phyml →
3:3.3.20220408-3 →
armhf → 2022-11-01 09:03:14
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| phyml 3:3.3.20220408-3 (armhf) Tue, 01 Nov 2022 08:56:54 +0000 |
+==============================================================================+
Package: phyml
Version: 3:3.3.20220408-3
Source Version: 3:3.3.20220408-3
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-3624c70c-c926-4e3e-aa76-3706ea8abc26' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.6 MB in 11s (2575 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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 1833 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main phyml 3:3.3.20220408-3 (dsc) [2258 B]
Get:2 http://172.17.4.1/private bookworm-staging/main phyml 3:3.3.20220408-3 (tar) [1804 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main phyml 3:3.3.20220408-3 (diff) [26.9 kB]
Fetched 1833 kB in 0s (6621 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phyml-XiIvkx/phyml-3.3.20220408' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phyml-XiIvkx' 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-PDMDpP/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-PDMDpP/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-PDMDpP/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-PDMDpP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (8854 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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap libperl5.34 netbase perl-modules-5.34 sensible-utils
Use 'apt autoremove' to remove them.
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-PDMDpP/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 (66.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14774 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-PDMDpP/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-PDMDpP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ Sources [513 B]
Get:5 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ Packages [595 B]
Fetched 2441 B in 0s (10.3 kB/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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap libperl5.34 netbase perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils chrpath debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-12 groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libbsd0 libcbor0.8 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 libgfortran-12-dev libgfortran5
libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev
libibverbs1 libicu71 libjs-jquery libjs-jquery-ui libltdl-dev libltdl7
libmagic-mgc libmagic1 libmd0 libmunge2 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
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 zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev gfortran-12-doc libcoarrays-dev groff
low-memory-monitor 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 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-12 groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libbsd0 libcbor0.8 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 libgfortran-12-dev libgfortran5
libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev
libibverbs1 libicu71 libjs-jquery libjs-jquery-ui libltdl-dev libltdl7
libmagic-mgc libmagic1 libmd0 libmunge2 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
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 zlib1g-dev
0 upgraded, 83 newly installed, 0 to remove and 30 not upgraded.
Need to get 37.8 MB of archives.
After this operation, 153 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-PDMDpP/apt_archive ./ sbuild-build-depends-phyml-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.0-1 [1299 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20221009-1 [76.0 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libcbor0.8 armhf 0.8.0-2 [22.8 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libfido2-1 armhf 1.12.0-1 [67.0 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf openssh-client armhf 1:9.0p1-1+b2 [890 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10.1 [79.9 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10.1 [940 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-3+rpi1 [238 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-12-dev armhf 12.2.0-3+rpi1 [285 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf gfortran-12 armhf 12.2.0-3+rpi1 [7509 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libibverbs1 armhf 42.0-1 [53.7 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf ibverbs-providers armhf 42.0-1 [28.8 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-5+b1 [166 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-5+b1 [125 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-5+b1 [102 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-5+b1 [57.6 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-5+b1 [62.5 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-5+b1 [280 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf librdmacm1 armhf 42.0-1 [60.3 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-3 [310 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.1-1 [1214 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.8.0-1 [130 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.15-1 [22.3 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.15-1 [35.5 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-4 [399 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.7-4 [161 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.8.0-1 [202 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.16-3 [51.2 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libxnvctrl0 armhf 510.85.02-2 [26.6 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.3 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.8.0-1 [20.4 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.7.0-0.2 [93.4 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.2 [163 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libibverbs-dev armhf 42.0-1 [188 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libmunge2 armhf 0.5.14-6 [18.6 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libpmix2 armhf 4.2.1-3 [530 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.4-2+rpi1 [1797 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf openmpi-common all 4.1.4-2+rpi1 [165 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libpmix-dev armhf 4.2.1-3 [844 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.4-2+rpi1 [192 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.4-2+rpi1 [920 kB]
Get:83 http://172.17.4.1/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
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Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 14774 files and directories currently installed.)
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Preparing to unpack .../02-bsdextrautils_2.38.1-1.1_armhf.deb ...
