Raspbian Package Auto-Building

Build log for phyml (3:3.3.20211021-1) on armhf

phyml3:3.3.20211021-1armhf → 2021-11-21 06:39:49

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04

+==============================================================================+
| phyml 3:3.3.20211021-1 (armhf)               Sun, 21 Nov 2021 06:21:27 +0000 |
+==============================================================================+

Package: phyml
Version: 3:3.3.20211021-1
Source Version: 3:3.3.20211021-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-eb758620-065c-4cff-ae0b-6fafe02cdcf2' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 26.0 MB in 26s (1018 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'phyml' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/phyml.git
Please use:
git clone https://salsa.debian.org/med-team/phyml.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1825 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main phyml 3:3.3.20211021-1 (dsc) [2138 B]
Get:2 http://172.17.0.1/private bookworm-staging/main phyml 3:3.3.20211021-1 (tar) [1802 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main phyml 3:3.3.20211021-1 (diff) [20.6 kB]
Fetched 1825 kB in 0s (5486 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phyml-BKfbkQ/phyml-3.3.20211021' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phyml-BKfbkQ' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-UZ5S6U/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-UZ5S6U/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2650 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 30 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12500 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), pkg-config, libopenmpi-dev, chrpath
Filtered Build-Depends: debhelper-compat (= 13), pkg-config, libopenmpi-dev, chrpath
dpkg-deb: building package 'sbuild-build-depends-phyml-dummy' in '/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive/sbuild-build-depends-phyml-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-phyml-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ Sources [513 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ Packages [592 B]
Fetched 2438 B in 1s (3247 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install phyml build dependencies (apt-based resolver)
-----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils chrpath cpp-11
  debhelper dh-autoreconf dh-strip-nondeterminism dwz file gcc-11 gettext
  gettext-base gfortran-11 groff-base ibverbs-providers intltool-debian
  libarchive-zip-perl libbsd0 libcbor0 libdebhelper-perl libedit2 libelf1
  libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
  libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1
  libfile-stripnondeterminism-perl libgcc-11-dev libgfortran-11-dev
  libgfortran5 libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc15
  libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libltdl-dev
  libltdl7 libmagic-mgc libmagic1 libmd0 libnl-3-200 libnl-3-dev
  libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
  libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 librdmacm1
  libsigsegv2 libsub-override-perl libtool libuchardet0 libx11-6 libx11-data
  libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db
  ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
  po-debconf sensible-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc gcc-11-locales dh-make
  gcc-11-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-11-doc
  libcoarrays-dev groff libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils
  gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran
  | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass
  libmail-box-perl
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs javascript-common libcoarrays-openmpi-dev xauth
  libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils chrpath cpp-11
  debhelper dh-autoreconf dh-strip-nondeterminism dwz file gcc-11 gettext
  gettext-base gfortran-11 groff-base ibverbs-providers intltool-debian
  libarchive-zip-perl libbsd0 libcbor0 libdebhelper-perl libedit2 libelf1
  libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
  libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1
  libfile-stripnondeterminism-perl libgcc-11-dev libgfortran-11-dev
  libgfortran5 libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc15
  libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libltdl-dev
  libltdl7 libmagic-mgc libmagic1 libmd0 libnl-3-200 libnl-3-dev
  libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
  libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 librdmacm1
  libsigsegv2 libsub-override-perl libtool libuchardet0 libx11-6 libx11-data
  libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db
  ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
  po-debconf sbuild-build-depends-phyml-dummy sensible-utils zlib1g-dev
0 upgraded, 87 newly installed, 0 to remove and 30 not upgraded.
Need to get 165 MB of archives.
After this operation, 541 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UZ5S6U/apt_archive ./ sbuild-build-depends-phyml-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libfido2-1 armhf 1.8.0-1 [55.9 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf openssh-client armhf 1:8.7p1-2 [881 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf cpp-11 armhf 11.2.0-10+rpi1 [42.3 MB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libgcc-11-dev armhf 11.2.0-10+rpi1 [697 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf gcc-11 armhf 11.2.0-10+rpi1 [48.3 MB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-10+rpi1 [234 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libgfortran-11-dev armhf 11.2.0-10+rpi1 [280 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf gfortran-11 armhf 11.2.0-10+rpi1 [43.8 MB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libibverbs1 armhf 36.0-2 [53.2 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf ibverbs-providers armhf 36.0-2 [27.6 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf librdmacm1 armhf 