I: pbuilder: network access will be disabled during build
I: Current time: Sat Jul 23 00:54:18 -12 2022
I: pbuilder-time-stamp: 1658580858
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [phyml_3.3.20200621-1.dsc]
I: copying [./phyml_3.3.20200621.orig.tar.gz]
I: copying [./phyml_3.3.20200621-1.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.NTfb35N0/trustedkeys.kbx': General error
gpgv: Signature made Wed Jul 22 07:49:47 2020 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./phyml_3.3.20200621-1.dsc
dpkg-source: info: extracting phyml in phyml-3.3.20200621
dpkg-source: info: unpacking phyml_3.3.20200621.orig.tar.gz
dpkg-source: info: unpacking phyml_3.3.20200621-1.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-stdc++.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
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/4391/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18'
DISTRIBUTION=''
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='c8b39f7f8af0405bbd722bfd098e3399'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='4391'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.zID2y5XD0Y/pbuilderrc_ppiw --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zID2y5XD0Y/b1 --logfile b1/build.log phyml_3.3.20200621-1.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos6-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux
I: ls -l /bin
total 5776
-rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash
-rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2
-rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep
-rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2
-rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore
-rwxr-xr-x 1 root root 38824 Sep 22 2020 cat
-rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp
-rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod
-rwxr-xr-x 1 root root 75752 Sep 22 2020 chown
-rwxr-xr-x 1 root root 157960 Sep 22 2020 cp
-rwxr-xr-x 1 root root 128724 Dec 10 2020 dash
-rwxr-xr-x 1 root root 124904 Sep 22 2020 date
-rwxr-xr-x 1 root root 92172 Sep 22 2020 dd
-rwxr-xr-x 1 root root 100752 Sep 22 2020 df
-rwxr-xr-x 1 root root 153964 Sep 22 2020 dir
-rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg
lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname
-rwxr-xr-x 1 root root 34664 Sep 22 2020 echo
-rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
-rwxr-xr-x 1 root root 34664 Sep 22 2020 false
-rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
-rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt
-rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount
-rwxr-xr-x 1 root root 210488 Nov 9 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip
-rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe
-rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip
-rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname
-rwxr-xr-x 1 root root 83980 Sep 22 2020 ln
-rwxr-xr-x 1 root root 55572 Feb 7 2020 login
-rwxr-xr-x 1 root root 153964 Sep 22 2020 ls
-rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk
-rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir
-rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod
-rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp
-rwxr-xr-x 1 root root 58920 Feb 7 2021 more
-rwsr-xr-x 1 root root 50720 Feb 7 2021 mount
-rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint
-rwxr-xr-x 1 root root 157996 Sep 22 2020 mv
lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd
lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash
-rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink
-rwxr-xr-x 1 root root 75720 Sep 22 2020 rm
-rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir
-rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts
-rwxr-xr-x 1 root root 125036 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Jul 22 03:48 sh -> dash
-rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep
-rwxr-xr-x 1 root root 83880 Sep 22 2020 stty
-rwsr-xr-x 1 root root 79396 Feb 7 2021 su
-rwxr-xr-x 1 root root 34696 Sep 22 2020 sync
-rwxr-xr-x 1 root root 602584 Feb 16 2021 tar
-rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile
-rwxr-xr-x 1 root root 108520 Sep 22 2020 touch
-rwxr-xr-x 1 root root 34664 Sep 22 2020 true
-rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Feb 7 2021 umount
-rwxr-xr-x 1 root root 34664 Sep 22 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress
-rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir
-rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl
lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat
-rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp
-rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff
-rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep
-rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce
-rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep
-rwxr-xr-x 1 root root 2206 Mar 2 2021 zless
-rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore
-rwxr-xr-x 1 root root 4553 Mar 2 2021 znew
I: user script /srv/workspace/pbuilder/4391/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 <pbuilder-maint@lists.alioth.debian.org>
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 ... 19675 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-10{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcbor0{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-10-dev{a} libgfortran5{a} libglib2.0-0{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu67{a} libjs-jquery{a} libjs-jquery-ui{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{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} libsigsegv2{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} pkg-config{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 libglib2.0-data libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs
0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded.
