I: pbuilder: network access will be disabled during build
I: Current time: Wed Nov 20 15:57:10 +14 2024
I: pbuilder-time-stamp: 1732067830
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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_3.3.20220408-4.dsc]
I: copying [./phyml_3.3.20220408.orig.tar.gz]
I: copying [./phyml_3.3.20220408-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Nov 9 19:15:00 2024
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_3.3.20220408-4.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_3.3.20220408-4.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 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/28381/tmp/hooks/D01_modify_environment starting
debug: Running on ff4a.
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 Nov 20 01:57 /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/28381/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/28381/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]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
BASH_VERSION='5.2.32(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=armhf
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=arm
HOST_ARCH=armhf
IFS='
'
INVOCATION_ID=d6beb83a187848618d764deaa4c2fc80
LANG=C
LANGUAGE=it_CH:it
LC_ALL=C
MACHTYPE=arm-unknown-linux-gnueabihf
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnueabihf
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=28381
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.h6gSqpUX/pbuilderrc_J9ww --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.h6gSqpUX/b2 --logfile b2/build.log phyml_3.3.20220408-4.dsc'
SUDO_GID=113
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://10.0.0.15:3142/
I: uname -a
Linux i-capture-the-hostname 6.1.0-27-armmp-lpae #1 SMP Debian 6.1.115-1 (2024-11-01) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/28381/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <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), pkgconf, mpi-default-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 ... 19686 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 pkgconf; however:
Package pkgconf is not installed.
pbuilder-satisfydepends-dummy depends on mpi-default-dev; however:
Package mpi-default-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-14{a} gfortran-14-arm-linux-gnueabihf{a} groff-base{a} hwloc-nox{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc15{a} libicu72{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpich-dev{a} libmpich12{a} libnuma-dev{a} libnuma1{a} libpipeline1{a} libpkgconf3{a} libslurm41t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mpi-default-dev{a} mpich{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libhwloc-plugins libmail-sendmail-perl lynx wget
0 packages upgraded, 49 newly installed, 0 to remove and 0 not upgraded.
Need to get 34.5 MB of archives. After unpacking 114 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf chrpath armhf 0.18-1 [12.6 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 22 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 23 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-8 [263 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf libgfortran-14-dev armhf 14.2.0-8 [315 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-8 [8724 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf gfortran-14 armhf 14.2.0-8 [12.2 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf libhwloc15 armhf 2.11.2-1 [134 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf hwloc-nox armhf 2.11.2-1 [201 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf libnuma1 armhf 2.0.18-1+b1 [18.9 kB]
Get: 38 http://deb.debian.org/debian unstable/main armhf libnuma-dev armhf 2.0.18-1+b1 [34.6 kB]
Get: 39 http://deb.debian.org/debian unstable/main armhf libltdl7 armhf 2.4.7-8 [390 kB]
Get: 40 http://deb.debian.org/debian unstable/main armhf libltdl-dev armhf 2.4.7-8 [162 kB]
Get: 41 http://deb.debian.org/debian unstable/main armhf libhwloc-dev armhf 2.11.2-1 [226 kB]
Get: 42 http://deb.debian.org/debian unstable/main armhf libmpich12 armhf 4.2.0-14 [1498 kB]
Get: 43 http://deb.debian.org/debian unstable/main armhf libslurm41t64 armhf 24.05.4-1 [683 kB]
Get: 44 http://deb.debian.org/debian unstable/main armhf mpich armhf 4.2.0-14 [223 kB]
Get: 45 http://deb.debian.org/debian unstable/main armhf libmpich-dev armhf 4.2.0-14 [2410 kB]
Get: 46 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB]
Get: 47 http://deb.debian.org/debian unstable/main armhf mpi-default-dev armhf 1.17 [3148 B]
Get: 48 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB]
Get: 49 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB]
Fetched 34.5 MB in 3s (13.0 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19686 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:armhf.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic1t64:armhf (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.22.5-2_armhf.deb ...
Unpacking gettext-base (0.22.5-2) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-5_armhf.deb ...
Unpacking groff-base (1.23.0-5) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.2-11_armhf.deb ...
Unpacking bsdextrautils (2.40.2-11) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ...
Unpacking autopoint (0.22.5-2) ...
Selecting previously unselected package chrpath.
Preparing to unpack .../15-chrpath_0.18-1_armhf.deb ...
Unpacking chrpath (0.18-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ...
Unpacking libdebhelper-perl (13.20) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-8_all.deb ...
Unpacking libtool (2.4.7-8) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:armhf.
Preparing to unpack .../22-libelf1t64_0.192-4_armhf.deb ...
Unpacking libelf1t64:armhf (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1+b2_armhf.deb ...
Unpacking dwz (0.15-1+b2) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../24-libicu72_72.1-5+b1_armhf.deb ...
Unpacking libicu72:armhf (72.1-5+b1) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ...
Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.22.5-2_armhf.deb ...
Unpacking gettext (0.22.5-2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.20_all.deb ...
Unpacking debhelper (13.20) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../30-libgfortran5_14.2.0-8_armhf.deb ...
Unpacking libgfortran5:armhf (14.2.0-8) ...
