Thu Sep 17 03:11:29 UTC 2020 I: starting to build ampliconnoise/buster/i386 on jenkins on '2020-09-17 03:11' Thu Sep 17 03:11:29 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_16/9501/console.log Thu Sep 17 03:11:29 UTC 2020 I: Downloading source for buster/ampliconnoise=1.29-8 --2020-09-17 03:11:29-- http://deb.debian.org/debian/pool/main/a/ampliconnoise/ampliconnoise_1.29-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2045 (2.0K) Saving to: ‘ampliconnoise_1.29-8.dsc’ 0K . 100% 240M=0s 2020-09-17 03:11:29 (240 MB/s) - ‘ampliconnoise_1.29-8.dsc’ saved [2045/2045] Thu Sep 17 03:11:30 UTC 2020 I: ampliconnoise_1.29-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: ampliconnoise Binary: ampliconnoise Architecture: any Version: 1.29-8 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://github.com/lanzen/ampliconnoise Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/ampliconnoise Vcs-Git: https://salsa.debian.org/med-team/ampliconnoise.git Build-Depends: debhelper (>= 11~), libgsl-dev, libopenmpi-dev Package-List: ampliconnoise deb science optional arch=any Checksums-Sha1: 743cbd53fa3410dea902f3dc82864041defc3c4b 1403119 ampliconnoise_1.29.orig.tar.gz 8eb6cf9bd6c28ed7ce85ade83aec34cc8680be4c 8796 ampliconnoise_1.29-8.debian.tar.xz Checksums-Sha256: 0bf946806d77ecaf0994ad8ebf9a5e98ad33c809f6def5c9340a16c367918167 1403119 ampliconnoise_1.29.orig.tar.gz 7ff546ef97ddd48b84896672d8635d7e663ae488635de55b5ba5788e575bfdee 8796 ampliconnoise_1.29-8.debian.tar.xz Files: d6723e6f9cc71d7eb6f1a65ba4643aac 1403119 ampliconnoise_1.29.orig.tar.gz 643517e05d1dab4524803071edad6bff 8796 ampliconnoise_1.29-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlvJ0xsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHzjA/9FgbX3aJl1zMunV9vZ1d4LiBVHd3XW4lB H43Y5M7WTtbp+cSrbeGDa8/ZuG7BZYKmNjbF5VPtNq1hVBk85O3qWmY3o9HGYaFg cNnB9MrQEVRVTyr3hYrXxsm81NESAjLY/OZWAe08IL9PM1LWeuZ3kiecY7Mcivgf tRQZhnusDrMw/q2ehiGQMN2Q5+DVrEr4ir0/8dZT6Icz9MYIG19qw7VEN2B+LF5k RDGpQ17SD3nlHp5FjdhypnWfEMpWJkty5bPUCh3r1ULuRN1YWMq0dQtx7tgt3VIv Y6KDhjuTr1OPda+Tw8dyhYVyRHLEmpJOM1cStFtY/aIs4gThe1vSrkK1Ip3mz5tY JNJeGiTRv2EAcmokb1O/qqpebhTIJMyMgEyL2+JlGBvotka2e3+tyf/ToJj2iMLp 3+wTxEpn+HRn0jmxtQy2l1tNLa5KDkKmM5N4tyBTbkWOg8MhHE8vyEtvuOx26EHW 6kSRDel33T+O7IPvFVh6MoyMqVqnIZLu6CsWaPahx6YIr+dppeEPaXKiq5dkRXKk 3pPSmaa31oweHwkJV5/PC8OFmS2phW3u/+t6ZhyKQU69DRuOiyEVddCQZX3j/VrO wmNyr7/aESGeMdekCVTz3yuL/ANVA73Ap+537YiIrQe6apaEJ22gcwkQu86Rs2oc 8Qfhhl10dfo= =HkF7 -----END PGP SIGNATURE----- Thu Sep 17 03:11:30 UTC 2020 I: Checking whether the package is not for us Thu Sep 17 03:11:30 UTC 2020 I: Starting 1st build on remote node profitbricks-build16-i386.debian.net. Thu Sep 17 03:11:30 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build16-i386.debian.net. Thu Sep 17 03:12:05 UTC 2020 I: Deleting $TMPDIR on profitbricks-build16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 19 21:34:29 -12 2021 I: pbuilder-time-stamp: 1634722469 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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: using eatmydata during job I: Copying source file I: copying [ampliconnoise_1.29-8.dsc] I: copying [./ampliconnoise_1.29.orig.tar.gz] I: copying [./ampliconnoise_1.29-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 19 00:50:35 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ampliconnoise_1.29-8.dsc dpkg-source: info: extracting ampliconnoise in ampliconnoise-1.29 dpkg-source: info: unpacking ampliconnoise_1.29.orig.tar.gz dpkg-source: info: unpacking ampliconnoise_1.29-8.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: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/27342/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='54cc19e569b141cb83794b3456970efe' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='27342' 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/tmp.KWt3reuQez/pbuilderrc_P0rb --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.KWt3reuQez/b1 --logfile b1/build.log ampliconnoise_1.29-8.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux profitbricks-build16-i386 4.19.0-10-amd64 #1 SMP Debian 4.19.132-1 (2020-07-24) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Oct 17 02:47 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/27342/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: i386 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 (>= 11~), 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 ... 