36.0-2 [60.4 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.1-1 [1210 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libhwloc15 armhf 2.6.0-1 [127 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.14-3 [21.8 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.14-3 [34.7 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.6.0-1 [198 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libxnvctrl0 armhf 470.82.00-1 [26.0 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-3 [39.9 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.6.0-1 [20.2 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libibverbs-dev armhf 36.0-2 [185 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-8 [315 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.0+dfsg-1 [250 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libpmix2 armhf 4.1.1~rc5-1 [476 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.2~rc1-5+rpi1 [1779 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf openmpi-common all 4.1.2~rc1-5+rpi1 [180 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libpmix-dev armhf 4.1.1~rc5-1 [640 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.2~rc1-5+rpi1 [209 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.2~rc1-5+rpi1 [937 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 165 MB in 18s (9352 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12500 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.37.2-4_armhf.deb ...
Unpacking bsdextrautils (2.37.2-4) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ...
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Preparing to unpack .../02-groff-base_1.22.4-7_armhf.deb ...
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Preparing to unpack .../03-libpipeline1_1.5.4-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.4-1) ...
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Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
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Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnuma-dev:armhf (2.0.14-3) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libjs-jquery-ui (1.13.0+dfsg-1) ...
Setting up libevent-dev (2.1.12-stable-1) ...
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Setting up groff-base (1.22.4-7) ...
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Setting up automake (1:1.16.5-1.1) ...
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Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up dh-autoreconf (20) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
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Setting up libopenmpi3:armhf (4.1.2~rc1-5+rpi1) ...
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Setting up openmpi-bin (4.1.2~rc1-5+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.1.2~rc1-5+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 gcc-10_10.3.0-11+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.9-2+rpi1
Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 chrpath_0.16-2 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-11+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-1 debconf_1.5.78 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-11+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran-11_11.2.0-10+rpi1 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 ibverbs-providers_36.0-2 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-4 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcbor0_0.5.0+dfsg-2 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libedit2_3.1-20210910-1 libelf1_0.185-2 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libext2fs2_1.46.4-1 libfabric1_1.11.0-2 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfido2-1_1.8.0-1 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-11+rpi1 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgfortran-11-dev_11.2.0-10+rpi1 libgfortran5_11.2.0-10+rpi1 libglib2.0-0_2.70.1-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhwloc-dev_2.6.0-1 libhwloc-plugins_2.6.0-1 libhwloc15_2.6.0-1 libibverbs-dev_36.0-2 libibverbs1_36.0-2 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjs-jquery_3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui_1.13.0+dfsg-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.4-1 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.14-3 libnuma1_2.0.14-3 libopenmpi-dev_4.1.2~rc1-5+rpi1 libopenmpi3_4.1.2~rc1-5+rpi1 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpciaccess0_0.16-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libpmix-dev_4.1.1~rc5-1 libpmix2_4.1.1~rc5-1 librdmacm1_36.0-2 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.2-2+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.5-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.5-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.12+dfsg-5 libxnvctrl0_470.82.00-1 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.9-2+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 ocl-icd-libopencl1_2.2.14-3 openmpi-bin_4.1.2~rc1-5+rpi1 openmpi-common_4.1.2~rc1-5+rpi1 openssh-client_1:8.7p1-2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.izBMBitM/trustedkeys.kbx': General error
gpgv: Signature made Fri Nov 19 00:24:41 2021 UTC
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./phyml_3.3.20211021-1.dsc
dpkg-source: info: extracting phyml in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking phyml_3.3.20211021.orig.tar.gz
dpkg-source: info: unpacking phyml_3.3.20211021-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying sse_only_if_supported.patch
dpkg-source: info: applying no-stdc++.patch
dpkg-source: info: applying no-configure-ac-date.patch
dpkg-source: info: applying fix_declaration_of_temp.patch
dpkg-source: info: applying fix_wrong_initialisation_of_array.patch
dpkg-source: info: applying no-march-native.patch
dpkg-source: info: applying cross.patch
dpkg-source: info: applying nodup-am-init-automake.patch
dpkg-source: info: applying apply-cflags.patch
dpkg-source: info: applying filter-sse3-intrinsics.patch
dpkg-source: info: applying apply-ldflags.patch