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Preparing to unpack .../03-libpipeline1_1.5.6-3_armhf.deb ...
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Setting up libbsd0:armhf (0.11.7-1) ...
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Setting up intltool-debian (0.35.0+20060710.6) ...
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Setting up libnl-route-3-200:armhf (3.7.0-0.2) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:armhf (2.4.7-4) ...
Setting up gfortran-12 (12.2.0-3+rpi1) ...
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Setting up libevent-dev (2.1.12-stable-5+b1) ...
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Setting up ibverbs-providers:armhf (42.0-1) ...
Setting up openssh-client (1:9.0p1-1+b2) ...
update-alternatives: using /usr/bin/ssh to provide /usr/bin/rsh (rsh) in auto mode
update-alternatives: using /usr/bin/slogin to provide /usr/bin/rlogin (rlogin) in auto mode
update-alternatives: using /usr/bin/scp to provide /usr/bin/rcp (rcp) in auto mode
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Setting up man-db (2.11.0-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up openmpi-bin (4.1.4-2+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 (4.1.4-2+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 (2.35-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1.1 bsdutils_1:2.38.1-1.1 build-essential_12.9 bzip2_1.0.8-5+b2 chrpath_0.16-2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+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_0.21-9 gettext-base_0.21-9 gfortran-12_12.2.0-3+rpi1 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 ibverbs-providers_42.0-1 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblkid1_2.38.1-1.1 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcbor0.8_0.8.0-2 libcc1-0_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.10.1 libdpkg-perl_1.21.9+rpi1 libedit2_3.1-20221009-1 libelf1_0.187-2+rpi2 libevent-2.1-7_2.1.12-stable-5+b1 libevent-core-2.1-7_2.1.12-stable-5+b1 libevent-dev_2.1.12-stable-5+b1 libevent-extra-2.1-7_2.1.12-stable-5+b1 libevent-openssl-2.1-7_2.1.12-stable-5+b1 libevent-pthreads-2.1-7_2.1.12-stable-5+b1 libext2fs2_1.46.6~rc1-1 libfabric1_1.11.0-3 libfakeroot_1.29-1 libffi8_3.4.2-4 libfido2-1_1.12.0-1 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-3+rpi1 libgfortran5_12.2.0-3+rpi1 libglib2.0-0_2.74.1-1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libhwloc-dev_2.8.0-1 libhwloc-plugins_2.8.0-1 libhwloc15_2.8.0-1 libibverbs-dev_42.0-1 libibverbs1_42.0-1 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.5-0_2.5.13+dfsg-2+rpi1 libltdl-dev_2.4.7-4 libltdl7_2.4.7-4 liblz4-1_1.9.4-1+rpi1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-1.1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libmunge2_0.5.14-6 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnl-3-200_3.7.0-0.2 libnl-3-dev_3.7.0-0.2 libnl-route-3-200_3.7.0-0.2 libnl-route-3-dev_3.7.0-0.2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.15-1 libnuma1_2.0.15-1 libopenmpi-dev_4.1.4-2+rpi1 libopenmpi3_4.1.4-2+rpi1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpciaccess0_0.16-3 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.6-3 libpmix-dev_4.2.1-3 libpmix2_4.2.1-3 librdmacm1_42.0-1 libreadline8_8.2-1 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1.1 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssl1.1_1.1.1o-1 libssl3_3.0.5-4 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-4 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-1.1 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libxau6_1:1.0.9-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.14+dfsg-1 libxnvctrl0_510.85.02-2 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.0-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-1.1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 ocl-icd-libopencl1_2.3.1-1 openmpi-bin_4.1.4-2+rpi1 openmpi-common_4.1.4-2+rpi1 openssh-client_1:9.0p1-1+b2 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 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 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-1.1 util-linux-extra_2.38.1-1.1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.9hIb4bd4/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 26 18:18:47 2022 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./phyml_3.3.20220408-3.dsc
dpkg-source: info: extracting phyml in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking phyml_3.3.20220408.orig.tar.gz
dpkg-source: info: unpacking phyml_3.3.20220408-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying sse_only_if_supported.patch
dpkg-source: info: applying no-configure-ac-date.patch
dpkg-source: info: applying fix_declaration_of_temp.patch
dpkg-source: info: applying fix_wrong_initialisation_of_array.patch
dpkg-source: info: applying no-march-native.patch
dpkg-source: info: applying cross.patch
dpkg-source: info: applying apply-cflags.patch
dpkg-source: info: applying filter-sse3-intrinsics.patch
dpkg-source: info: applying apply-ldflags.patch
dpkg-source: info: applying typos.patch
Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-3624c70c-c926-4e3e-aa76-3706ea8abc26
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package phyml
dpkg-buildpackage: info: source version 3:3.3.20220408-3
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:31: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:31: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:31: the top level
configure.ac:52: warning: The macro `AC_FUNC_SETVBUF_REVERSED' is obsolete. Remove it and all references to SETVBUF_REVERSED.