19234 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 (>= 11~); however: Package debhelper 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{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} libpmix2{a} libpsm-infinipath1{a} librdmacm1{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{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} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 32.5 MB of archives. After unpacking 120 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libedit2 i386 3.1-20181209-1 [98.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libkeyutils1 i386 1.6-6 [15.4 kB] Get: 14 http://deb.debian.org/debian buster/main i386 libkrb5support0 i386 1.17-3 [68.6 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libk5crypto3 i386 1.17-3 [126 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 17 http://deb.debian.org/debian buster/main i386 libkrb5-3 i386 1.17-3 [396 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libgssapi-krb5-2 i386 1.17-3 [168 kB] Get: 19 http://deb.debian.org/debian buster/main i386 openssh-client i386 1:7.9p1-10+deb10u2 [834 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 21 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 22 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 23 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 24 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 25 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 27 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 30 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 31 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 32 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 33 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 38 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 39 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 40 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 41 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libnl-3-200 i386 3.4.0-1 [65.8 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libnl-route-3-200 i386 3.4.0-1 [170 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libibverbs1 i386 22.1-1 [53.9 kB] Get: 45 http://deb.debian.org/debian buster/main i386 ibverbs-providers i386 22.1-1 [201 kB] Get: 46 http://deb.debian.org/debian buster/main i386 libevent-2.1-6 i386 2.1.8-stable-4 [191 kB] Get: 47 http://deb.debian.org/debian buster/main i386 libevent-core-2.1-6 i386 2.1.8-stable-4 [137 kB] Get: 48 http://deb.debian.org/debian buster/main i386 libevent-pthreads-2.1-6 i386 2.1.8-stable-4 [48.1 kB] Get: 49 http://deb.debian.org/debian buster/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6 [178 kB] Get: 50 http://deb.debian.org/debian buster/main i386 librdmacm1 i386 22.1-1 [68.8 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libfabric1 i386 1.6.2-3 [364 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 53 http://deb.debian.org/debian buster/main i386 libgslcblas0 i386 2.5+dfsg-6 [99.2 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libgsl23 i386 2.5+dfsg-6 [855 kB] Get: 55 http://deb.debian.org/debian buster/main i386 libgsl-dev i386 2.5+dfsg-6 [1076 kB] Get: 56 http://deb.debian.org/debian buster/main i386 libltdl7 i386 2.4.6-9 [392 kB] Get: 57 http://deb.debian.org/debian buster/main i386 libnuma1 i386 2.0.12-1 [27.7 kB] Get: 58 http://deb.debian.org/debian buster/main i386 libhwloc5 i386 1.11.12-3 [119 kB] Get: 59 http://deb.debian.org/debian buster/main i386 libnuma-dev i386 2.0.12-1 [40.9 kB] Get: 60 http://deb.debian.org/debian buster/main i386 libltdl-dev i386 2.4.6-9 [164 kB] Get: 61 http://deb.debian.org/debian buster/main i386 libhwloc-dev i386 1.11.12-3 [185 kB] Get: 62 http://deb.debian.org/debian buster/main i386 libpciaccess0 i386 0.14-1 [55.7 kB] Get: 63 http://deb.debian.org/debian buster/main i386 ocl-icd-libopencl1 i386 2.2.12-2 [37.2 kB] Get: 64 http://deb.debian.org/debian buster/main i386 libhwloc-plugins i386 1.11.12-3 [17.8 kB] Get: 65 http://deb.debian.org/debian buster/main i386 libnl-3-dev i386 3.4.0-1 [107 kB] Get: 66 http://deb.debian.org/debian buster/main i386 libnl-route-3-dev i386 3.4.0-1 [193 kB] Get: 67 http://deb.debian.org/debian buster/main i386 libibverbs-dev i386 22.1-1 [385 kB] Get: 68 http://deb.debian.org/debian buster/main i386 libpmix2 i386 3.1.2-3 [541 kB] Get: 69 http://deb.debian.org/debian buster/main i386 libopenmpi3 i386 3.1.3-11 [2236 kB] Get: 70 http://deb.debian.org/debian buster/main i386 openmpi-common all 3.1.3-11 [165 kB] Get: 71 http://deb.debian.org/debian buster/main i386 openmpi-bin i386 3.1.3-11 [200 kB] Get: 72 http://deb.debian.org/debian buster/main i386 libopenmpi-dev i386 3.1.3-11 [963 kB] Fetched 32.5 MB in 0s (69.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... 