Check disc space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-eb758620-065c-4cff-ae0b-6fafe02cdcf2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package phyml
dpkg-buildpackage: info: source version 3:3.3.20211021-1
dpkg-buildpackage: info: source distribution unstable
 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 '/<<PKGBUILDDIR>>'
# 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 '/<<PKGBUILDDIR>>'
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   debian/rules override_dh_autoreconf
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_autoreconf --as-needed
configure.ac:33: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:33: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:33: the top level
configure.ac:54: warning: The macro `AC_FUNC_SETVBUF_REVERSED' is obsolete.  Remove it and all references to SETVBUF_REVERSED.
./lib/autoconf/functions.m4:1766: AC_FUNC_SETVBUF_REVERSED is expanded from...
configure.ac:54: the top level
configure.ac:16: installing './compile'
configure.ac:14: installing './config.guess'
configure.ac:14: installing './config.sub'
configure.ac:5: installing './install-sh'
configure.ac:5: installing './missing'
src/Makefile.am: installing './depcomp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# 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... /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... /bin/grep
checking for egrep... /bin/grep -E
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now"
	make -j4 "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make  all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c

gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utilities.o utilities.c

gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o optimiz.o optimiz.c
.:  Building [phyml]. Version 3.3.3:3.3.20211021-1 :.


gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lk.o lk.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bionj.o bionj.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o models.o models.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o free.o free.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simu.o simu.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eigen.o eigen.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pars.o pars.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alrt.o alrt.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o interface.o interface.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cl.o cl.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o spr.o spr.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o draw.o draw.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stats.o stats.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o make.o make.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o nexus.o nexus.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o init.o init.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xml.o xml.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sse.o sse.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o avx.o avx.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tbe.o tbe.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ancestral.o ancestral.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mixt.o mixt.c
gcc  -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o io.o make.o nexus.o init.o xml.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm 

