I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 18 00:13:35 +14 2024 I: pbuilder-time-stamp: 1718619215 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [phyml_3.3.20220408-3.dsc] I: copying [./phyml_3.3.20220408.orig.tar.gz] I: copying [./phyml_3.3.20220408-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Oct 27 08:18:47 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-3.dsc: no acceptable signature found dpkg-source: info: extracting phyml in phyml-3.3.20220408 dpkg-source: info: unpacking phyml_3.3.20220408.orig.tar.gz dpkg-source: info: unpacking phyml_3.3.20220408-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sse_only_if_supported.patch dpkg-source: info: applying no-configure-ac-date.patch dpkg-source: info: applying fix_declaration_of_temp.patch dpkg-source: info: applying fix_wrong_initialisation_of_array.patch dpkg-source: info: applying no-march-native.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying apply-cflags.patch dpkg-source: info: applying filter-sse3-intrinsics.patch dpkg-source: info: applying apply-ldflags.patch dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1860095/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. 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 18 00:13 /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/1860095/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1860095/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]="x86_64-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=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=8c12b718ac694e7fa470a907615b3b7a LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-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=1860095 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.HL5un3j3/pbuilderrc_x9Hl --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.HL5un3j3/b2 --logfile b2/build.log --extrapackages usrmerge phyml_3.3.20220408-3.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 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 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 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 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 2023 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 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 2023 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 2023 more -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 Jun 18 00:13 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 2023 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 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/1860095/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkg-config, libopenmpi-dev, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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 pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath 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} chrpath{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} 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} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libucx0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{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, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 45.5 MB of archives. After unpacking 179 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libevent-2.1-7 amd64 2.1.12-stable-8 [180 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-8 [107 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-8 [60.6 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libevent-dev amd64 2.1.12-stable-8 [305 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libnuma-dev amd64 2.0.16-1 [35.0 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libltdl-dev amd64 2.4.7-5 [164 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libhwloc-dev amd64 2.9.0-1 [241 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libnl-3-dev amd64 3.7.0-0.2+b1 [104 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-dev amd64 3.7.0-0.2+b1 [203 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libibverbs-dev amd64 44.0-2 [633 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libpmix-dev amd64 4.2.2-1+b1 [902 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libopenmpi-dev amd64 4.1.4-3+b1 [970 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Fetched 45.5 MB in 7s (6574 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 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_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... 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Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../28-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../29-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../30-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../31-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../32-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../33-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../34-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../35-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../36-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran-12-dev:amd64. Preparing to unpack .../37-libgfortran-12-dev_12.2.0-14_amd64.deb ... Unpacking libgfortran-12-dev:amd64 (12.2.0-14) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../38-gfortran-12_12.2.0-14_amd64.deb ... Unpacking gfortran-12 (12.2.0-14) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../39-libnl-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../40-libnl-route-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../41-libibverbs1_44.0-2_amd64.deb ... Unpacking libibverbs1:amd64 (44.0-2) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../42-ibverbs-providers_44.0-2_amd64.deb ... Unpacking ibverbs-providers:amd64 (44.0-2) ... Selecting previously unselected package libevent-2.1-7:amd64. Preparing