Need to get 43.7 MB of archives. After unpacking 163 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB]
Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB]
Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB]
Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB]
Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB]
Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB]
Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB]
Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB]
Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB]
Get: 11 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB]
Get: 12 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB]
Get: 13 http://deb.debian.org/debian bullseye/main i386 libedit2 i386 3.1-20191231-2+b1 [101 kB]
Get: 14 http://deb.debian.org/debian bullseye/main i386 libcbor0 i386 0.5.0+dfsg-2 [26.2 kB]
Get: 15 http://deb.debian.org/debian bullseye/main i386 libfido2-1 i386 1.6.0-2 [59.9 kB]
Get: 16 http://deb.debian.org/debian bullseye/main i386 openssh-client i386 1:8.4p1-5 [991 kB]
Get: 17 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB]
Get: 18 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB]
Get: 19 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB]
Get: 20 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 21 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB]
Get: 22 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB]
Get: 23 http://deb.debian.org/debian bullseye/main i386 chrpath i386 0.16-2+b1 [17.5 kB]
Get: 24 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB]
Get: 25 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB]
Get: 26 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 27 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 28 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB]
Get: 29 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get: 30 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get: 31 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB]
Get: 32 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB]
Get: 33 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB]
Get: 34 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB]
Get: 35 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB]
Get: 36 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 37 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 38 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB]
Get: 39 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB]
Get: 40 http://deb.debian.org/debian bullseye/main i386 libgfortran-10-dev i386 10.2.1-6 [705 kB]
Get: 41 http://deb.debian.org/debian bullseye/main i386 gfortran-10 i386 10.2.1-6 [9642 kB]
Get: 42 http://deb.debian.org/debian bullseye/main i386 libnl-3-200 i386 3.4.0-1+b1 [66.4 kB]
Get: 43 http://deb.debian.org/debian bullseye/main i386 libnl-route-3-200 i386 3.4.0-1+b1 [168 kB]
Get: 44 http://deb.debian.org/debian bullseye/main i386 libibverbs1 i386 33.2-1 [64.6 kB]
Get: 45 http://deb.debian.org/debian bullseye/main i386 ibverbs-providers i386 33.2-1 [275 kB]
Get: 46 http://deb.debian.org/debian bullseye/main i386 libevent-2.1-7 i386 2.1.12-stable-1 [203 kB]
Get: 47 http://deb.debian.org/debian bullseye/main i386 libevent-core-2.1-7 i386 2.1.12-stable-1 [148 kB]
Get: 48 http://deb.debian.org/debian bullseye/main i386 libevent-extra-2.1-7 i386 2.1.12-stable-1 [116 kB]
Get: 49 http://deb.debian.org/debian bullseye/main i386 libevent-pthreads-2.1-7 i386 2.1.12-stable-1 [57.3 kB]
Get: 50 http://deb.debian.org/debian bullseye/main i386 libevent-openssl-2.1-7 i386 2.1.12-stable-1 [64.9 kB]
Get: 51 http://deb.debian.org/debian bullseye/main i386 libevent-dev i386 2.1.12-stable-1 [332 kB]
Get: 52 http://deb.debian.org/debian bullseye/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.1 [178 kB]
Get: 53 http://deb.debian.org/debian bullseye/main i386 librdmacm1 i386 33.2-1 [75.2 kB]
Get: 54 http://deb.debian.org/debian bullseye/main i386 libfabric1 i386 1.11.0-2 [518 kB]
Get: 55 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB]
Get: 56 http://deb.debian.org/debian bullseye/main i386 libhwloc15 i386 2.4.1+dfsg-1 [164 kB]
Get: 57 http://deb.debian.org/debian bullseye/main i386 libnuma1 i386 2.0.12-1+b1 [27.9 kB]
Get: 58 http://deb.debian.org/debian bullseye/main i386 libnuma-dev i386 2.0.12-1+b1 [41.2 kB]
Get: 59 http://deb.debian.org/debian bullseye/main i386 libltdl7 i386 2.4.6-15 [392 kB]
Get: 60 http://deb.debian.org/debian bullseye/main i386 libltdl-dev i386 2.4.6-15 [164 kB]
Get: 61 http://deb.debian.org/debian bullseye/main i386 libhwloc-dev i386 2.4.1+dfsg-1 [250 kB]
Get: 62 http://deb.debian.org/debian bullseye/main i386 libpciaccess0 i386 0.16-1 [55.7 kB]
Get: 63 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB]
Get: 64 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB]
Get: 65 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB]
Get: 66 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.1-1 [310 kB]
Get: 67 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.1-1 [796 kB]
Get: 68 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB]
Get: 69 http://deb.debian.org/debian bullseye/main i386 libxnvctrl0 i386 460.56-1 [26.8 kB]
Get: 70 http://deb.debian.org/debian bullseye/main i386 ocl-icd-libopencl1 i386 2.2.14-2 [45.0 kB]
Get: 71 http://deb.debian.org/debian bullseye/main i386 libhwloc-plugins i386 2.4.1+dfsg-1 [22.0 kB]
Get: 72 http://deb.debian.org/debian bullseye/main i386 libnl-3-dev i386 3.4.0-1+b1 [107 kB]
Get: 73 http://deb.debian.org/debian bullseye/main i386 libnl-route-3-dev i386 3.4.0-1+b1 [192 kB]
Get: 74 http://deb.debian.org/debian bullseye/main i386 libibverbs-dev i386 33.2-1 [521 kB]
Get: 75 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get: 76 http://deb.debian.org/debian bullseye/main i386 libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get: 77 http://deb.debian.org/debian bullseye/main i386 libpmix2 i386 4.0.0-4 [582 kB]
Get: 78 http://deb.debian.org/debian bullseye/main i386 libopenmpi3 i386 4.1.0-10 [2144 kB]
Get: 79 http://deb.debian.org/debian bullseye/main i386 openmpi-common all 4.1.0-10 [179 kB]
Get: 80 http://deb.debian.org/debian bullseye/main i386 libpmix-dev i386 4.0.0-4 [717 kB]
Get: 81 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB]
Get: 82 http://deb.debian.org/debian bullseye/main i386 openmpi-bin i386 4.1.0-10 [209 kB]
Get: 83 http://deb.debian.org/debian bullseye/main i386 libopenmpi-dev i386 4.1.0-10 [1142 kB]
Get: 84 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB]
Fetched 43.7 MB in 0s (89.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(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 ... 19675 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ...