Done.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# move phyml binary to temporary dir inside debian/
mkdir -p /<<PKGBUILDDIR>>/debian/bin
mv src/phyml /<<PKGBUILDDIR>>/debian/bin/phyml
/usr/bin/make distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making distclean in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
test -z "phyml" || rm -f phyml
rm -f *.o
rm -f *.tab.c
test -z "" || rm -f 
test . = "." || test -z "" || rm -f 
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
rm -f ./.deps/alrt.Po
rm -f ./.deps/ancestral.Po
rm -f ./.deps/avx.Po
rm -f ./.deps/beagle_utils.Po
rm -f ./.deps/bionj.Po
rm -f ./.deps/checkpoint.Po
rm -f ./.deps/cl.Po
rm -f ./.deps/date.Po
rm -f ./.deps/draw.Po
rm -f ./.deps/eigen.Po
rm -f ./.deps/free.Po
rm -f ./.deps/geo.Po
rm -f ./.deps/help.Po
rm -f ./.deps/init.Po
rm -f ./.deps/interface.Po
rm -f ./.deps/invitee.Po
rm -f ./.deps/io.Po
rm -f ./.deps/lk.Po
rm -f ./.deps/location.Po
rm -f ./.deps/main.Po
rm -f ./.deps/make.Po
rm -f ./.deps/mcmc.Po
rm -f ./.deps/mg.Po
rm -f ./.deps/mixt.Po
rm -f ./.deps/models.Po
rm -f ./.deps/nexus.Po
rm -f ./.deps/optimiz.Po
rm -f ./.deps/pars.Po
rm -f ./.deps/phyml_mpi-alrt.Po
rm -f ./.deps/phyml_mpi-ancestral.Po
rm -f ./.deps/phyml_mpi-avx.Po
rm -f ./.deps/phyml_mpi-bionj.Po
rm -f ./.deps/phyml_mpi-cl.Po
rm -f ./.deps/phyml_mpi-draw.Po
rm -f ./.deps/phyml_mpi-eigen.Po
rm -f ./.deps/phyml_mpi-free.Po
rm -f ./.deps/phyml_mpi-help.Po
rm -f ./.deps/phyml_mpi-init.Po
rm -f ./.deps/phyml_mpi-interface.Po
rm -f ./.deps/phyml_mpi-io.Po
rm -f ./.deps/phyml_mpi-lk.Po
rm -f ./.deps/phyml_mpi-main.Po
rm -f ./.deps/phyml_mpi-make.Po
rm -f ./.deps/phyml_mpi-mixt.Po
rm -f ./.deps/phyml_mpi-models.Po
rm -f ./.deps/phyml_mpi-mpi_boot.Po
rm -f ./.deps/phyml_mpi-nexus.Po
rm -f ./.deps/phyml_mpi-optimiz.Po
rm -f ./.deps/phyml_mpi-pars.Po
rm -f ./.deps/phyml_mpi-simu.Po
rm -f ./.deps/phyml_mpi-spr.Po
rm -f ./.deps/phyml_mpi-sse.Po
rm -f ./.deps/phyml_mpi-stats.Po
rm -f ./.deps/phyml_mpi-tbe.Po
rm -f ./.deps/phyml_mpi-utilities.Po
rm -f ./.deps/phyml_mpi-xml.Po
rm -f ./.deps/phyrex.Po
rm -f ./.deps/rates.Po
rm -f ./.deps/rrw.Po
rm -f ./.deps/rw.Po
rm -f ./.deps/simu.Po
rm -f ./.deps/slfv.Po
rm -f ./.deps/spr.Po
rm -f ./.deps/sse.Po
rm -f ./.deps/stats.Po
rm -f ./.deps/tbe.Po
rm -f ./.deps/times.Po
rm -f ./.deps/tiporder.Po
rm -f ./.deps/utilities.Po
rm -f ./.deps/xml.Po
rm -f Makefile
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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... /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... /bin/grep
checking for egrep... /bin/grep -E
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for mpi-c... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now"
	make -j4 "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make  all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c

gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c

.:  Building [phyml-mpi]. Version 3.3.3:3.3.20211021-1 :.


gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c
In file included from lk.h:18,
                 from lk.c:14:
utilities.h:18: warning: "_POSIX_C_SOURCE" redefined
   18 | #define _POSIX_C_SOURCE 200112L
      | 
In file included from /usr/include/assert.h:35,
                 from lk.c:13:
/usr/include/features.h:310: note: this is the location of the previous definition
  310 | # define _POSIX_C_SOURCE 199506L
      | 
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c
In file included from cl.h:21,
                 from cl.c:13:
utilities.h:18: warning: "_POSIX_C_SOURCE" redefined
   18 | #define _POSIX_C_SOURCE 200112L
      | 
In file included from /usr/include/unistd.h:25,
                 from cl.h:19,
                 from cl.c:13:
/usr/include/features.h:310: note: this is the location of the previous definition
  310 | # define _POSIX_C_SOURCE 199506L
      | 
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c
In file included from sse.h:18,
                 from sse.c:14:
utilities.h:18: warning: "_POSIX_C_SOURCE" redefined
   18 | #define _POSIX_C_SOURCE 200112L
      | 
In file included from /usr/include/assert.h:35,
                 from sse.c:13:
/usr/include/features.h:310: note: this is the location of the previous definition
  310 | # define _POSIX_C_SOURCE 199506L
      | 
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c
In file included from avx.h:18,
                 from avx.c:14:
utilities.h:18: warning: "_POSIX_C_SOURCE" redefined
   18 | #define _POSIX_C_SOURCE 200112L
      | 
In file included from /usr/include/assert.h:35,
                 from avx.c:13:
/usr/include/features.h:310: note: this is the location of the previous definition
  310 | # define _POSIX_C_SOURCE 199506L
      | 
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c
gcc  -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c
gcc -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm 