to unpack .../43-libevent-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-core-2.1-7:amd64. Preparing to unpack .../44-libevent-core-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-extra-2.1-7:amd64. Preparing to unpack .../45-libevent-extra-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-extra-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-pthreads-2.1-7:amd64. Preparing to unpack .../46-libevent-pthreads-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-openssl-2.1-7:amd64. Preparing to unpack .../47-libevent-openssl-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-openssl-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../48-libevent-dev_2.1.12-stable-8_amd64.deb ... Unpacking libevent-dev (2.1.12-stable-8) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../49-libpsm-infinipath1_3.3+20.604758e7-6.2_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.2) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../50-libnuma1_2.0.16-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.16-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../51-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../52-librdmacm1_44.0-2_amd64.deb ... Unpacking librdmacm1:amd64 (44.0-2) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../53-libfabric1_1.17.0-3_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../54-libhwloc15_2.9.0-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.9.0-1) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../55-libnuma-dev_2.0.16-1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.16-1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../56-libltdl7_2.4.7-5_amd64.deb ... Unpacking libltdl7:amd64 (2.4.7-5) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../57-libltdl-dev_2.4.7-5_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.7-5) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../58-libhwloc-dev_2.9.0-1_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.9.0-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../59-libpciaccess0_0.17-2_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../60-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../61-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../62-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../63-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../64-libx11-6_2%3a1.8.4-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.4-2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../65-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../66-libxnvctrl0_525.85.05-1_amd64.deb ... Unpacking libxnvctrl0:amd64 (525.85.05-1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../67-ocl-icd-libopencl1_2.3.1-1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.1-1) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../68-libhwloc-plugins_2.9.0-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.9.0-1) ... Selecting previously unselected package libnl-3-dev:amd64. Preparing to unpack .../69-libnl-3-dev_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-3-dev:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-dev:amd64. Preparing to unpack .../70-libnl-route-3-dev_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-route-3-dev:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs-dev:amd64. Preparing to unpack .../71-libibverbs-dev_44.0-2_amd64.deb ... Unpacking libibverbs-dev:amd64 (44.0-2) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../72-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../73-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libmunge2. Preparing to unpack .../74-libmunge2_0.5.15-2_amd64.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../75-libpmix2_4.2.2-1+b1_amd64.deb ... Unpacking libpmix2:amd64 (4.2.2-1+b1) ... Selecting previously unselected package libucx0:amd64. Preparing to unpack .../76-libucx0_1.13.1-1_amd64.deb ... Unpacking libucx0:amd64 (1.13.1-1) ... Selecting previously unselected package libopenmpi3:amd64. Preparing to unpack .../77-libopenmpi3_4.1.4-3+b1_amd64.deb ... Unpacking libopenmpi3:amd64 (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:amd64. Preparing to unpack .../79-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpmix-dev:amd64. Preparing to unpack .../80-libpmix-dev_4.2.2-1+b1_amd64.deb ... Unpacking libpmix-dev:amd64 (4.2.2-1+b1) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../81-openmpi-bin_4.1.4-3+b1_amd64.deb ... Unpacking openmpi-bin (4.1.4-3+b1) ... Selecting previously unselected package libopenmpi-dev:amd64. Preparing to unpack .../82-libopenmpi-dev_4.1.4-3+b1_amd64.deb ... Unpacking libopenmpi-dev:amd64 (4.1.4-3+b1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../83-libpkgconf3_1.8.1-1_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../84-pkgconf-bin_1.8.1-1_amd64.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../85-pkgconf_1.8.1-1_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-1) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../86-pkg-config_1.8.1-1_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libcbor0.8:amd64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libltdl7:amd64 (2.4.7-5) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libpsm2-2 (11.2.185-2) ... 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/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.12.0-2+b1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libelf1:amd64 (0.188-2.1) ... 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Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up libpmix-dev:amd64 (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:amd64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Processing triggers for libc-bin (2.36-9) ... 