phyml →
3:3.3.20200621-2 →
armhf → 2021-10-09 07:03:00
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| phyml 3:3.3.20200621-2 (armhf) Sat, 09 Oct 2021 06:47:20 +0000 |
+==============================================================================+
Package: phyml
Version: 3:3.3.20200621-2
Source Version: 3:3.3.20200621-2
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-f4ad5e11-7f7e-419b-ae39-37119ddc24b6' 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 [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 26s (996 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 2255 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main phyml 3:3.3.20200621-2 (dsc) [2094 B]
Get:2 http://172.17.0.1/private bookworm-staging/main phyml 3:3.3.20200621-2 (tar) [2235 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main phyml 3:3.3.20200621-2 (diff) [17.3 kB]
Fetched 2255 kB in 1s (2669 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phyml-Y2ZYxu/phyml-3.3.20200621' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phyml-Y2ZYxu' 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-L0do0Y/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-L0do0Y/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-L0do0Y/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-L0do0Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-L0do0Y/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-L0do0Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-L0do0Y/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-L0do0Y/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2704 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 22 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-L0do0Y/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 (22.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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-L0do0Y/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-L0do0Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-L0do0Y/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-L0do0Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-L0do0Y/apt_archive ./ Sources [513 B]
Get:5 copy:/<<BUILDDIR>>/resolver-L0do0Y/apt_archive ./ Packages [595 B]
Fetched 2441 B in 1s (2967 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-10
debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-10 gcc-10
gcc-10-base gcc-11-base gettext gettext-base gfortran-10 groff-base
ibverbs-providers intltool-debian libarchive-zip-perl libasan6 libatomic1
libbsd0 libcbor0 libcc1-0 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 libffi8 libfido2-1
libfile-stripnondeterminism-perl libgcc-10-dev libgcc-s1 libgfortran-10-dev
libgfortran5 libglib2.0-0 libgomp1 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 libstdc++-10-dev libstdc++6 libsub-override-perl libtool
libubsan1 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-10-locales dh-make
gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-10-doc
libcoarrays-dev groff libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils
libstdc++-10-doc 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-10 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 libffi8 libfido2-1
libfile-stripnondeterminism-perl libgfortran-10-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
The following packages will be upgraded:
cpp-10 g++-10 gcc-10 gcc-10-base gcc-11-base libasan6 libatomic1 libcc1-0
libgcc-10-dev libgcc-s1 libgomp1 libstdc++-10-dev libstdc++6 libubsan1
14 upgraded, 85 newly installed, 0 to remove and 8 not upgraded.
Need to get 70.6 MB of archives.
After this operation, 136 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-L0do0Y/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 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-7+rpi1 [1944 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-7+rpi1 [797 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-7+rpi1 [88.1 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-7+rpi1 [205 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-7+rpi1 [36.2 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-7+rpi1 [37.7 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-7+rpi1 [8188 B]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-7+rpi1 [465 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf g++-10 armhf 10.3.0-11+rpi1 [7350 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf gcc-10 armhf 10.3.0-11+rpi1 [13.4 MB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf libstdc++-10-dev armhf 10.3.0-11+rpi1 [1755 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libgcc-10-dev armhf 10.3.0-11+rpi1 [678 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf cpp-10 armhf 10.3.0-11+rpi1 [6690 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf gcc-10-base armhf 10.3.0-11+rpi1 [206 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libfido2-1 armhf 1.8.0-1 [55.9 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf openssh-client armhf 1:8.4p1-6 [794 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-7+rpi1 [235 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libgfortran-10-dev armhf 10.3.0-11+rpi1 [277 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf gfortran-10 armhf 10.3.0-11+rpi1 [7201 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libibverbs1 armhf 36.0-1 [53.2 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf ibverbs-providers armhf 36.0-1 [27.3 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:64 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:65 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:66 http://172.17.0.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf librdmacm1 armhf 36.0-1 [60.1 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libhwloc15 armhf 2.5.0+dfsg-2 [126 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.14-3 [21.8 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.14-3 [34.7 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.5.0+dfsg-2 [197 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libxnvctrl0 armhf 470.57.02-2 [26.0 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.9 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.5.0+dfsg-2 [20.0 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf libibverbs-dev armhf 36.0-1 [186 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libpmix2 armhf 4.1.1~rc2-1 [476 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.1-5+rpi1 [1772 kB]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf openmpi-common all 4.1.1-5+rpi1 [179 kB]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf libpmix-dev armhf 4.1.1~rc2-1 [640 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.1-5+rpi1 [207 kB]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.1-5+rpi1 [1145 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
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Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libxcb1:armhf (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libglib2.0-0:armhf (2.70.0-1) ...