Unpacking bsdextrautils (2.36.1-7) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ...
Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ...
Unpacking sensible-utils (0.0.14) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_i386.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../07-libmagic1_1%3a5.39-3_i386.deb ...
Unpacking libmagic1:i386 (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../08-file_1%3a5.39-3_i386.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../09-gettext-base_0.21-4_i386.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libmd0:i386.
Preparing to unpack .../10-libmd0_1.0.3-3_i386.deb ...
Unpacking libmd0:i386 (1.0.3-3) ...
Selecting previously unselected package libbsd0:i386.
Preparing to unpack .../11-libbsd0_0.11.3-1_i386.deb ...
Unpacking libbsd0:i386 (0.11.3-1) ...
Selecting previously unselected package libedit2:i386.
Preparing to unpack .../12-libedit2_3.1-20191231-2+b1_i386.deb ...
Unpacking libedit2:i386 (3.1-20191231-2+b1) ...
Selecting previously unselected package libcbor0:i386.
Preparing to unpack .../13-libcbor0_0.5.0+dfsg-2_i386.deb ...
Unpacking libcbor0:i386 (0.5.0+dfsg-2) ...
Selecting previously unselected package libfido2-1:i386.
Preparing to unpack .../14-libfido2-1_1.6.0-2_i386.deb ...
Unpacking libfido2-1:i386 (1.6.0-2) ...
Selecting previously unselected package openssh-client.
Preparing to unpack .../15-openssh-client_1%3a8.4p1-5_i386.deb ...
Unpacking openssh-client (1:8.4p1-5) ...
Selecting previously unselected package libsigsegv2:i386.
Preparing to unpack .../16-libsigsegv2_2.13-1_i386.deb ...
Unpacking libsigsegv2:i386 (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../17-m4_1.4.18-5_i386.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../18-autoconf_2.69-14_all.deb ...
Unpacking autoconf (2.69-14) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../19-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../20-automake_1%3a1.16.3-2_all.deb ...
Unpacking automake (1:1.16.3-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../21-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package chrpath.
Preparing to unpack .../22-chrpath_0.16-2+b1_i386.deb ...
Unpacking chrpath (0.16-2+b1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../23-libdebhelper-perl_13.3.4_all.deb ...
Unpacking libdebhelper-perl (13.3.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../24-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../25-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../26-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../27-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../28-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../29-dh-strip-nondeterminism_1.11.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.11.0-1) ...
Selecting previously unselected package libelf1:i386.
Preparing to unpack .../30-libelf1_0.183-1_i386.deb ...
Unpacking libelf1:i386 (0.183-1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../31-dwz_0.13+20210201-1_i386.deb ...
Unpacking dwz (0.13+20210201-1) ...
Selecting previously unselected package libicu67:i386.
Preparing to unpack .../32-libicu67_67.1-6_i386.deb ...
Unpacking libicu67:i386 (67.1-6) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../33-libxml2_2.9.10+dfsg-6.7_i386.deb ...
Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ...
Selecting previously unselected package gettext.
Preparing to unpack .../34-gettext_0.21-4_i386.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../35-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../36-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../37-debhelper_13.3.4_all.deb ...
Unpacking debhelper (13.3.4) ...
Selecting previously unselected package libgfortran5:i386.
Preparing to unpack .../38-libgfortran5_10.2.1-6_i386.deb ...
Unpacking libgfortran5:i386 (10.2.1-6) ...