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Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:i386 (63.1-6+deb10u1) ... Setting up libkrb5support0:i386 (1.17-3) ... Setting up autotools-dev (20180224.1) ... Setting up libgsl23:i386 (2.5+dfsg-6) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:i386 (1.17-3) ... Setting up libltdl7:i386 (2.4.6-9) ... Setting up libevent-core-2.1-6:i386 (2.1.8-stable-4) ... Setting up libgfortran5:i386 (8.3.0-6) ... Setting up libevent-2.1-6:i386 (2.1.8-stable-4) ... Setting up libnuma1:i386 (2.0.12-1) ... Setting up sensible-utils (0.0.12) ... Setting up ocl-icd-libopencl1:i386 (2.2.12-2) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libnl-3-200:i386 (3.4.0-1) ... Setting up openmpi-common (3.1.3-11) ... Setting up libkrb5-3:i386 (1.17-3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/i386-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libevent-pthreads-2.1-6:i386 (2.1.8-stable-4) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libtool (2.4.6-9) ... Setting up libhwloc5:i386 (1.11.12-3) ... Setting up libedit2:i386 (3.1-20181209-1) ... Setting up m4 (1.4.18-2) ... Setting up libhwloc-plugins:i386 (1.11.12-3) ... Setting up libnuma-dev:i386 (2.0.12-1) ... Setting up libnl-route-3-200:i386 (3.4.0-1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:i386 (1.17-3) ... Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up libnl-3-dev:i386 (3.4.0-1) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:i386 (22.1-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libpmix2:i386 (3.1.2-3) ... Setting up ibverbs-providers:i386 (22.1-1) ... Setting up openssh-client (1:7.9p1-10+deb10u2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnl-route-3-dev:i386 (3.4.0-1) ... Setting up libltdl-dev:i386 (2.4.6-9) ... Setting up libhwloc-dev:i386 (1.11.12-3) ... Setting up librdmacm1:i386 (22.1-1) ... Setting up po-debconf (1.0.21) ... Setting up libibverbs-dev:i386 (22.1-1) ... Setting up libfabric1 (1.6.2-3) ... Setting up libopenmpi3:i386 (3.1.3-11) ... Setting up openmpi-bin (3.1.3-11) ... 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:i386 (3.1.3-11) ... update-alternatives: using /usr/lib/i386-linux-gnu/openmpi/include to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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 dpkg-buildpackage: info: source package ampliconnoise dpkg-buildpackage: info: source version 1.29-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_auto_clean make -j18 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 build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j18 "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] 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] UpdateMinCacheForRow(asMin,i,aafDistMatrix); ^~~~~~~~~~~~~~~~~~~~ UpdateMinCacheForMarkedRows FCluster.c: At top level: FCluster.c:237:1: warning: return type defaults to 'int' [-Wimplicit-int] 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:707:52: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); ^~~~~~~ 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] 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:854:52: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); ^~~~~~~ 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] 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] if(bVerbose){printf("%d: Broadcast distance matrix\n", rank, nSize, nPacket); fflush(stdout);} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SeqNoise.c: In function 'readData': SeqNoise.c:652:52: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); ^~~~~~~ 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] 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=] 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 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=] 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 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=] 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 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=] 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 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=] 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 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=] 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 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] 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=] 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 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=] 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 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:856:52: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); ^~~~~~~ 