No schema files found: doing nothing.
Setting up libgcc-10-dev:armhf (10.3.0-11+rpi1) ...
Setting up libedit2:armhf (3.1-20210910-1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnuma-dev:armhf (2.0.14-3) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-8) ...
Setting up libevent-dev (2.1.12-stable-1) ...
Setting up pkg-config (0.29.2-1) ...
Setting up gcc-10 (10.3.0-11+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up libx11-6:armhf (2:1.7.2-2) ...
Setting up libgfortran-10-dev:armhf (10.3.0-11+rpi1) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:armhf (36.0-1) ...
Setting up libstdc++-10-dev:armhf (10.3.0-11+rpi1) ...
Setting up g++-10 (10.3.0-11+rpi1) ...
Setting up ibverbs-providers:armhf (36.0-1) ...
Setting up openssh-client (1:8.4p1-6) ...
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'.
Setting up libxnvctrl0:armhf (470.57.02-2) ...
Setting up dh-autoreconf (20) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-15) ...
Setting up gfortran-10 (10.3.0-11+rpi1) ...
Setting up libhwloc-dev:armhf (2.5.0+dfsg-2) ...
Setting up librdmacm1:armhf (36.0-1) ...
Setting up debhelper (13.5.2) ...
Setting up libibverbs-dev:armhf (36.0-1) ...
Setting up libhwloc-plugins:armhf (2.5.0+dfsg-2) ...
Setting up libfabric1 (1.11.0-2) ...
Setting up libpmix2:armhf (4.1.1~rc2-1) ...
Setting up libopenmpi3:armhf (4.1.1-5+rpi1) ...
Setting up libpmix-dev:armhf (4.1.1~rc2-1) ...
Setting up openmpi-bin (4.1.1-5+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 (4.1.1-5+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.2-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 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-7+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 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 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 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-base_11.2.0-7+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-10_10.3.0-11+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_36.0-1 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-7+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-7+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 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 libcbor0_0.5.0+dfsg-2 libcc1-0_11.2.0-7+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 libffi7_3.3-6 libffi8_3.4.2-2 libfido2-1_1.8.0-1 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-11+rpi1 libgcc-s1_11.2.0-7+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgfortran-10-dev_10.3.0-11+rpi1 libgfortran5_11.2.0-7+rpi1 libglib2.0-0_2.70.0-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-7+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhwloc-dev_2.5.0+dfsg-2 libhwloc-plugins_2.5.0+dfsg-2 libhwloc15_2.5.0+dfsg-2 libibverbs-dev_36.0-1 libibverbs1_36.0-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 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_2.37.2-1 libmpc3_1.2.0-1 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_4.1.1-5+rpi1 libopenmpi3_4.1.1-5+rpi1 libp11-kit0_0.24.0-2 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_5.32.1-5 libpipeline1_1.5.3-1 libpmix-dev_4.1.1~rc2-1 libpmix2_4.1.1~rc2-1 librdmacm1_36.0-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 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_11.2.0-7+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+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_11.2.0-7+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 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_470.57.02-2 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+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_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 ocl-icd-libopencl1_2.2.14-2 openmpi-bin_4.1.1-5+rpi1 openmpi-common_4.1.1-5+rpi1 openssh-client_1:8.4p1-6 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 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_2021a-1 util-linux_2.37.2-1 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.KsTTT7x4/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 6 15:39:18 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./phyml_3.3.20200621-2.dsc
dpkg-source: info: extracting phyml in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking phyml_3.3.20200621.orig.tar.gz
dpkg-source: info: unpacking phyml_3.3.20200621-2.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
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-f4ad5e11-7f7e-419b-ae39-37119ddc24b6
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 3:3.3.20200621-2
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