Done.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# move phyml binary to temporary dir inside debian/
# mkdir -p /<<PKGBUILDDIR>>/debian/bin
mv src/phyml-mpi /<<PKGBUILDDIR>>/debian/bin/phyml-mpi
mv phyml-manual.pdf doc
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -a
	make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'


gcc -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm 
.:  Building [phyml-mpi]. Version 3.3.3:3.3.20211021-1 :.



Done.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_prep -a
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
	make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/phyml AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'


.:  Building [phyml-mpi]. Version 3.3.3:3.3.20211021-1 :.



Done.
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Nothing to be done for 'install-data-am'.
 /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/phyml/usr/bin'
  /usr/bin/install -c phyml-mpi '/<<PKGBUILDDIR>>/debian/phyml/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# install phyml binary we have kept safe above
mkdir -p /<<PKGBUILDDIR>>/debian/phyml/usr/lib/phyml/bin
mv /<<PKGBUILDDIR>>/debian/bin/* /<<PKGBUILDDIR>>/debian/phyml/usr/lib/phyml/bin
chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -a
   debian/rules override_dh_installdocs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installdocs
mv /<<PKGBUILDDIR>>/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /<<PKGBUILDDIR>>/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installchangelogs -a
   dh_installexamples -a
   dh_installman -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   debian/rules override_dh_compress
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
   dh_missing -a
   debian/rules override_dh_dwz
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "Do not run dh_dwz"
Do not run dh_dwz
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyml/usr/bin/phyml-mpi debian/phyml/usr/lib/phyml/bin/phyml debian/phyml/usr/lib/phyml/bin/phyml-mpi were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'phyml' in '../phyml_3.3.20211021-1_armhf.deb'.
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20211021-1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../phyml_3.3.20211021-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-11-21T06:39:40Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


phyml_3.3.20211021-1_armhf.changes:
-----------------------------------

Format: 1.8
Date: Fri, 19 Nov 2021 00:22:37 +0100
Source: phyml
Binary: phyml phyml-dbgsym
Architecture: armhf
Version: 3:3.3.20211021-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
 phyml      - Phylogenetic estimation using Maximum Likelihood
Changes:
 phyml (3:3.3.20211021-1) unstable; urgency=medium
 .
   * New upstream version.
   * Refresh most patches.
   * Add apply-cflags.patch: ensure standard Debian CFLAGS are propagated
     throughout the build process.
   * Add filter-sse3-intrinsics.patch: fixes FTBFS when built with -msse but
     without -msse3, as the codebase also now includes SSE3 instructions;
     however this means that SSE acceleration is thus now disabled on amd64.
   * Add apply-ldflags.patch: ensure standard Debian LDFLAGS are propagated
     throughout the build process for proper hardening.
   * d/rules: autoconfigure with --enable-phyml-mpi, replacing --enable-mpi.
   * d/rules: fix permissions of example files nucleic and proteic.
   * d/{links,phyml.1}: also provide phyml-mpi manual page.
   * d/control: add myself to Uploaders.
   * d/copyright: bump project to GPL-3 and document the file src/mxml.h
   * d/copyright: update copyright entry of package maintenance
Checksums-Sha1:
 c6f878c79210c33d8fea62750eed120d048234bf 1938384 phyml-dbgsym_3.3.20211021-1_armhf.deb
 963bee54902f7cdf9ba22113538a39b188b4f068 6736 phyml_3.3.20211021-1_armhf.buildinfo
 c7644eda398d4662d2b913fded18b70ff7258957 955600 phyml_3.3.20211021-1_armhf.deb
Checksums-Sha256:
 78bc6fa8c70daf6d29a72c061267569a6480105902d582bdd23d1995799d653e 1938384 phyml-dbgsym_3.3.20211021-1_armhf.deb
 880d0db40f5133eb669d88782d5882256466b602b51ce7624fe4657f1a2a4ab6 6736 phyml_3.3.20211021-1_armhf.buildinfo
 5ea0d12fea654f5491e325227b509fd3243909b7ac9754d694306cfd868000c6 955600 phyml_3.3.20211021-1_armhf.deb
Files:
 bc2245bab0f70d4ad412fe2508db0d80 1938384 debug optional phyml-dbgsym_3.3.20211021-1_armhf.deb
 14126bbca42ca1f768c76306dfec7f27 6736 science optional phyml_3.3.20211021-1_armhf.buildinfo
 fbbfd6a5934f1227dc618d37a0f38c64 955600 science optional phyml_3.3.20211021-1_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