Selecting previously unselected package libgfortran-10-dev:i386.
Preparing to unpack .../39-libgfortran-10-dev_10.2.1-6_i386.deb ...
Unpacking libgfortran-10-dev:i386 (10.2.1-6) ...
Selecting previously unselected package gfortran-10.
Preparing to unpack .../40-gfortran-10_10.2.1-6_i386.deb ...
Unpacking gfortran-10 (10.2.1-6) ...
Selecting previously unselected package libnl-3-200:i386.
Preparing to unpack .../41-libnl-3-200_3.4.0-1+b1_i386.deb ...
Unpacking libnl-3-200:i386 (3.4.0-1+b1) ...
Selecting previously unselected package libnl-route-3-200:i386.
Preparing to unpack .../42-libnl-route-3-200_3.4.0-1+b1_i386.deb ...
Unpacking libnl-route-3-200:i386 (3.4.0-1+b1) ...
Selecting previously unselected package libibverbs1:i386.
Preparing to unpack .../43-libibverbs1_33.2-1_i386.deb ...
Unpacking libibverbs1:i386 (33.2-1) ...
Selecting previously unselected package ibverbs-providers:i386.
Preparing to unpack .../44-ibverbs-providers_33.2-1_i386.deb ...
Unpacking ibverbs-providers:i386 (33.2-1) ...
Selecting previously unselected package libevent-2.1-7:i386.
Preparing to unpack .../45-libevent-2.1-7_2.1.12-stable-1_i386.deb ...
Unpacking libevent-2.1-7:i386 (2.1.12-stable-1) ...
Selecting previously unselected package libevent-core-2.1-7:i386.
Preparing to unpack .../46-libevent-core-2.1-7_2.1.12-stable-1_i386.deb ...
Unpacking libevent-core-2.1-7:i386 (2.1.12-stable-1) ...
Selecting previously unselected package libevent-extra-2.1-7:i386.
Preparing to unpack .../47-libevent-extra-2.1-7_2.1.12-stable-1_i386.deb ...
Unpacking libevent-extra-2.1-7:i386 (2.1.12-stable-1) ...
Selecting previously unselected package libevent-pthreads-2.1-7:i386.
Preparing to unpack .../48-libevent-pthreads-2.1-7_2.1.12-stable-1_i386.deb ...
Unpacking libevent-pthreads-2.1-7:i386 (2.1.12-stable-1) ...
Selecting previously unselected package libevent-openssl-2.1-7:i386.
Preparing to unpack .../49-libevent-openssl-2.1-7_2.1.12-stable-1_i386.deb ...
Unpacking libevent-openssl-2.1-7:i386 (2.1.12-stable-1) ...
Selecting previously unselected package libevent-dev.
Preparing to unpack .../50-libevent-dev_2.1.12-stable-1_i386.deb ...
Unpacking libevent-dev (2.1.12-stable-1) ...
Selecting previously unselected package libpsm-infinipath1.
Preparing to unpack .../51-libpsm-infinipath1_3.3+20.604758e7-6.1_i386.deb ...
Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.1) ...
Selecting previously unselected package librdmacm1:i386.
Preparing to unpack .../52-librdmacm1_33.2-1_i386.deb ...
Unpacking librdmacm1:i386 (33.2-1) ...
Selecting previously unselected package libfabric1.
Preparing to unpack .../53-libfabric1_1.11.0-2_i386.deb ...
Unpacking libfabric1 (1.11.0-2) ...
Selecting previously unselected package libglib2.0-0:i386.
Preparing to unpack .../54-libglib2.0-0_2.66.8-1_i386.deb ...
Unpacking libglib2.0-0:i386 (2.66.8-1) ...
Selecting previously unselected package libhwloc15:i386.
Preparing to unpack .../55-libhwloc15_2.4.1+dfsg-1_i386.deb ...
Unpacking libhwloc15:i386 (2.4.1+dfsg-1) ...
Selecting previously unselected package libnuma1:i386.
Preparing to unpack .../56-libnuma1_2.0.12-1+b1_i386.deb ...
Unpacking libnuma1:i386 (2.0.12-1+b1) ...
Selecting previously unselected package libnuma-dev:i386.
Preparing to unpack .../57-libnuma-dev_2.0.12-1+b1_i386.deb ...
Unpacking libnuma-dev:i386 (2.0.12-1+b1) ...
Selecting previously unselected package libltdl7:i386.
Preparing to unpack .../58-libltdl7_2.4.6-15_i386.deb ...
Unpacking libltdl7:i386 (2.4.6-15) ...
Selecting previously unselected package libltdl-dev:i386.
Preparing to unpack .../59-libltdl-dev_2.4.6-15_i386.deb ...