checking dependency style of gcc... (cached) 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 -c -o main.o main.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o utilities.o utilities.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o optimiz.o optimiz.c
.: Building [phyml]. Version 3.3.3:3.3.20200621-2 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o lk.o lk.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o bionj.o bionj.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o models.o models.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o free.o free.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o help.o help.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o simu.o simu.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o eigen.o eigen.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o pars.o pars.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o alrt.o alrt.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o interface.o interface.c
utilities.c: In function 'Assign_State_With_Ambiguity':
utilities.c:3073:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
3073 | sprintf(format,"%%%dd",stepsize);
| ^~
utilities.c:3073:26: note: directive argument in the range [0, 2147483647]
3073 | sprintf(format,"%%%dd",stepsize);
| ^~~~~~~
In file included from /usr/include/stdio.h:866,
from utilities.h:21,
from utilities.c:12:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:38:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o cl.o cl.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o spr.o spr.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o draw.o draw.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o stats.o stats.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o rates.o rates.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o mcmc.o mcmc.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o times.o times.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o tiporder.o tiporder.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o io.o io.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o make.o make.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o nexus.o nexus.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o init.o init.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o xml.o xml.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o date.o date.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o sse.o sse.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o avx.o avx.c
io.c: In function 'Print_Fp_Out':
io.c:2315:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision);
| ^~
io.c:2315:43: note: directive argument in the range [1, 2147483647]
2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision);
| ^~~~~~~~
In file included from /usr/include/stdio.h:866,
from utilities.h:21,
from io.h:18,
from io.c:13:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o tbe.o tbe.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o ancestral.o ancestral.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o mixt.o mixt.c
gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o io.o make.o nexus.o init.o xml.o date.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm
Done.
make[4]: Leaving directory '/<<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/main.Po
rm -f ./.deps/make.Po
rm -f ./.deps/mcmc.Po
rm -f ./.deps/mg.Po
rm -f ./.deps/mixt.Po
rm -f ./.deps/models.Po
rm -f ./.deps/nexus.Po
rm -f ./.deps/optimiz.Po
rm -f ./.deps/pars.Po
rm -f ./.deps/phyml_mpi-alrt.Po
rm -f ./.deps/phyml_mpi-ancestral.Po
rm -f ./.deps/phyml_mpi-avx.Po
rm -f ./.deps/phyml_mpi-bionj.Po
rm -f ./.deps/phyml_mpi-cl.Po
rm -f ./.deps/phyml_mpi-date.Po
rm -f ./.deps/phyml_mpi-draw.Po
rm -f ./.deps/phyml_mpi-eigen.Po
rm -f ./.deps/phyml_mpi-free.Po
rm -f ./.deps/phyml_mpi-help.Po
rm -f ./.deps/phyml_mpi-init.Po
rm -f ./.deps/phyml_mpi-interface.Po
rm -f ./.deps/phyml_mpi-io.Po
rm -f ./.deps/phyml_mpi-lk.Po
rm -f ./.deps/phyml_mpi-main.Po
rm -f ./.deps/phyml_mpi-make.Po
rm -f ./.deps/phyml_mpi-mcmc.Po
rm -f ./.deps/phyml_mpi-mg.Po
rm -f ./.deps/phyml_mpi-mixt.Po
rm -f ./.deps/phyml_mpi-models.Po
rm -f ./.deps/phyml_mpi-mpi_boot.Po
rm -f ./.deps/phyml_mpi-nexus.Po
rm -f ./.deps/phyml_mpi-optimiz.Po
rm -f ./.deps/phyml_mpi-pars.Po
rm -f ./.deps/phyml_mpi-rates.Po
rm -f ./.deps/phyml_mpi-simu.Po
rm -f ./.deps/phyml_mpi-spr.Po
rm -f ./.deps/phyml_mpi-sse.Po
rm -f ./.deps/phyml_mpi-stats.Po
rm -f ./.deps/phyml_mpi-tbe.Po
rm -f ./.deps/phyml_mpi-times.Po
rm -f ./.deps/phyml_mpi-tiporder.Po
rm -f ./.deps/phyml_mpi-utilities.Po
rm -f ./.deps/phyml_mpi-xml.Po
rm -f ./.deps/phyrex.Po
rm -f ./.deps/rates.Po
rm -f ./.deps/rrw.Po
rm -f ./.deps/rw.Po
rm -f ./.deps/simu.Po
rm -f ./.deps/slfv.Po
rm -f ./.deps/spr.Po
rm -f ./.deps/sse.Po
rm -f ./.deps/stats.Po
rm -f ./.deps/tbe.Po
rm -f ./.deps/times.Po