phyml-dbgsym_3.3.20211021-1_armhf.deb
-------------------------------------

 new Debian package, version 2.0.
 size 1938384 bytes: control archive=600 bytes.
     422 bytes,    12 lines      control              
     212 bytes,     2 lines      md5sums              
 Package: phyml-dbgsym
 Source: phyml
 Version: 3:3.3.20211021-1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2083
 Depends: phyml (= 3:3.3.20211021-1)
 Section: debug
 Priority: optional
 Description: debug symbols for phyml
 Build-Ids: ada624b71b0a095b79496e2a3e2199f350f758a4 f31d615230c8699a3219f981d4b6855864223238

drwxr-xr-x root/root         0 2021-11-18 23:22 ./
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/lib/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/lib/debug/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/lib/debug/.build-id/ad/
-rw-r--r-- root/root   1071916 2021-11-18 23:22 ./usr/lib/debug/.build-id/ad/a624b71b0a095b79496e2a3e2199f350f758a4.debug
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/lib/debug/.build-id/f3/
-rw-r--r-- root/root   1049328 2021-11-18 23:22 ./usr/lib/debug/.build-id/f3/1d615230c8699a3219f981d4b6855864223238.debug
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/doc/
lrwxrwxrwx root/root         0 2021-11-18 23:22 ./usr/share/doc/phyml-dbgsym -> phyml


phyml_3.3.20211021-1_armhf.deb
------------------------------

 new Debian package, version 2.0.
 size 955600 bytes: control archive=1900 bytes.
    1682 bytes,    31 lines      control              
    1779 bytes,    25 lines      md5sums              
 Package: phyml
 Version: 3:3.3.20211021-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3578
 Depends: libc6 (>= 2.29), libopenmpi3 (>= 4.1.2~rc1), openmpi-bin
 Section: science
 Priority: optional
 Homepage: http://www.atgc-montpellier.fr/phyml
 Description: Phylogenetic estimation using Maximum Likelihood
  PhyML is a software that estimates maximum likelihood phylogenies from
  alignments of nucleotide or amino acid sequences. It provides a wide
  range of options that were designed to facilitate standard phylogenetic
  analyses. The main strengths of PhyML lies in the large number of
  substitution models coupled to various options to search the space of
  phylogenetic tree topologies, going from very fast and efficient methods
  to slower but generally more accurate approaches. It also implements
  two methods to evaluate branch supports in a sound statistical framework
  (the non-parametric bootstrap and the approximate likelihood ratio test).
  .
  PhyML was designed to process moderate to large data sets. In theory,
  alignments with up to 4,000 sequences 2,000,000 character-long can
  be analyzed. In  practice however, the amount of memory required to process
  a data set is proportional of the product of the number of sequences by their
  length. Hence, a large number of sequences can only be processed provided
  that they are short. Also, PhyML can handle long sequences provided that
  they are not numerous. With most standard personal computers, the “comfort
  zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
  character long.
  .
  This package also includes PhyTime.