Unpacking libltdl-dev:i386 (2.4.6-15) ...
Selecting previously unselected package libhwloc-dev:i386.
Preparing to unpack .../60-libhwloc-dev_2.4.1+dfsg-1_i386.deb ...
Unpacking libhwloc-dev:i386 (2.4.1+dfsg-1) ...
Selecting previously unselected package libpciaccess0:i386.
Preparing to unpack .../61-libpciaccess0_0.16-1_i386.deb ...
Unpacking libpciaccess0:i386 (0.16-1) ...
Selecting previously unselected package libxau6:i386.
Preparing to unpack .../62-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 .../63-libxdmcp6_1%3a1.1.2-3_i386.deb ...
Unpacking libxdmcp6:i386 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:i386.
Preparing to unpack .../64-libxcb1_1.14-3_i386.deb ...
Unpacking libxcb1:i386 (1.14-3) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../65-libx11-data_2%3a1.7.1-1_all.deb ...
Unpacking libx11-data (2:1.7.1-1) ...
Selecting previously unselected package libx11-6:i386.
Preparing to unpack .../66-libx11-6_2%3a1.7.1-1_i386.deb ...
Unpacking libx11-6:i386 (2:1.7.1-1) ...
Selecting previously unselected package libxext6:i386.
Preparing to unpack .../67-libxext6_2%3a1.3.3-1.1_i386.deb ...
Unpacking libxext6:i386 (2:1.3.3-1.1) ...
Selecting previously unselected package libxnvctrl0:i386.
Preparing to unpack .../68-libxnvctrl0_460.56-1_i386.deb ...
Unpacking libxnvctrl0:i386 (460.56-1) ...
Selecting previously unselected package ocl-icd-libopencl1:i386.
Preparing to unpack .../69-ocl-icd-libopencl1_2.2.14-2_i386.deb ...
Unpacking ocl-icd-libopencl1:i386 (2.2.14-2) ...
Selecting previously unselected package libhwloc-plugins:i386.
Preparing to unpack .../70-libhwloc-plugins_2.4.1+dfsg-1_i386.deb ...
Unpacking libhwloc-plugins:i386 (2.4.1+dfsg-1) ...
Selecting previously unselected package libnl-3-dev:i386.
Preparing to unpack .../71-libnl-3-dev_3.4.0-1+b1_i386.deb ...
Unpacking libnl-3-dev:i386 (3.4.0-1+b1) ...
Selecting previously unselected package libnl-route-3-dev:i386.
Preparing to unpack .../72-libnl-route-3-dev_3.4.0-1+b1_i386.deb ...
Unpacking libnl-route-3-dev:i386 (3.4.0-1+b1) ...
Selecting previously unselected package libibverbs-dev:i386.
Preparing to unpack .../73-libibverbs-dev_33.2-1_i386.deb ...
Unpacking libibverbs-dev:i386 (33.2-1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../74-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ...
Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../75-libjs-jquery-ui_1.12.1+dfsg-8_all.deb ...
Unpacking libjs-jquery-ui (1.12.1+dfsg-8) ...
Selecting previously unselected package libpmix2:i386.
Preparing to unpack .../76-libpmix2_4.0.0-4_i386.deb ...
Unpacking libpmix2:i386 (4.0.0-4) ...
Selecting previously unselected package libopenmpi3:i386.
Preparing to unpack .../77-libopenmpi3_4.1.0-10_i386.deb ...
Unpacking libopenmpi3:i386 (4.1.0-10) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../78-openmpi-common_4.1.0-10_all.deb ...
Unpacking openmpi-common (4.1.0-10) ...
Selecting previously unselected package libpmix-dev:i386.
Preparing to unpack .../79-libpmix-dev_4.0.0-4_i386.deb ...
Unpacking libpmix-dev:i386 (4.0.0-4) ...
Selecting previously unselected package zlib1g-dev:i386.
Preparing to unpack .../80-zlib1g-dev_1%3a1.2.11.dfsg-2_i386.deb ...
Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../81-openmpi-bin_4.1.0-10_i386.deb ...
Unpacking openmpi-bin (4.1.0-10) ...
Selecting previously unselected package libopenmpi-dev:i386.
Preparing to unpack .../82-libopenmpi-dev_4.1.0-10_i386.deb ...
Unpacking libopenmpi-dev:i386 (4.1.0-10) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../83-pkg-config_0.29.2-1_i386.deb ...
Unpacking pkg-config (0.29.2-1) ...
Setting up libpipeline1:i386 (1.5.3-1) ...
Setting up libpciaccess0:i386 (0.16-1) ...
Setting up libxau6:i386 (1:1.0.9-1) ...
