I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 14 13:36:42 +14 2023 I: pbuilder-time-stamp: 1686699402 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: using eatmydata during job 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 Sat Oct 9 11:04:27 2021 +14 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/28096/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 14 13:36 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/28096/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/28096/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=9ec3aecf5a6646dfa4e56a8144a7105b LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=28096 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.37bIaRj9/pbuilderrc_SBUA --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.37bIaRj9/b2 --logfile b2/build.log --extrapackages usrmerge ampliconnoise_1.29-10.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-9-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.27-1 (2023-05-08) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Jun 14 13:36 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/28096/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-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 ... 19599 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} libpsm-infinipath1{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, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 47.0 MB of archives. After unpacking 184 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 libcbor0.8 i386 0.8.0-2+b1 [29.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 libfido2-1 i386 1.12.0-2+b1 [87.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 openssh-client i386 1:9.2p1-2 [1004 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 26 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 28 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libgfortran-12-dev i386 12.2.0-14 [761 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 gfortran-12 i386 12.2.0-14 [10.5 MB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libnl-3-200 i386 3.7.0-0.2+b1 [66.2 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libnl-route-3-200 i386 3.7.0-0.2+b1 [196 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libibverbs1 i386 44.0-2 [65.8 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 ibverbs-providers i386 44.0-2 [368 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libevent-2.1-7 i386 2.1.12-stable-8 [194 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 libevent-core-2.1-7 i386 2.1.12-stable-8 [139 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libevent-extra-2.1-7 i386 2.1.12-stable-8 [112 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 libevent-pthreads-2.1-7 i386 2.1.12-stable-8 [53.7 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libevent-openssl-2.1-7 i386 2.1.12-stable-8 [61.5 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 libevent-dev i386 2.1.12-stable-8 [325 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.2 [177 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 librdmacm1 i386 44.0-2 [74.6 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libfabric1 i386 1.17.0-3 [538 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libgslcblas0 i386 2.7.1+dfsg-5 [99.6 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libgsl27 i386 2.7.1+dfsg-5 [921 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libgsl-dev i386 2.7.1+dfsg-5 [1176 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libhwloc15 i386 2.9.0-1 [168 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 libnuma1 i386 2.0.16-1 [22.7 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libnuma-dev i386 2.0.16-1 [37.3 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libltdl7 i386 2.4.7-5 [394 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libltdl-dev i386 2.4.7-5 [167 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libhwloc-dev i386 2.9.0-1 [259 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libpciaccess0 i386 0.17-2 [53.4 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2 [292 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2 [782 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libxnvctrl0 i386 525.85.05-1 [13.3 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 ocl-icd-libopencl1 i386 2.3.1-1 [45.4 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libhwloc-plugins i386 2.9.0-1 [17.8 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libnl-3-dev i386 3.7.0-0.2+b1 [109 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libnl-route-3-dev i386 3.7.0-0.2+b1 [226 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libibverbs-dev i386 44.0-2 [683 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libmunge2 i386 0.5.15-2 [20.3 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 libpmix2 i386 4.2.2-1+b1 [652 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 libopenmpi3 i386 4.1.4-3+b1 [2183 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 openmpi-common all 4.1.4-3 [167 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 libpmix-dev i386 4.2.2-1+b1 [975 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 openmpi-bin i386 4.1.4-3+b1 [196 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 libopenmpi-dev i386 4.1.4-3+b1 [920 kB] Fetched 47.0 MB in 1s (48.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19599 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_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ... 