Selecting previously unselected package libgfortran-14-dev:armhf.
Preparing to unpack .../31-libgfortran-14-dev_14.2.0-8_armhf.deb ...
Unpacking libgfortran-14-dev:armhf (14.2.0-8) ...
Selecting previously unselected package gfortran-14-arm-linux-gnueabihf.
Preparing to unpack .../32-gfortran-14-arm-linux-gnueabihf_14.2.0-8_armhf.deb ...
Unpacking gfortran-14-arm-linux-gnueabihf (14.2.0-8) ...
Selecting previously unselected package gfortran-14.
Preparing to unpack .../33-gfortran-14_14.2.0-8_armhf.deb ...
Unpacking gfortran-14 (14.2.0-8) ...
Selecting previously unselected package libhwloc15:armhf.
Preparing to unpack .../34-libhwloc15_2.11.2-1_armhf.deb ...
Unpacking libhwloc15:armhf (2.11.2-1) ...
Selecting previously unselected package hwloc-nox.
Preparing to unpack .../35-hwloc-nox_2.11.2-1_armhf.deb ...
Unpacking hwloc-nox (2.11.2-1) ...
Selecting previously unselected package libnuma1:armhf.
Preparing to unpack .../36-libnuma1_2.0.18-1+b1_armhf.deb ...
Unpacking libnuma1:armhf (2.0.18-1+b1) ...
Selecting previously unselected package libnuma-dev:armhf.
Preparing to unpack .../37-libnuma-dev_2.0.18-1+b1_armhf.deb ...
Unpacking libnuma-dev:armhf (2.0.18-1+b1) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../38-libltdl7_2.4.7-8_armhf.deb ...
Unpacking libltdl7:armhf (2.4.7-8) ...
Selecting previously unselected package libltdl-dev:armhf.
Preparing to unpack .../39-libltdl-dev_2.4.7-8_armhf.deb ...
Unpacking libltdl-dev:armhf (2.4.7-8) ...
Selecting previously unselected package libhwloc-dev:armhf.
Preparing to unpack .../40-libhwloc-dev_2.11.2-1_armhf.deb ...
Unpacking libhwloc-dev:armhf (2.11.2-1) ...
Selecting previously unselected package libmpich12:armhf.
Preparing to unpack .../41-libmpich12_4.2.0-14_armhf.deb ...
Unpacking libmpich12:armhf (4.2.0-14) ...
Selecting previously unselected package libslurm41t64.
Preparing to unpack .../42-libslurm41t64_24.05.4-1_armhf.deb ...
Unpacking libslurm41t64 (24.05.4-1) ...
Selecting previously unselected package mpich.
Preparing to unpack .../43-mpich_4.2.0-14_armhf.deb ...
Unpacking mpich (4.2.0-14) ...
Selecting previously unselected package libmpich-dev:armhf.
Preparing to unpack .../44-libmpich-dev_4.2.0-14_armhf.deb ...
Unpacking libmpich-dev:armhf (4.2.0-14) ...
Selecting previously unselected package libpkgconf3:armhf.
Preparing to unpack .../45-libpkgconf3_1.8.1-4_armhf.deb ...
Unpacking libpkgconf3:armhf (1.8.1-4) ...
Selecting previously unselected package mpi-default-dev.
Preparing to unpack .../46-mpi-default-dev_1.17_armhf.deb ...
Unpacking mpi-default-dev (1.17) ...
Selecting previously unselected package pkgconf-bin.
Preparing to unpack .../47-pkgconf-bin_1.8.1-4_armhf.deb ...
Unpacking pkgconf-bin (1.8.1-4) ...
Selecting previously unselected package pkgconf:armhf.
Preparing to unpack .../48-pkgconf_1.8.1-4_armhf.deb ...
Unpacking pkgconf:armhf (1.8.1-4) ...
Setting up libpipeline1:armhf (1.5.8-1) ...
Setting up libicu72:armhf (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-11) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.20) ...
Setting up libmagic1t64:armhf (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-2) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:armhf (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libpkgconf3:armhf (1.8.1-4) ...
Setting up libhwloc15:armhf (2.11.2-1) ...
Setting up autopoint (0.22.5-2) ...
Setting up pkgconf-bin (1.8.1-4) ...
Setting up libltdl7:armhf (2.4.7-8) ...
Setting up libgfortran5:armhf (14.2.0-8) ...
Setting up autoconf (2.72-3) ...
Setting up libnuma1:armhf (2.0.18-1+b1) ...
Setting up dwz (0.15-1+b2) ...
Setting up libmpich12:armhf (4.2.0-14) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:armhf (0.0.8-1+b2) ...
Setting up libslurm41t64 (24.05.4-1) ...
Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up chrpath (0.18-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libgfortran-14-dev:armhf (14.2.0-8) ...
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.22.5-2) ...
Setting up libtool (2.4.7-8) ...
Setting up hwloc-nox (2.11.2-1) ...
Setting up pkgconf:armhf (1.8.1-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnuma-dev:armhf (2.0.18-1+b1) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:armhf (2.4.7-8) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-5) ...