Setting up bsdextrautils (2.36.1-7) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:i386 (67.1-6) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:i386 (2.66.8-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.3.4) ...
Setting up libcbor0:i386 (0.5.0+dfsg-2) ...
Setting up libmagic1:i386 (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libx11-data (2:1.7.1-1) ...
Setting up libsigsegv2:i386 (2.13-1) ...
Setting up libhwloc15:i386 (2.4.1+dfsg-1) ...
Setting up libevent-core-2.1-7:i386 (2.1.12-stable-1) ...
Setting up libevent-2.1-7:i386 (2.1.12-stable-1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libltdl7:i386 (2.4.6-15) ...
Setting up libgfortran5:i386 (10.2.1-6) ...
Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ...
Setting up libnuma1:i386 (2.0.12-1+b1) ...
Setting up libmd0:i386 (1.0.3-3) ...
Setting up sensible-utils (0.0.14) ...
Setting up ocl-icd-libopencl1:i386 (2.2.14-2) ...
Setting up libuchardet0:i386 (0.0.7-1) ...
Setting up libnl-3-200:i386 (3.4.0-1+b1) ...
Setting up openmpi-common (4.1.0-10) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libgfortran-10-dev:i386 (10.2.1-6) ...
Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ...
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 (3.5.1+dfsg+~3.5.5-7) ...
Setting up libfido2-1:i386 (1.6.0-2) ...
Setting up libbsd0:i386 (0.11.3-1) ...
Setting up libelf1:i386 (0.183-1) ...
Setting up libxml2:i386 (2.9.10+dfsg-6.7) ...
Setting up chrpath (0.16-2+b1) ...
Setting up libevent-pthreads-2.1-7:i386 (2.1.12-stable-1) ...
Setting up libfile-stripnondeterminism-perl (1.11.0-1) ...
Setting up libxdmcp6:i386 (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:i386 (2.1.12-stable-1) ...
Setting up libxcb1:i386 (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libedit2:i386 (3.1-20191231-2+b1) ...
Setting up libevent-openssl-2.1-7:i386 (2.1.12-stable-1) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnuma-dev:i386 (2.0.12-1+b1) ...
Setting up libnl-route-3-200:i386 (3.4.0-1+b1) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-8) ...
Setting up libevent-dev (2.1.12-stable-1) ...
Setting up gfortran-10 (10.2.1-6) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.11.0-1) ...
Setting up dwz (0.13+20210201-1) ...
Setting up libnl-3-dev:i386 (3.4.0-1+b1) ...
Setting up groff-base (1.22.4-6) ...
Setting up libx11-6:i386 (2:1.7.1-1) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:i386 (33.2-1) ...
Setting up ibverbs-providers:i386 (33.2-1) ...
Setting up openssh-client (1:8.4p1-5) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:i386 (2:1.3.3-1.1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:i386 (460.56-1) ...
Setting up dh-autoreconf (20) ...
Setting up libnl-route-3-dev:i386 (3.4.0-1+b1) ...
Setting up libltdl-dev:i386 (2.4.6-15) ...
Setting up libhwloc-dev:i386 (2.4.1+dfsg-1) ...
Setting up librdmacm1:i386 (33.2-1) ...
Setting up debhelper (13.3.4) ...
Setting up libibverbs-dev:i386 (33.2-1) ...
Setting up libhwloc-plugins:i386 (2.4.1+dfsg-1) ...
Setting up libfabric1 (1.11.0-2) ...
Setting up libpmix2:i386 (4.0.0-4) ...
Setting up libopenmpi3:i386 (4.1.0-10) ...
Setting up libpmix-dev:i386 (4.0.0-4) ...
Setting up openmpi-bin (4.1.0-10) ...
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 (4.1.0-10) ...