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Selecting previously unselected package libltdl7:i386. Preparing to unpack .../57-libltdl7_2.4.7-5_i386.deb ... Unpacking libltdl7:i386 (2.4.7-5) ... Selecting previously unselected package libltdl-dev:i386. Preparing to unpack .../58-libltdl-dev_2.4.7-5_i386.deb ... Unpacking libltdl-dev:i386 (2.4.7-5) ... Selecting previously unselected package libhwloc-dev:i386. Preparing to unpack .../59-libhwloc-dev_2.9.0-1_i386.deb ... Unpacking libhwloc-dev:i386 (2.9.0-1) ... Selecting previously unselected package libpciaccess0:i386. Preparing to unpack .../60-libpciaccess0_0.17-2_i386.deb ... Unpacking libpciaccess0:i386 (0.17-2) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../61-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../62-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. 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Selecting previously unselected package libmunge2. Preparing to unpack .../75-libmunge2_0.5.15-2_i386.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libpmix2:i386. Preparing to unpack .../76-libpmix2_4.2.2-1+b1_i386.deb ... Unpacking libpmix2:i386 (4.2.2-1+b1) ... Selecting previously unselected package libopenmpi3:i386. Preparing to unpack .../77-libopenmpi3_4.1.4-3+b1_i386.deb ... Unpacking libopenmpi3:i386 (4.1.4-3+b1) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../78-openmpi-common_4.1.4-3_all.deb ... Unpacking openmpi-common (4.1.4-3) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../79-zlib1g-dev_1%3a1.2.13.dfsg-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpmix-dev:i386. Preparing to unpack .../80-libpmix-dev_4.2.2-1+b1_i386.deb ... Unpacking libpmix-dev:i386 (4.2.2-1+b1) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../81-openmpi-bin_4.1.4-3+b1_i386.deb ... Unpacking openmpi-bin (4.1.4-3+b1) ... Selecting previously unselected package libopenmpi-dev:i386. Preparing to unpack .../82-libopenmpi-dev_4.1.4-3+b1_i386.deb ... Unpacking libopenmpi-dev:i386 (4.1.4-3+b1) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libpciaccess0:i386 (0.17-2) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libicu72:i386 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libgslcblas0:i386 (2.7.1+dfsg-5) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libcbor0.8:i386 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:i386 (2.7.1+dfsg-5) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libhwloc15:i386 (2.9.0-1) ... Setting up libevent-core-2.1-7:i386 (2.1.12-stable-8) ... Setting up libevent-2.1-7:i386 (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up libltdl7:i386 (2.4.7-5) ... Setting up libgfortran5:i386 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up libnuma1:i386 (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:i386 (2.3.1-1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libnl-3-200:i386 (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... 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 libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:i386 (1.12.0-2+b1) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.2) ... Setting up libevent-pthreads-2.1-7:i386 (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:i386 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:i386 (2.1.12-stable-8) ... Setting up libxcb1:i386 (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:i386 (3.1-20221030-2) ... Setting up libevent-openssl-2.1-7:i386 (2.1.12-stable-8) ... Setting up libgfortran-12-dev:i386 (12.2.0-14) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:i386 (2.0.16-1) ... Setting up libnl-route-3-200:i386 (3.7.0-0.2+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:i386 (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:i386 (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libx11-6:i386 (2:1.8.4-2) ... Setting up libhwloc-dev:i386 (2.9.0-1) ... Setting up libibverbs1:i386 (44.0-2) ... Setting up ibverbs-providers:i386 (44.0-2) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:i386 (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:i386 (525.85.05-1) ... Setting up libnl-route-3-dev:i386 (3.7.0-0.2+b1) ... Setting up librdmacm1:i386 (44.0-2) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:i386 (44.0-2) ... Setting up libhwloc-plugins:i386 (2.9.0-1) ... Setting up libfabric1:i386 (1.17.0-3) ... Setting up libpmix2:i386 (4.2.2-1+b1) ... Setting up libopenmpi3:i386 (4.1.4-3+b1) ... Setting up libpmix-dev:i386 (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:i386 (4.1.4-3+b1) ... 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 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/28096/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/28096/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/ampliconnoise-1.29/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 i386 debian/rules clean dh clean dh_auto_clean make -j7 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 -j7 "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' in '../ampliconnoise_1.29-10_i386.deb'. dpkg-deb: building package 'ampliconnoise-dbgsym' in '../ampliconnoise-dbgsym_1.29-10_i386.deb'. dpkg-genbuildinfo --build=binary -O../ampliconnoise_1.29-10_i386.buildinfo dpkg-genchanges --build=binary -O../ampliconnoise_1.29-10_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/28096/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/28096/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/28096 and its subdirectories I: Current time: Wed Jun 14 13:37:53 +14 2023 I: pbuilder-time-stamp: 1686699473