29' dh_clean rm -f *.o rm -f *.1 make[1]: Leaving directory '/build/ampliconnoise-1.29' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/ampliconnoise-1.29' (cd FCluster && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/FCluster' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c FCluster.c FCluster.c:223:1: warning: return type defaults to 'int' [-Wimplicit-int] 223 | UpdateMinCacheForMarkedRows(struct t_Min* asMin,float** aafDistMatrix,int nN) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ FCluster.c: In function 'UpdateMinCacheForMarkedRows': FCluster.c:230:13: warning: implicit declaration of function 'UpdateMinCacheForRow'; did you mean 'UpdateMinCacheForMarkedRows'? [-Wimplicit-function-declaration] 230 | UpdateMinCacheForRow(asMin,i,aafDistMatrix); | ^~~~~~~~~~~~~~~~~~~~ | UpdateMinCacheForMarkedRows FCluster.c: At top level: FCluster.c:237:1: warning: return type defaults to 'int' [-Wimplicit-int] 237 | UpdateMinCacheForRow(struct t_Min* asMin,int i,float** aafDistMatrix) | ^~~~~~~~~~~~~~~~~~~~ linking... cc -Wl,-z,relro -Wl,-z,now -o FCluster FCluster.o -lm make[2]: Leaving directory '/build/ampliconnoise-1.29/FCluster' (cd FastaUnique && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/FastaUnique' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c FastaUnique.c linking... cc -Wl,-z,relro -Wl,-z,now -o FastaUnique FastaUnique.o -lm make[2]: Leaving directory '/build/ampliconnoise-1.29/FastaUnique' (cd NDist && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/NDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c NDist.c NDist.c: In function 'readData': NDist.c:707:59: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] 707 | ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); | ^~~~~~~ NDist.c:17:1: note: include '' or provide a declaration of 'toupper' 16 | #include "NDist.h" +++ |+#include 17 | linking... mpicc -Wl,-z,relro -Wl,-z,now -o NDist NDist.o -lm make[2]: Leaving directory '/build/ampliconnoise-1.29/NDist' (cd PyroDist && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/PyroDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c PyroDist.c linking... mpicc -Wl,-z,relro -Wl,-z,now -o PyroDist PyroDist.o -lm make[2]: Leaving directory '/build/ampliconnoise-1.29/PyroDist' (cd PyroNoise && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/PyroNoise' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -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/ampliconnoise-1.29/PyroNoise' (cd SeqDist && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/SeqDist' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c SeqDist.c SeqDist.c: In function 'readData': SeqDist.c:854:59: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] 854 | ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); | ^~~~~~~ SeqDist.c:17:1: note: include '' or provide a declaration of 'toupper' 16 | #include "SeqDist.h" +++ |+#include 17 | linking... mpicc -Wl,-z,relro -Wl,-z,now -o SeqDist SeqDist.o -lm make[2]: Leaving directory '/build/ampliconnoise-1.29/SeqDist' (cd PyroNoiseM && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/PyroNoiseM' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -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/ampliconnoise-1.29/PyroNoiseM' (cd PyroNoiseA && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/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/ampliconnoise-1.29/PyroNoiseA' (cd SeqNoise && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/SeqNoise' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mpicc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c SeqNoise.c SeqNoise.c: In function 'main': SeqNoise.c:120:25: warning: too many arguments for format [-Wformat-extra-args] 120 | if(bVerbose){printf("%d: Broadcast distance matrix\n", rank, nSize, nPacket); fflush(stdout);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SeqNoise.c: In function 'readData': SeqNoise.c:652:59: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] 652 | ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); | ^~~~~~~ SeqNoise.c:9:1: note: include '' or provide a declaration of 'toupper' 8 | #include "SeqNoise.h" +++ |+#include 9 | linking... mpicc -Wl,-z,relro -Wl,-z,now -o SeqNoise SeqNoise.o -lm make[2]: Leaving directory '/build/ampliconnoise-1.29/SeqNoise' (cd SplitClusterEven && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/SplitClusterEven' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -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/ampliconnoise-1.29/SplitClusterEven' (cd SplitClusterClust && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/SplitClusterClust' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. gcc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -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/ampliconnoise-1.29/SplitClusterClust' (cd Perseus && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/Perseus' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c Perseus.c Perseus.c: In function 'readData': Perseus.c:856:59: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] 856 | ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); | ^~~~~~~ Perseus.c:17:1: note: include '' or provide a declaration of 'toupper' 16 | #include "Perseus.h" +++ |+#include 17 | Perseus.c: In function 'calcLoonIndex': Perseus.c:1637:34: warning: '%s' directive writing up to 65535 bytes into a region of size 65524 [-Wformat-overflow=] 1637 | sprintf(szCommand,"mafft-linsi %s > %s 2> %s",szTempFasta,szTempAlign, TEMP_ERROR_FILE); | ^~ ~~~~~~~~~~~ Perseus.c:1637:3: note: 'sprintf' output between 28 and 131098 bytes into a destination of size 65536 1637 | 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/ampliconnoise-1.29/Perseus' (cd PerseusD && CFLAGS="-g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make) make[2]: Entering directory '/build/ampliconnoise-1.29/PerseusD' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -ffile-prefix-map=/build/ampliconnoise-1.29=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c PerseusD.c PerseusD.c: In function 'readData': PerseusD.c:908:59: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] 908 | ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); | ^~~~~~~ PerseusD.c:17:1: note: include '' or provide a declaration of 'toupper' 16 | #include "PerseusD.h" +++ |+#include 17 | PerseusD.c: In function 'calcLoonIndex': PerseusD.c:1648:34: warning: '%s' directive writing up to 65535 bytes into a region of size 65524 [-Wformat-overflow=] 1648 | sprintf(szCommand,"mafft-linsi %s > %s 2> %s",szTempFasta,szTempAlign, TEMP_ERROR_FILE); | ^~ ~~~~~~~~~~~ PerseusD.c:1648:3: note: 'sprintf' output between 28 and 131098 bytes into a destination of size 65536 1648 | 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/ampliconnoise-1.29/PerseusD' make[1]: Leaving directory '/build/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/ampliconnoise-1.29' make install make[2]: Entering directory '/build/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/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/ampliconnoise-1.29' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/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/ampliconnoise-1.29' dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/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/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-dbgsym' in '../ampliconnoise-dbgsym_1.29-10_armhf.deb'. dpkg-deb: building package 'ampliconnoise' in '../ampliconnoise_1.29-10_armhf.deb'. dpkg-genbuildinfo --build=binary -O../ampliconnoise_1.29-10_armhf.buildinfo dpkg-genchanges --build=binary -O../ampliconnoise_1.29-10_armhf.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/32257 and its subdirectories I: Current time: Sun Jun 4 06:59:48 -12 2023 I: pbuilder-time-stamp: 1685905188 Sun Jun 4 18:59:57 UTC 2023 I: 1st build successful. Starting 2nd build on remote node jtx1c-armhf-rb.debian.net. Sun Jun 4 18:59:57 UTC 2023 I: Preparing to do remote build '2' on jtx1c-armhf-rb.debian.net. Sun Jun 4 19:02:37 UTC 2023 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. Sun Jun 4 19:02:39 UTC 2023 I: ampliconnoise_1.29-10_armhf.changes: Format: 1.8 Date: Fri, 08 Oct 2021 23:00:19 +0200 Source: ampliconnoise Binary: ampliconnoise ampliconnoise-dbgsym Architecture: armhf Version: 1.29-10 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: ampliconnoise - removal of noise from 454 sequenced PCR amplicons Changes: ampliconnoise (1.29-10) unstable; urgency=medium . * Fix watchfile to detect new versions on github * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: 9652eeafbae40694a0e118164bc81335bf230805 306988 ampliconnoise-dbgsym_1.29-10_armhf.deb d56f11923798d3a4af075bdede247c6e0610e58a 6724 ampliconnoise_1.29-10_armhf.buildinfo 425d57ac7dd3f336b205b3b072b820e43d360eb3 1084848 ampliconnoise_1.29-10_armhf.deb Checksums-Sha256: 564d5d70bb40b114c137dedfb49021dc8d8bfffdc4f1a5e3b700d7d958241565 306988 ampliconnoise-dbgsym_1.29-10_armhf.deb fd46eeb15163cfd2c23af50d4fad0cbe9f38dd48fb04cec5c85809a8321f7bbb 6724 ampliconnoise_1.29-10_armhf.buildinfo 2ec81b552ea608bf8a793db4f31faf598d71f9c402f35b45ed16967ba0201248 1084848 ampliconnoise_1.29-10_armhf.deb Files: ad8d15f551dbfbf4ebd5f88877399b5a 306988 debug optional ampliconnoise-dbgsym_1.29-10_armhf.deb 96673461bc322094fd196558f1c0a221 6724 science optional ampliconnoise_1.29-10_armhf.buildinfo 8d1fb3cf1509f64b7a789ee6dd4c01c7 1084848 science optional ampliconnoise_1.29-10_armhf.deb Sun Jun 4 19:02:40 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zetasRRS/ampliconnoise_1.29-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zetasRRS/ampliconnoise_1.29-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zetasRRS/ampliconnoise_1.29-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zetasRRS/b1/ampliconnoise_1.29-10_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.zetasRRS/b2/ampliconnoise_1.29-10_armhf.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: 0.515s) 0.515s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.036s) 0.036s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sun Jun 4 19:02:41 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Sun Jun 4 19:02:41 UTC 2023 I: ampliconnoise from bookworm built successfully and reproducibly on armhf. Sun Jun 4 19:02:43 UTC 2023 I: Submitting .buildinfo files to external archives: Sun Jun 4 19:02:43 UTC 2023 I: Submitting 8.0K b1/ampliconnoise_1.29-10_armhf.buildinfo.asc Sun Jun 4 19:02:43 UTC 2023 I: Submitting 8.0K b2/ampliconnoise_1.29-10_armhf.buildinfo.asc Sun Jun 4 19:02:44 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jun 4 19:02:44 UTC 2023 I: Done submitting .buildinfo files. Sun Jun 4 19:02:44 UTC 2023 I: Removing signed ampliconnoise_1.29-10_armhf.buildinfo.asc files: removed './b1/ampliconnoise_1.29-10_armhf.buildinfo.asc' removed './b2/ampliconnoise_1.29-10_armhf.buildinfo.asc'