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/1860095/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/1860095/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/phyml-3.3.20220408/ && 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 > ../phyml_3.3.20220408-3_source.changes dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20220408-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phyml-3.3.20220408' # save pdf from cleaning mv doc/phyml-manual.pdf . dh_auto_clean mv phyml-manual.pdf doc # remove temporary bin dir for phyml (see above hack) rm -rf debian/bin rm -rf doc/Makefile make[1]: Leaving directory '/build/phyml-3.3.20220408' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/phyml-3.3.20220408' dh_autoreconf --as-needed configure.ac:31: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:31: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:31: the top level configure.ac:52: warning: The macro `AC_FUNC_SETVBUF_REVERSED' is obsolete. Remove it and all references to SETVBUF_REVERSED. ./lib/autoconf/functions.m4:1766: AC_FUNC_SETVBUF_REVERSED is expanded from... configure.ac:52: the top level configure.ac:14: installing './compile' configure.ac:12: installing './config.guess' configure.ac:12: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/phyml-3.3.20220408' debian/rules override_dh_auto_build make[1]: Entering directory '/build/phyml-3.3.20220408' # According to README you need different configure options to get different executables # Here we hack in a full build process for phyml executable # The hack includes saving the documentation from beeing cleaned up mv doc/phyml-manual.pdf . dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none configure: "On arch x86_64-pc-linux-gnu use MSSE = -msse" checking for log in -lm... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j16 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/phyml-3.3.20220408' make all-recursive make[3]: Entering directory '/build/phyml-3.3.20220408' Making all in src make[4]: Entering directory '/build/phyml-3.3.20220408/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utilities.o utilities.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o optimiz.o optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lk.o lk.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bionj.o bionj.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o models.o models.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o free.o free.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o help.o help.c .: Building [phyml]. Version 3.3.3:3.3.20220408-3 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simu.o simu.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eigen.o eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pars.o pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alrt.o alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o interface.o interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cl.o cl.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o spr.o spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o draw.o draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stats.o stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o make.o make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o nexus.o nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o init.o init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xml.o xml.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sse.o sse.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o avx.o avx.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tbe.o tbe.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ancestral.o ancestral.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mixt.o mixt.c io.c: In function 'Sub_Trees': io.c:511:25: warning: 'subs' may be used uninitialized [-Wmaybe-uninitialized] 511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:479:10: note: 'subs' was declared here 479 | char **subs; | ^~~~ gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o io.o make.o nexus.o init.o xml.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm Done. make[4]: Leaving directory '/build/phyml-3.3.20220408/src' make[4]: Entering directory '/build/phyml-3.3.20220408' make[4]: Leaving directory '/build/phyml-3.3.20220408' make[3]: Leaving directory '/build/phyml-3.3.20220408' make[2]: Leaving directory '/build/phyml-3.3.20220408' # move phyml binary to temporary dir inside debian/ mkdir -p /build/phyml-3.3.20220408/debian/bin mv src/phyml /build/phyml-3.3.20220408/debian/bin/phyml /usr/bin/make distclean make[2]: Entering directory '/build/phyml-3.3.20220408' Making distclean in src make[3]: Entering directory '/build/phyml-3.3.20220408/src' test -z "phyml" || rm -f phyml rm -f *.o rm -f *.tab.c test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/alrt.Po rm -f ./.deps/ancestral.Po rm -f ./.deps/avx.Po rm -f ./.deps/bionj.Po rm -f ./.deps/cl.Po rm -f ./.deps/date.Po rm -f ./.deps/draw.Po rm -f ./.deps/eigen.Po rm -f ./.deps/free.Po rm -f ./.deps/help.Po rm -f ./.deps/init.Po rm -f ./.deps/interface.Po rm -f ./.deps/io.Po rm -f ./.deps/lk.Po rm -f ./.deps/location.Po rm -f ./.deps/main.Po rm -f ./.deps/make.Po rm -f ./.deps/mcmc.Po rm -f ./.deps/mg.Po rm -f ./.deps/mixt.Po rm -f ./.deps/models.Po rm -f ./.deps/nexus.Po rm -f ./.deps/optimiz.Po rm -f ./.deps/pars.Po rm -f ./.deps/phyml_mpi-alrt.Po rm -f ./.deps/phyml_mpi-ancestral.Po rm -f ./.deps/phyml_mpi-avx.Po rm -f ./.deps/phyml_mpi-bionj.Po rm -f ./.deps/phyml_mpi-cl.Po rm -f ./.deps/phyml_mpi-draw.Po rm -f ./.deps/phyml_mpi-eigen.Po rm -f ./.deps/phyml_mpi-free.Po rm -f ./.deps/phyml_mpi-help.Po rm -f ./.deps/phyml_mpi-init.Po rm -f ./.deps/phyml_mpi-interface.Po rm -f ./.deps/phyml_mpi-io.Po rm -f ./.deps/phyml_mpi-lk.Po rm -f ./.deps/phyml_mpi-main.Po rm -f ./.deps/phyml_mpi-make.Po rm -f ./.deps/phyml_mpi-mixt.Po rm -f ./.deps/phyml_mpi-models.Po rm -f ./.deps/phyml_mpi-mpi_boot.Po rm -f ./.deps/phyml_mpi-nexus.Po rm -f ./.deps/phyml_mpi-optimiz.Po rm -f ./.deps/phyml_mpi-pars.Po