./lib/autoconf/functions.m4:1766: AC_FUNC_SETVBUF_REVERSED is expanded from...
configure.ac:52: the top level
configure.ac:14: installing './compile'
configure.ac:12: installing './config.guess'
configure.ac:12: installing './config.sub'
configure.ac:5: installing './install-sh'
configure.ac:5: installing './missing'
src/Makefile.am: installing './depcomp'
make[1]: Leaving directory '/<<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 3.3.3:3.3.20220408-3 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/<<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
io.c: In function 'Sub_Trees':
io.c:511:25: warning: 'subs' may be used uninitialized [-Wmaybe-uninitialized]
511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:479:10: note: 'subs' was declared here
479 | char **subs;
| ^~~~
gcc -I. -I.. -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/bionj.Po
rm -f ./.deps/cl.Po
rm -f ./.deps/date.Po
rm -f ./.deps/draw.Po
rm -f ./.deps/eigen.Po
rm -f ./.deps/free.Po
rm -f ./.deps/help.Po
rm -f ./.deps/init.Po
rm -f ./.deps/interface.Po
rm -f ./.deps/io.Po
rm -f ./.deps/lk.Po
rm -f ./.deps/location.Po
rm -f ./.deps/main.Po
rm -f ./.deps/make.Po
rm -f ./.deps/mcmc.Po
rm -f ./.deps/mg.Po
rm -f ./.deps/mixt.Po
rm -f ./.deps/models.Po
rm -f ./.deps/nexus.Po
rm -f ./.deps/optimiz.Po
rm -f ./.deps/pars.Po
rm -f ./.deps/phyml_mpi-alrt.Po
rm -f ./.deps/phyml_mpi-ancestral.Po
rm -f ./.deps/phyml_mpi-avx.Po
rm -f ./.deps/phyml_mpi-bionj.Po
rm -f ./.deps/phyml_mpi-cl.Po
rm -f ./.deps/phyml_mpi-draw.Po
rm -f ./.deps/phyml_mpi-eigen.Po
rm -f ./.deps/phyml_mpi-free.Po
rm -f ./.deps/phyml_mpi-help.Po
rm -f ./.deps/phyml_mpi-init.Po
rm -f ./.deps/phyml_mpi-interface.Po
rm -f ./.deps/phyml_mpi-io.Po
rm -f ./.deps/phyml_mpi-lk.Po
rm -f ./.deps/phyml_mpi-main.Po
rm -f ./.deps/phyml_mpi-make.Po
rm -f ./.deps/phyml_mpi-mixt.Po
rm -f ./.deps/phyml_mpi-models.Po
rm -f ./.deps/phyml_mpi-mpi_boot.Po
rm -f ./.deps/phyml_mpi-nexus.Po
rm -f ./.deps/phyml_mpi-optimiz.Po
rm -f ./.deps/phyml_mpi-pars.Po
rm -f ./.deps/phyml_mpi-simu.Po
rm -f ./.deps/phyml_mpi-spr.Po
rm -f ./.deps/phyml_mpi-sse.Po
rm -f ./.deps/phyml_mpi-stats.Po
rm -f ./.deps/phyml_mpi-tbe.Po
rm -f ./.deps/phyml_mpi-utilities.Po
rm -f ./.deps/phyml_mpi-xml.Po
rm -f ./.deps/phyrex.Po
rm -f ./.deps/rates.Po
rm -f ./.deps/rrw.Po
rm -f ./.deps/rw.Po
rm -f ./.deps/simu.Po
rm -f ./.deps/slfv.Po
rm -f ./.deps/spr.Po
rm -f ./.deps/sse.Po
rm -f ./.deps/stats.Po
rm -f ./.deps/tbe.Po
rm -f ./.deps/times.Po
rm -f ./.deps/utilities.Po
rm -f ./.deps/xml.Po
rm -f Makefile
make[3]: Leaving directory '/<<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 -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 -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 -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 3.3.3:3.3.20220408-3 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 -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 -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 -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 -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
io.c: In function 'Sub_Trees':
io.c:511:25: warning: 'subs' may be used uninitialized [-Wmaybe-uninitialized]
511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:479:10: note: 'subs' was declared here
479 | char **subs;
| ^~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 -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 -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 -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 -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 -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
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 -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 -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 "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -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 3.3.3:3.3.20220408-3 :.