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 (2.31-12) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/phyml-3.3.20200621/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
dpkg-buildpackage: info: source package phyml
dpkg-buildpackage: info: source version 3:3.3.20200621-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Shayan Doust <hello@shayandoust.me>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/phyml-3.3.20200621'
# 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-3.3.20200621'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
debian/rules override_dh_autoreconf
make[1]: Entering directory '/build/phyml-3.3.20200621'
dh_autoreconf --as-needed
configure.ac:16: installing './compile'
configure.ac:14: installing './config.guess'
configure.ac:14: 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-3.3.20200621'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/phyml-3.3.20200621'
# 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=i686-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/i386-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 thread-safe mkdir -p... /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... i686-pc-linux-gnu
checking host system type... i686-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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... 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
checking dependency style of gcc... (cached) none
configure: "Do not use MSSE = because not available on arch i686-pc-linux-gnu"
checking for log in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
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 stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
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 -j18 "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/build/phyml-3.3.20200621'
make all-recursive
make[3]: Entering directory '/build/phyml-3.3.20200621'
Making all in src
make[4]: Entering directory '/build/phyml-3.3.20200621/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -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 -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 -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 -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 -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 -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 -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 -c -o help.o help.c
.: Building [phyml]. Version 3.3.3:3.3.20200621-1 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -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 -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 -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 -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 -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 -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 -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 -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 -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 -c -o rates.o rates.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o mcmc.o mcmc.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o times.o times.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o tiporder.o tiporder.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -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 -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 -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 -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 -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 -c -o date.o date.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -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 -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 -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 -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 -c -o mixt.o mixt.c
io.c: In function 'Print_Fp_Out':
io.c:2315:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision);
| ^~
io.c:2315:43: note: directive argument in the range [1, 2147483647]
2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision);
| ^~~~~~~~
In file included from /usr/include/stdio.h:867,
from utilities.h:21,
from io.h:18,
from io.c:13:
/usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -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 rates.o mcmc.o times.o tiporder.o io.o make.o nexus.o init.o xml.o date.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm
Done.
make[4]: Leaving directory '/build/phyml-3.3.20200621/src'
make[4]: Entering directory '/build/phyml-3.3.20200621'
make[4]: Leaving directory '/build/phyml-3.3.20200621'
make[3]: Leaving directory '/build/phyml-3.3.20200621'
make[2]: Leaving directory '/build/phyml-3.3.20200621'
# move phyml binary to temporary dir inside debian/
mkdir -p /build/phyml-3.3.20200621/debian/bin
mv src/phyml /build/phyml-3.3.20200621/debian/bin/phyml
/usr/bin/make distclean
make[2]: Entering directory '/build/phyml-3.3.20200621'
Making distclean in src
make[3]: Entering directory '/build/phyml-3.3.20200621/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/beagle_utils.Po
rm -f ./.deps/bionj.Po
rm -f ./.deps/checkpoint.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/geo.Po
rm -f ./.deps/help.Po
rm -f ./.deps/init.Po
rm -f ./.deps/interface.Po
rm -f ./.deps/invitee.Po
rm -f ./.deps/io.Po
rm -f ./.deps/lk.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-date.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-mcmc.Po
rm -f ./.deps/phyml_mpi-mg.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-rates.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-times.Po
rm -f ./.deps/phyml_mpi-tiporder.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/tiporder.Po
rm -f ./.deps/utilities.Po
rm -f ./.deps/xml.Po
rm -f Makefile
make[3]: Leaving directory '/build/phyml-3.3.20200621/src'
make[3]: Entering directory '/build/phyml-3.3.20200621'
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-3.3.20200621'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/build/phyml-3.3.20200621'
dh_auto_configure -- --enable-mpi
./configure --build=i686-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/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-mpi
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /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... i686-pc-linux-gnu
checking host system type... i686-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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... 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
checking dependency style of gcc... (cached) none
configure: "Do not use MSSE = because not available on arch i686-pc-linux-gnu"
checking for log in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
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 stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
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 -j18 "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/build/phyml-3.3.20200621'
make all-recursive
make[3]: Entering directory '/build/phyml-3.3.20200621'
Making all in src
make[4]: Entering directory '/build/phyml-3.3.20200621/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c
.: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c
In file included from lk.h:18,
from lk.c:14:
utilities.h:18: warning: "_POSIX_C_SOURCE" redefined
18 | #define _POSIX_C_SOURCE 200112L
|
In file included from /usr/include/assert.h:35,
from lk.c:13:
/usr/include/features.h:310: note: this is the location of the previous definition
310 | # define _POSIX_C_SOURCE 199506L
|
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-rates.o `test -f 'rates.c' || echo './'`rates.c
In file included from cl.h:21,
from cl.c:13:
utilities.h:18: warning: "_POSIX_C_SOURCE" redefined
18 | #define _POSIX_C_SOURCE 200112L
|
In file included from /usr/include/unistd.h:25,
from cl.h:19,
from cl.c:13:
/usr/include/features.h:310: note: this is the location of the previous definition
310 | # define _POSIX_C_SOURCE 199506L
|
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-times.o `test -f 'times.c' || echo './'`times.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-tiporder.o `test -f 'tiporder.c' || echo './'`tiporder.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mg.o `test -f 'mg.c' || echo './'`mg.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-date.o `test -f 'date.c' || echo './'`date.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c
In file included from sse.h:18,
from sse.c:14:
utilities.h:18: warning: "_POSIX_C_SOURCE" redefined
18 | #define _POSIX_C_SOURCE 200112L
|
In file included from /usr/include/assert.h:35,
from sse.c:13:
/usr/include/features.h:310: note: this is the location of the previous definition
310 | # define _POSIX_C_SOURCE 199506L
|
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c
In file included from avx.h:18,
from avx.c:14:
utilities.h:18: warning: "_POSIX_C_SOURCE" redefined
18 | #define _POSIX_C_SOURCE 200112L
|
In file included from /usr/include/assert.h:35,
from avx.c:13:
/usr/include/features.h:310: note: this is the location of the previous definition
310 | # define _POSIX_C_SOURCE 199506L
|
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c
io.c: In function 'Print_Fp_Out':
io.c:2315:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision);
| ^~
io.c:2315:43: note: directive argument in the range [1, 2147483647]
2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision);
| ^~~~~~~~
In file included from /usr/include/stdio.h:867,
from utilities.h:21,
from io.h:18,
from io.c:13:
/usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -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-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.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-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/i386-linux-gnu/openmpi/lib -lmpi -lm
Done.