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=] 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 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:908:52: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] ptData->acSequences[(nSequences - 1)*nM + nPos] = toupper(szLine[i]); ^~~~~~~ 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=] 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 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 fakeroot debian/rules binary dh binary dh_testroot 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 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' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/ampliconnoise-1.29' dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/PerseusD debian/ampliconnoise/usr/bin/Perseus were not linked against libgslcblas.so.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/PyroDist debian/ampliconnoise/usr/bin/PyroNoiseM debian/ampliconnoise/usr/bin/SeqDist debian/ampliconnoise/usr/bin/PyroNoise debian/ampliconnoise/usr/bin/SeqNoise debian/ampliconnoise/usr/bin/NDist debian/ampliconnoise/usr/bin/PyroNoiseA were not linked against libpthread.so.0 (they use none of the library's symbols) 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_1.29-8_i386.deb'. dpkg-deb: building package 'ampliconnoise' in '../ampliconnoise_1.29-8_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../ampliconnoise_1.29-8_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/27342 and its subdirectories I: Current time: Tue Oct 19 21:35:03 -12 2021 I: pbuilder-time-stamp: 1634722503 Thu Sep 17 03:12:06 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build12-i386.debian.net. Thu Sep 17 03:12:06 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build12-i386.debian.net. Thu Sep 17 03:18:50 UTC 2020 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. Thu Sep 17 03:18:51 UTC 2020 I: ampliconnoise_1.29-8_i386.changes: Format: 1.8 Date: Fri, 19 Oct 2018 14:20:25 +0200 Source: ampliconnoise Binary: ampliconnoise ampliconnoise-dbgsym Architecture: i386 Version: 1.29-8 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 (1.29-8) unstable; urgency=medium . * Set Homepage to automatic clone from googlecode to Github * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: f8beeeff97bfabd9c1168339715d2710a8f38d1f 305120 ampliconnoise-dbgsym_1.29-8_i386.deb 33179a5a17c29970a67c5e4fb58f24bcdaef1393 5951 ampliconnoise_1.29-8_i386.buildinfo ccf3a98d3cb83360cbad59d171bed7c50cfadfc2 471496 ampliconnoise_1.29-8_i386.deb Checksums-Sha256: bf2e7fc2943488fceba07d498d1ac72eaf656adab9f5d1861803c69c1efbeeae 305120 ampliconnoise-dbgsym_1.29-8_i386.deb 8d9f49e97bd0b2fd98657fa439e5bfad267741bade473e8b955742ee45c372c9 5951 ampliconnoise_1.29-8_i386.buildinfo 6de16b9fd678766e218c6244b13b77b88e274dcea49bc6f4f8c6a3aedcc91cf4 471496 ampliconnoise_1.29-8_i386.deb Files: e6ce157fab30eb4791f22b08aee1d036 305120 debug optional ampliconnoise-dbgsym_1.29-8_i386.deb 398f4e8d9ca416911ef83f4020c38911 5951 science optional ampliconnoise_1.29-8_i386.buildinfo 97d869c3b01a2933de907c70eda6beae 471496 science optional ampliconnoise_1.29-8_i386.deb Thu Sep 17 03:18:51 UTC 2020 I: diffoscope 160 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.KWt3reuQez/ampliconnoise_1.29-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.KWt3reuQez/ampliconnoise_1.29-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.KWt3reuQez/ampliconnoise_1.29-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.KWt3reuQez/b1/ampliconnoise_1.29-8_i386.changes /srv/reproducible-results/rbuild-debian/tmp.KWt3reuQez/b2/ampliconnoise_1.29-8_i386.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: 0.211s) 0.211s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.028s) 0.028s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Sep 17 03:18:54 UTC 2020 I: diffoscope 160 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 17 03:18:54 UTC 2020 I: ampliconnoise from buster built successfully and reproducibly on i386. Thu Sep 17 03:18:57 UTC 2020 I: Submitting .buildinfo files to external archives: Thu Sep 17 03:18:57 UTC 2020 I: Submitting 8.0K b1/ampliconnoise_1.29-8_i386.buildinfo.asc Thu Sep 17 03:18:58 UTC 2020 I: Submitting 8.0K b2/ampliconnoise_1.29-8_i386.buildinfo.asc Thu Sep 17 03:18:59 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Sep 17 03:18:59 UTC 2020 I: Done submitting .buildinfo files. Thu Sep 17 03:18:59 UTC 2020 I: Removing signed ampliconnoise_1.29-8_i386.buildinfo.asc files: removed './b1/ampliconnoise_1.29-8_i386.buildinfo.asc' removed './b2/ampliconnoise_1.29-8_i386.buildinfo.asc'