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 3.3.3:3.3.20220408-3 :.
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/lib/phyml/bin/phyml debian/phyml/usr/bin/phyml-mpi 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-dbgsym' in '../phyml-dbgsym_3.3.20220408-3_armhf.deb'.
dpkg-deb: building package 'phyml' in '../phyml_3.3.20220408-3_armhf.deb'.
dpkg-genbuildinfo --build=any -O../phyml_3.3.20220408-3_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../phyml_3.3.20220408-3_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 2022-11-01T09:03:11Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phyml_3.3.20220408-3_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 26 Oct 2022 19:56:40 +0200
Source: phyml
Binary: phyml phyml-dbgsym
Architecture: armhf
Version: 3:3.3.20220408-3
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Changes:
phyml (3:3.3.20220408-3) unstable; urgency=medium
.
* d/watch: move to git tag scanning; fixes uscan following github changes.
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Checksums-Sha256:
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ab22245026adf633d163d00090cfb8821fe0142f8277523b52aa4b4953386997 969400 phyml_3.3.20220408-3_armhf.deb
Files:
abdb8c6ecc07d23c1d51b6c5bc09b47f 1923036 debug optional phyml-dbgsym_3.3.20220408-3_armhf.deb
55380fde7c82f22b22cc7436dbba4e6c 6666 science optional phyml_3.3.20220408-3_armhf.buildinfo
732361f2a7742ae64e8dab11162ce869 969400 science optional phyml_3.3.20220408-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phyml-dbgsym_3.3.20220408-3_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 1923036 bytes: control archive=604 bytes.
422 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: phyml-dbgsym
Source: phyml
Version: 3:3.3.20220408-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2062
Depends: phyml (= 3:3.3.20220408-3)
Section: debug
Priority: optional
Description: debug symbols for phyml
Build-Ids: 64b8e0f4ba545697d8dbc55c4ae5b4384a603f97 d2ffb9db22b0c5ac743b793d81f470272f3a103d
drwxr-xr-x root/root 0 2022-10-26 17:56 ./
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/lib/debug/.build-id/64/
-rw-r--r-- root/root 1060964 2022-10-26 17:56 ./usr/lib/debug/.build-id/64/b8e0f4ba545697d8dbc55c4ae5b4384a603f97.debug
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/lib/debug/.build-id/d2/
-rw-r--r-- root/root 1038224 2022-10-26 17:56 ./usr/lib/debug/.build-id/d2/ffb9db22b0c5ac743b793d81f470272f3a103d.debug
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-10-26 17:56 ./usr/share/doc/phyml-dbgsym -> phyml
phyml_3.3.20220408-3_armhf.deb
------------------------------
new Debian package, version 2.0.
size 969400 bytes: control archive=1896 bytes.
