I: pbuilder: network access will be disabled during build
I: Current time: Tue Mar 24 14:27:01 +14 2026
I: pbuilder-time-stamp: 1774312021
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
dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-4.dsc: unsupported subcommand
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/3666850/tmp/hooks/D01_modify_environment starting
debug: Running on ionos5-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Mar 24 00:27 /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/3666850/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/3666850/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=bb6e79a1be884dbbac1e84731bdd7f89
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=3666850
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.wftqQSiU/pbuilderrc_4ioR --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.wftqQSiU/b2 --logfile b2/build.log phyml_3.3.20220408-4.dsc'
SUDO_GID=110
SUDO_UID=105
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3666850/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <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 ... 19798 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-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libcbor0.10{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1t64{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth
0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded.
Need to get 108 MB of archives. After unpacking 436 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.9p2-1 [970 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 33 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-17 [879 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17 [11.7 MB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-17 [14.0 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 56.0-1 [62.1 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 56.0-1 [356 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-21 [23.6 MB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 56.0-1 [70.1 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-3 [415 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-3 [167 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.12.0-1 [255 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.12.0-1 [18.1 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 56.0-1 [29.7 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 56.0-1 [44.3 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 56.0-1 [653 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.6-3 [651 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.7-1 [2365 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.7-1 [97.2 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.6-3 [3961 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.7-1 [189 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.7-1 [1089 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.18 [3372 B]
Get: 104 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Fetched 108 MB in 6s (18.2 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
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Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libffi8:amd64 (3.4.7-1) ...
Setting up libnuma1:amd64 (2.0.18-1+b1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ...
Setting up libpsm2-2 (11.2.185-2.1) ...
Setting up openmpi-common (5.0.7-1) ...
Setting up libx11-6:amd64 (2:1.8.10-2) ...
Setting up libkrb5-3:amd64 (1.21.3-4) ...
Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ...
update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libfido2-1:amd64 (1.15.0-1+b1) ...
Setting up libdrm-common (2.4.123-1) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up chrpath (0.18-1) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libgfortran-14-dev:amd64 (14.2.0-17) ...
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b3) ...
Setting up gfortran-14-x86-64-linux-gnu (14.2.0-17) ...
Setting up pkgconf:amd64 (1.8.1-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnuma-dev:amd64 (2.0.18-1+b1) ...
Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ...
Setting up libxnvctrl0:amd64 (535.171.04-1+b2) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:amd64 (2.5.4-3) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libllvm17t64:amd64 (1:17.0.6-21) ...
Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ...
Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up libdrm2:amd64 (2.4.123-1) ...
Setting up libnl-3-dev:amd64 (3.7.0-0.3+b1) ...
Setting up groff-base (1.23.0-7) ...
Setting up libhwloc-dev:amd64 (2.12.0-1) ...
Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ...
Setting up gfortran-14 (14.2.0-17) ...
Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ...
Setting up libibverbs1:amd64 (56.0-1) ...
Setting up ibverbs-providers:amd64 (56.0-1) ...
Setting up openssh-client (1:9.9p2-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhwloc-plugins:amd64 (2.12.0-1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ...
Setting up libevent-dev (2.1.12-stable-10+b1) ...
Setting up libpmix2t64:amd64 (5.0.6-3) ...
Setting up librdmacm1t64:amd64 (56.0-1) ...
Setting up libpmix-dev:amd64 (5.0.6-3) ...
Setting up libhsakmt1:amd64 (6.2.4+ds-1) ...
Setting up libfabric1:amd64 (1.17.0-3.1) ...
Setting up debhelper (13.24.1) ...
Setting up libibverbs-dev:amd64 (56.0-1) ...
Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ...
Setting up libamdhip64-5 (5.7.1-5) ...
Setting up libucx0:amd64 (1.17.0+ds-3) ...
Setting up libopenmpi40:amd64 (5.0.7-1) ...
Setting up openmpi-bin (5.0.7-1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:amd64 (5.0.7-1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode
Setting up mpi-default-dev (1.18) ...
Processing triggers for libc-bin (2.40-7) ...