drwxr-xr-x root/root         0 2021-11-18 23:22 ./
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/bin/
-rwxr-xr-x root/root       579 2020-06-16 19:49 ./usr/bin/phyml
-rwxr-xr-x root/root    935480 2021-11-18 23:22 ./usr/bin/phyml-mpi
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/lib/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/lib/phyml/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/lib/phyml/bin/
-rwxr-xr-x root/root    927288 2021-11-18 23:22 ./usr/lib/phyml/bin/phyml
-rwxr-xr-x root/root    935480 2021-11-18 23:22 ./usr/lib/phyml/bin/phyml-mpi
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/doc-base/
-rw-r--r-- root/root       202 2020-06-16 19:49 ./usr/share/doc-base/phyml.phyml
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/doc/phyml/
-rw-r--r-- root/root      2446 2020-06-16 19:49 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root      3825 2021-11-18 23:22 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root      3897 2021-11-18 23:19 ./usr/share/doc/phyml/copyright
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/doc/phyml/examples/
-rw-r--r-- root/root     20905 2020-06-16 19:49 ./usr/share/doc/phyml/examples/example.nex
drwxr-xr-x root/root         0 2021-10-21 16:09 ./usr/share/doc/phyml/examples/lg4x/
-rw-r--r-- root/root      1900 2021-10-21 16:09 ./usr/share/doc/phyml/examples/lg4x/X1.mat
-rw-r--r-- root/root      1899 2021-10-21 16:09 ./usr/share/doc/phyml/examples/lg4x/X2.mat
-rw-r--r-- root/root      1893 2021-10-21 16:09 ./usr/share/doc/phyml/examples/lg4x/X3.mat
-rw-r--r-- root/root      1895 2021-10-21 16:09 ./usr/share/doc/phyml/examples/lg4x/X4.mat
-rw-r--r-- root/root      1994 2021-10-21 16:09 ./usr/share/doc/phyml/examples/lg4x/lg4x.xml
-rw-r--r-- root/root      2175 2021-10-21 16:09 ./usr/share/doc/phyml/examples/nexus_example.nxs
-rw-r--r-- root/root     60771 2021-10-21 16:09 ./usr/share/doc/phyml/examples/nucleic
drwxr-xr-x root/root         0 2021-10-21 16:09 ./usr/share/doc/phyml/examples/phyrex/
-rw-r--r-- root/root      9115 2021-10-21 16:09 ./usr/share/doc/phyml/examples/phyrex/flu.xml
-rw-r--r-- root/root     70310 2021-10-21 16:09 ./usr/share/doc/phyml/examples/phyrex/h1n1.nxs
-rw-r--r-- root/root      1784 2021-10-21 16:09 ./usr/share/doc/phyml/examples/phyrex/usa_coord.txt
drwxr-xr-x root/root         0 2021-10-21 16:09 ./usr/share/doc/phyml/examples/phytime/
-rw-r--r-- root/root      2248 2021-10-21 16:09 ./usr/share/doc/phyml/examples/phytime/dating_example.xml
-rw-r--r-- root/root    100171 2021-10-21 16:09 ./usr/share/doc/phyml/examples/phytime/seq.txt
-rw-r--r-- root/root     25990 2021-10-21 16:09 ./usr/share/doc/phyml/examples/proteic
-rw-r--r-- root/root    518808 2021-10-21 16:09 ./usr/share/doc/phyml/phyml_manual.pdf
-rw-r--r-- root/root      1257 2020-06-16 19:49 ./usr/share/doc/phyml/run-unit-test
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/man/
drwxr-xr-x root/root         0 2021-11-18 23:22 ./usr/share/man/man1/
lrwxrwxrwx root/root         0 2021-11-18 23:22 ./usr/share/man/man1/phyml-mpi.1.gz -> phyml.1.gz
-rw-r--r-- root/root      2908 2021-11-18 23:22 ./usr/share/man/man1/phyml.1.gz


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 25080
Build-Time: 374
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 671
Job: phyml_3:3.3.20211021-1
Machine Architecture: armhf
Package: phyml
Package-Time: 1093
Source-Version: 3:3.3.20211021-1
Space: 25080
Status: successful
Version: 3:3.3.20211021-1
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Finished at 2021-11-21T06:39:40Z
Build needed 00:18:13, 25080k disc space