1678 bytes, 31 lines control
1779 bytes, 25 lines md5sums
Package: phyml
Version: 3:3.3.20220408-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3747
Depends: libc6 (>= 2.34), libopenmpi3 (>= 4.1.4), 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 2022-10-26 17:56 ./
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/bin/
-rwxr-xr-x root/root 579 2022-10-26 17:56 ./usr/bin/phyml
-rwxr-xr-x root/root 984632 2022-10-26 17:56 ./usr/bin/phyml-mpi
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/lib/phyml/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/lib/phyml/bin/
-rwxr-xr-x root/root 984632 2022-10-26 17:56 ./usr/lib/phyml/bin/phyml
-rwxr-xr-x root/root 984632 2022-10-26 17:56 ./usr/lib/phyml/bin/phyml-mpi
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/doc-base/
-rw-r--r-- root/root 202 2022-10-26 17:56 ./usr/share/doc-base/phyml.phyml
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/doc/phyml/
-rw-r--r-- root/root 2446 2022-10-26 17:56 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root 1614 2022-10-26 17:56 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root 23260 2022-10-26 17:56 ./usr/share/doc/phyml/copyright
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/doc/phyml/examples/
-rw-r--r-- root/root 20905 2022-10-26 17:56 ./usr/share/doc/phyml/examples/example.nex
drwxr-xr-x root/root 0 2022-04-08 15:01 ./usr/share/doc/phyml/examples/lg4x/
-rw-r--r-- root/root 1900 2022-04-08 15:01 ./usr/share/doc/phyml/examples/lg4x/X1.mat
-rw-r--r-- root/root 1899 2022-04-08 15:01 ./usr/share/doc/phyml/examples/lg4x/X2.mat
-rw-r--r-- root/root 1893 2022-04-08 15:01 ./usr/share/doc/phyml/examples/lg4x/X3.mat
-rw-r--r-- root/root 1895 2022-04-08 15:01 ./usr/share/doc/phyml/examples/lg4x/X4.mat
-rw-r--r-- root/root 1994 2022-04-08 15:01 ./usr/share/doc/phyml/examples/lg4x/lg4x.xml
-rw-r--r-- root/root 2175 2022-04-08 15:01 ./usr/share/doc/phyml/examples/nexus_example.nxs
-rw-r--r-- root/root 60771 2022-04-08 15:01 ./usr/share/doc/phyml/examples/nucleic
drwxr-xr-x root/root 0 2022-04-08 15:01 ./usr/share/doc/phyml/examples/phyrex/
-rw-r--r-- root/root 9115 2022-04-08 15:01 ./usr/share/doc/phyml/examples/phyrex/flu.xml
-rw-r--r-- root/root 70310 2022-04-08 15:01 ./usr/share/doc/phyml/examples/phyrex/h1n1.nxs
-rw-r--r-- root/root 1784 2022-04-08 15:01 ./usr/share/doc/phyml/examples/phyrex/usa_coord.txt
drwxr-xr-x root/root 0 2022-04-08 15:01 ./usr/share/doc/phyml/examples/phytime/
-rw-r--r-- root/root 2248 2022-04-08 15:01 ./usr/share/doc/phyml/examples/phytime/dating_example.xml
-rw-r--r-- root/root 100171 2022-04-08 15:01 ./usr/share/doc/phyml/examples/phytime/seq.txt
-rw-r--r-- root/root 25990 2022-04-08 15:01 ./usr/share/doc/phyml/examples/proteic
-rw-r--r-- root/root 518525 2022-04-08 15:01 ./usr/share/doc/phyml/phyml_manual.pdf
-rw-r--r-- root/root 1257 2022-10-26 17:56 ./usr/share/doc/phyml/run-unit-test
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/man/
drwxr-xr-x root/root 0 2022-10-26 17:56 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2022-10-26 17:56 ./usr/share/man/man1/phyml-mpi.1.gz -> phyml.1.gz
-rw-r--r-- root/root 2906 2022-10-26 17:56 ./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: 25188
Build-Time: 123
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 234
Job: phyml_3:3.3.20220408-3
Machine Architecture: armhf
Package: phyml
Package-Time: 377
Source-Version: 3:3.3.20220408-3
Space: 25188
Status: successful
Version: 3:3.3.20220408-3
--------------------------------------------------------------------------------
Finished at 2022-11-01T09:03:11Z
Build needed 00:06:17, 25188k disk space