Setting up libhwloc-dev:armhf (2.11.2-1) ...
Setting up gfortran-14-arm-linux-gnueabihf (14.2.0-8) ...
Setting up mpich (4.2.0-14) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran-14 (14.2.0-8) ...
Setting up debhelper (13.20) ...
Setting up libmpich-dev:armhf (4.2.0-14) ...
update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up mpi-default-dev (1.17) ...
Processing triggers for libc-bin (2.40-3) ...
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: user script /srv/workspace/pbuilder/28381/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/28381/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/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_3.3.20220408-4_source.changes
dpkg-buildpackage: info: source package phyml
dpkg-buildpackage: info: source version 3:3.3.20220408-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/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.m4:663: 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.m4:1785: 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/reproducible-path/phyml-3.3.20220408'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
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: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
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 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 -j4 "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
make all-recursive
make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
Making all in src
make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src'
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o main.o main.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o utilities.o utilities.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o optimiz.o optimiz.c
.: Building [phyml]. Version 3.3.3:3.3.20220408-4 :.
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o lk.o lk.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o bionj.o bionj.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o models.o models.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o free.o free.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o help.o help.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o simu.o simu.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o eigen.o eigen.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o pars.o pars.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o alrt.o alrt.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o interface.o interface.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o cl.o cl.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o spr.o spr.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o draw.o draw.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o stats.o stats.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o io.o io.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o make.o make.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. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o nexus.o nexus.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o init.o init.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o xml.o xml.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sse.o sse.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o avx.o avx.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o tbe.o tbe.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o ancestral.o ancestral.c
gcc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mixt.o mixt.c
gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -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/reproducible-path/phyml-3.3.20220408/src'
make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
# move phyml binary to temporary dir inside debian/
mkdir -p /build/reproducible-path/phyml-3.3.20220408/debian/bin
mv src/phyml /build/reproducible-path/phyml-3.3.20220408/debian/bin/phyml
/usr/bin/make distclean
make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
Making distclean in src
make[3]: Entering directory '/build/reproducible-path/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/mpi_boot.Po
rm -f ./.deps/nexus.Po
rm -f ./.deps/optimiz.Po
rm -f ./.deps/pars.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/reproducible-path/phyml-3.3.20220408/src'
make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/phyml-3.3.20220408'
dh_auto_configure -- --enable-phyml-mpi
./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
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: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
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 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 -j4 "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
make all-recursive
make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
Making all in src
make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src'
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o main.o main.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o utilities.o utilities.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o optimiz.o optimiz.c
.: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-4 :.
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o lk.o lk.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o bionj.o bionj.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o models.o models.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o free.o free.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o help.o help.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o simu.o simu.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o eigen.o eigen.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o pars.o pars.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o alrt.o alrt.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o interface.o interface.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o cl.o cl.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o spr.o spr.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o draw.o draw.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o stats.o stats.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o io.o io.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o make.o make.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;
| ^~~~
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o nexus.o nexus.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o init.o init.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o xml.o xml.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mixt.o mixt.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o tbe.o tbe.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sse.o sse.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o avx.o avx.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o ancestral.o ancestral.c
mpicc -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mpi_boot.o mpi_boot.c
mpicc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml-mpi 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 mixt.o tbe.o sse.o avx.o ancestral.o mpi_boot.o -lm -lm
Done.
make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src'
make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
# move phyml binary to temporary dir inside debian/
# mkdir -p /build/reproducible-path/phyml-3.3.20220408/debian/bin
mv src/phyml-mpi /build/reproducible-path/phyml-3.3.20220408/debian/bin/phyml-mpi
mv phyml-manual.pdf doc
make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
dh_auto_test
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
Making check in src
make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src'
mpicc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml-mpi 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 mixt.o tbe.o sse.o avx.o ancestral.o mpi_boot.o -lm -lm
.: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-4 :.
Done.
make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src'
make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
dh_auto_install
make -j4 install DESTDIR=/build/reproducible-path/phyml-3.3.20220408/debian/phyml AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
Making install in src
make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src'
.: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-4 :.
Done.
make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src'
/usr/bin/mkdir -p '/build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/bin'
make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c phyml-mpi '/build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src'
make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src'
make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/phyml-3.3.20220408'
make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
# install phyml binary we have kept safe above
mkdir -p /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin
mv /build/reproducible-path/phyml-3.3.20220408/debian/bin/* /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin
chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml*
make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
dh_install
debian/rules override_dh_installdocs
make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
dh_installdocs
mv /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf
make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/phyml-3.3.20220408'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/phyml-3.3.20220408'
dh_missing
debian/rules override_dh_dwz
make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408'
echo "Do not run dh_dwz"
Do not run dh_dwz
make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'phyml' in '../phyml_3.3.20220408-4_armhf.deb'.
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20220408-4_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../phyml_3.3.20220408-4_armhf.buildinfo
dpkg-genchanges --build=binary -O../phyml_3.3.20220408-4_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/28381/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/28381/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/28381 and its subdirectories
I: Current time: Wed Nov 20 16:01:50 +14 2024
I: pbuilder-time-stamp: 1732068110