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/3666850/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/3666850/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 amd64
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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
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 xargs -n works... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
configure: "On arch x86_64-pc-linux-gnu use MSSE = -msse"
checking for log in -lm... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
checking 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 -j42 "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.. -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 -fcf-protection -c -o main.o main.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o utilities.o utilities.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o optimiz.o optimiz.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o lk.o lk.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o bionj.o bionj.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o models.o models.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o free.o free.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o help.o help.c
gcc -I. -I.. -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 -fcf-protection -c -o simu.o simu.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o eigen.o eigen.c
.: Building [phyml]. Version 3.3.3:3.3.20220408-4 :.
gcc -I. -I.. -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 -fcf-protection -c -o pars.o pars.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alrt.o alrt.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o interface.o interface.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cl.o cl.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o spr.o spr.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o draw.o draw.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o stats.o stats.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o io.o io.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o make.o make.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o nexus.o nexus.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o init.o init.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o xml.o xml.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sse.o sse.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o avx.o avx.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o tbe.o tbe.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ancestral.o ancestral.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o mixt.o mixt.c
io.c: In function 'Sub_Trees':
io.c:511:25: warning: 'subs' may be used uninitialized [-Wmaybe-uninitialized]
511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:479:10: note: 'subs' was declared here
479 | char **subs;
| ^~~~
gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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'
rm -f phyml
rm -f *.o
rm -f *.tab.c
rm -f
test . = "." || 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'
rm -f
test . = "." || 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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-phyml-mpi
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
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 xargs -n works... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
configure: "On arch x86_64-pc-linux-gnu use MSSE = -msse"
checking for log in -lm... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
checking 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 -j42 "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.. -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 -fcf-protection -c -o main.o main.c
mpicc -I. -I.. -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 -fcf-protection -c -o utilities.o utilities.c
mpicc -I. -I.. -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 -fcf-protection -c -o optimiz.o optimiz.c
mpicc -I. -I.. -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 -fcf-protection -c -o lk.o lk.c
mpicc -I. -I.. -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 -fcf-protection -c -o bionj.o bionj.c
mpicc -I. -I.. -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 -fcf-protection -c -o models.o models.c
mpicc -I. -I.. -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 -fcf-protection -c -o free.o free.c
mpicc -I. -I.. -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 -fcf-protection -c -o help.o help.c
mpicc -I. -I.. -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 -fcf-protection -c -o simu.o simu.c
.: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-4 :.
mpicc -I. -I.. -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 -fcf-protection -c -o eigen.o eigen.c
mpicc -I. -I.. -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 -fcf-protection -c -o pars.o pars.c
mpicc -I. -I.. -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 -fcf-protection -c -o alrt.o alrt.c
mpicc -I. -I.. -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 -fcf-protection -c -o interface.o interface.c
mpicc -I. -I.. -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 -fcf-protection -c -o cl.o cl.c
mpicc -I. -I.. -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 -fcf-protection -c -o spr.o spr.c
mpicc -I. -I.. -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 -fcf-protection -c -o draw.o draw.c
mpicc -I. -I.. -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 -fcf-protection -c -o stats.o stats.c
mpicc -I. -I.. -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 -fcf-protection -c -o io.o io.c
mpicc -I. -I.. -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 -fcf-protection -c -o make.o make.c
mpicc -I. -I.. -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 -fcf-protection -c -o nexus.o nexus.c
mpicc -I. -I.. -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 -fcf-protection -c -o init.o init.c
mpicc -I. -I.. -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 -fcf-protection -c -o xml.o xml.c
mpicc -I. -I.. -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 -fcf-protection -c -o mixt.o mixt.c
mpicc -I. -I.. -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 -fcf-protection -c -o tbe.o tbe.c
mpicc -I. -I.. -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 -fcf-protection -c -o sse.o sse.c
mpicc -I. -I.. -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 -fcf-protection -c -o avx.o avx.c
mpicc -I. -I.. -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 -fcf-protection -c -o ancestral.o ancestral.c
mpicc -I. -I.. -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 -fcf-protection -c -o mpi_boot.o mpi_boot.c
io.c: In function 'Sub_Trees':
io.c:511:25: warning: 'subs' may be used uninitialized [-Wmaybe-uninitialized]
511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:479:10: note: 'subs' was declared here
479 | char **subs;
| ^~~~
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 -fcf-protection -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 -j42 check "TESTSUITEFLAGS=-j42 --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 -fcf-protection -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 -j42 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'
make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/bin'
/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
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'phyml' in '../phyml_3.3.20220408-4_amd64.deb'.
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20220408-4_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../phyml_3.3.20220408-4_amd64.buildinfo
dpkg-genchanges --build=binary -O../phyml_3.3.20220408-4_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/3666850/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/3666850/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/3666850 and its subdirectories
I: Current time: Tue Mar 24 14:28:45 +14 2026
I: pbuilder-time-stamp: 1774312125