make[4]: Leaving directory '/build/phyml-3.3.20200621/src'
make[4]: Entering directory '/build/phyml-3.3.20200621'
make[4]: Leaving directory '/build/phyml-3.3.20200621'
make[3]: Leaving directory '/build/phyml-3.3.20200621'
make[2]: Leaving directory '/build/phyml-3.3.20200621'
# move phyml binary to temporary dir inside debian/
# mkdir -p /build/phyml-3.3.20200621/debian/bin
mv src/phyml-mpi /build/phyml-3.3.20200621/debian/bin/phyml-mpi
mv phyml-manual.pdf doc
make[1]: Leaving directory '/build/phyml-3.3.20200621'
dh_auto_test
make -j18 check VERBOSE=1
make[1]: Entering directory '/build/phyml-3.3.20200621'
Making check in src
make[2]: Entering directory '/build/phyml-3.3.20200621/src'
gcc -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -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-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.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-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/i386-linux-gnu/openmpi/lib -lmpi -lm
.: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :.
Done.
make[2]: Leaving directory '/build/phyml-3.3.20200621/src'
make[2]: Entering directory '/build/phyml-3.3.20200621'
make[2]: Leaving directory '/build/phyml-3.3.20200621'
make[1]: Leaving directory '/build/phyml-3.3.20200621'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/phyml-3.3.20200621'
dh_auto_install
make -j18 install DESTDIR=/build/phyml-3.3.20200621/debian/phyml AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/phyml-3.3.20200621'
Making install in src
make[3]: Entering directory '/build/phyml-3.3.20200621/src'
.: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :.
Done.
make[4]: Entering directory '/build/phyml-3.3.20200621/src'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/build/phyml-3.3.20200621/debian/phyml/usr/bin'
/usr/bin/install -c phyml-mpi '/build/phyml-3.3.20200621/debian/phyml/usr/bin'
make[4]: Leaving directory '/build/phyml-3.3.20200621/src'
make[3]: Leaving directory '/build/phyml-3.3.20200621/src'
make[3]: Entering directory '/build/phyml-3.3.20200621'
make[4]: Entering directory '/build/phyml-3.3.20200621'
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-3.3.20200621'
make[3]: Leaving directory '/build/phyml-3.3.20200621'
make[2]: Leaving directory '/build/phyml-3.3.20200621'
# install phyml binary we have kept safe above
mkdir -p /build/phyml-3.3.20200621/debian/phyml/usr/lib/phyml/bin
mv /build/phyml-3.3.20200621/debian/bin/* /build/phyml-3.3.20200621/debian/phyml/usr/lib/phyml/bin
chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml*
make[1]: Leaving directory '/build/phyml-3.3.20200621'
dh_install
debian/rules override_dh_installdocs
make[1]: Entering directory '/build/phyml-3.3.20200621'
dh_installdocs
mv /build/phyml-3.3.20200621/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /build/phyml-3.3.20200621/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf
make[1]: Leaving directory '/build/phyml-3.3.20200621'
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
debian/rules override_dh_compress
make[1]: Entering directory '/build/phyml-3.3.20200621'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/build/phyml-3.3.20200621'
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/phyml-3.3.20200621'
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 \{\} \;
make[1]: Leaving directory '/build/phyml-3.3.20200621'
dh_missing
debian/rules override_dh_dwz
make[1]: Entering directory '/build/phyml-3.3.20200621'
echo "Do not run dh_dwz"
Do not run dh_dwz
make[1]: Leaving directory '/build/phyml-3.3.20200621'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'phyml' in '../phyml_3.3.20200621-1_i386.deb'.
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20200621-1_i386.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../phyml_3.3.20200621-1_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/4391 and its subdirectories
I: Current time: Sat Jul 23 00:55:14 -12 2022
I: pbuilder-time-stamp: 1658580914