rm -f ./.deps/phyml_mpi-simu.Po rm -f ./.deps/phyml_mpi-spr.Po rm -f ./.deps/phyml_mpi-sse.Po rm -f ./.deps/phyml_mpi-stats.Po rm -f ./.deps/phyml_mpi-tbe.Po rm -f ./.deps/phyml_mpi-utilities.Po rm -f ./.deps/phyml_mpi-xml.Po rm -f ./.deps/phyrex.Po rm -f ./.deps/rates.Po rm -f ./.deps/rrw.Po rm -f ./.deps/rw.Po rm -f ./.deps/simu.Po rm -f ./.deps/slfv.Po rm -f ./.deps/spr.Po rm -f ./.deps/sse.Po rm -f ./.deps/stats.Po rm -f ./.deps/tbe.Po rm -f ./.deps/times.Po rm -f ./.deps/utilities.Po rm -f ./.deps/xml.Po rm -f Makefile make[3]: Leaving directory '/build/phyml-3.3.20220408/src' make[3]: Entering directory '/build/phyml-3.3.20220408' test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/build/phyml-3.3.20220408' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/phyml-3.3.20220408' dh_auto_configure -- --enable-phyml-mpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-phyml-mpi checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none configure: "On arch x86_64-pc-linux-gnu use MSSE = -msse" checking for log in -lm... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for mpi-c... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j16 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/phyml-3.3.20220408' make all-recursive make[3]: Entering directory '/build/phyml-3.3.20220408' Making all in src make[4]: Entering directory '/build/phyml-3.3.20220408/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-3 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c io.c: In function 'Sub_Trees': io.c:511:25: warning: 'subs' may be used uninitialized [-Wmaybe-uninitialized] 511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:479:10: note: 'subs' was declared here 479 | char **subs; | ^~~~ gcc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -lm Done. make[4]: Leaving directory '/build/phyml-3.3.20220408/src' make[4]: Entering directory '/build/phyml-3.3.20220408' make[4]: Leaving directory '/build/phyml-3.3.20220408' make[3]: Leaving directory '/build/phyml-3.3.20220408' make[2]: Leaving directory '/build/phyml-3.3.20220408' # move phyml binary to temporary dir inside debian/ # mkdir -p /build/phyml-3.3.20220408/debian/bin mv src/phyml-mpi /build/phyml-3.3.20220408/debian/bin/phyml-mpi mv phyml-manual.pdf doc make[1]: Leaving directory '/build/phyml-3.3.20220408' dh_auto_test make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 make[1]: Entering directory '/build/phyml-3.3.20220408' Making check in src make[2]: Entering directory '/build/phyml-3.3.20220408/src' gcc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -lm .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-3 :. Done. make[2]: Leaving directory '/build/phyml-3.3.20220408/src' make[2]: Entering directory '/build/phyml-3.3.20220408' make[2]: Leaving directory '/build/phyml-3.3.20220408' make[1]: Leaving directory '/build/phyml-3.3.20220408' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/phyml-3.3.20220408' dh_auto_install make -j16 install DESTDIR=/build/phyml-3.3.20220408/debian/phyml AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/phyml-3.3.20220408' Making install in src make[3]: Entering directory '/build/phyml-3.3.20220408/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-3 :. Done. make[4]: Entering directory '/build/phyml-3.3.20220408/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/phyml-3.3.20220408/debian/phyml/usr/bin' /usr/bin/install -c phyml-mpi '/build/phyml-3.3.20220408/debian/phyml/usr/bin' make[4]: Leaving directory '/build/phyml-3.3.20220408/src' make[3]: Leaving directory '/build/phyml-3.3.20220408/src' make[3]: Entering directory '/build/phyml-3.3.20220408' make[4]: Entering directory '/build/phyml-3.3.20220408' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/phyml-3.3.20220408' make[3]: Leaving directory '/build/phyml-3.3.20220408' make[2]: Leaving directory '/build/phyml-3.3.20220408' # install phyml binary we have kept safe above mkdir -p /build/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin mv /build/phyml-3.3.20220408/debian/bin/* /build/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml* make[1]: Leaving directory '/build/phyml-3.3.20220408' dh_install debian/rules override_dh_installdocs make[1]: Entering directory '/build/phyml-3.3.20220408' dh_installdocs mv /build/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /build/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf make[1]: Leaving directory '/build/phyml-3.3.20220408' dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/phyml-3.3.20220408' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/phyml-3.3.20220408' debian/rules override_dh_fixperms make[1]: Entering directory '/build/phyml-3.3.20220408' dh_fixperms find debian/*/usr/share/doc -name "*.nxs" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.xml" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.mat" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.txt" -exec chmod -x \{\} \; chmod -x debian/*/usr/share/doc/phyml/examples/nucleic chmod -x debian/*/usr/share/doc/phyml/examples/proteic make[1]: Leaving directory '/build/phyml-3.3.20220408' dh_missing debian/rules override_dh_dwz make[1]: Entering directory '/build/phyml-3.3.20220408' echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/build/phyml-3.3.20220408' dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phyml' in '../phyml_3.3.20220408-3_amd64.deb'. dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20220408-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../phyml_3.3.20220408-3_amd64.buildinfo dpkg-genchanges --build=binary -O../phyml_3.3.20220408-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1860095/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1860095/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/1860095 and its subdirectories I: Current time: Tue Jun 18 00:15:07 +14 2024 I: pbuilder-time-stamp: 1718619307