rm -f ./.deps/tiporder.Po
rm -f ./.deps/utilities.Po
rm -f ./.deps/xml.Po
rm -f Makefile
make[3]: Leaving directory '/<<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-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-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
checking dependency style of gcc... (cached) 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 -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 -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 -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c
.: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-2 :.
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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c
utilities.c: In function 'Assign_State_With_Ambiguity':
utilities.c:3073:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
3073 | sprintf(format,"%%%dd",stepsize);
| ^~
utilities.c:3073:26: note: directive argument in the range [0, 2147483647]
3073 | sprintf(format,"%%%dd",stepsize);
| ^~~~~~~
In file included from /usr/include/stdio.h:866,
from utilities.h:21,
from utilities.c:12:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:38:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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 -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 -c -o phyml_mpi-rates.o `test -f 'rates.c' || echo './'`rates.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 -c -o phyml_mpi-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/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 -c -o phyml_mpi-times.o `test -f 'times.c' || echo './'`times.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/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 -c -o phyml_mpi-tiporder.o `test -f 'tiporder.c' || echo './'`tiporder.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/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 -c -o phyml_mpi-mg.o `test -f 'mg.c' || echo './'`mg.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/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 -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 -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 -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 -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 -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 -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c
io.c: In function 'Print_Fp_Out':
io.c:2315:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision);
| ^~
io.c:2315:43: note: directive argument in the range [1, 2147483647]
2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision);
| ^~~~~~~~
In file included from /usr/include/stdio.h:866,
from utilities.h:21,
from io.h:18,
from io.c:13:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -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 -c -o phyml_mpi-date.o `test -f 'date.c' || echo './'`date.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/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 -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 -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 -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 -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 -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/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 -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm
.: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-2 :.
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 3.3.3:3.3.20200621-2 :.
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 \{\} \;
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
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'phyml' in '../phyml_3.3.20200621-2_armhf.deb'.
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20200621-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../phyml_3.3.20200621-2_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 2021-10-09T07:02:53Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phyml_3.3.20200621-2_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 06 Oct 2021 17:30:05 +0200
Source: phyml
Binary: phyml phyml-dbgsym
Architecture: armhf
Version: 3:3.3.20200621-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Changes:
phyml (3:3.3.20200621-2) unstable; urgency=medium
.
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
Checksums-Sha1:
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Checksums-Sha256:
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05d3ac642a3119be235dd31e21ed41c7df3e704d84b712d28799c9f87c6a233b 6605 phyml_3.3.20200621-2_armhf.buildinfo
49b6ca06d39ecea1c9b421d96969b69388a5cacaecf4577cab891532236cdcda 1537564 phyml_3.3.20200621-2_armhf.deb
Files:
8e5b581368376bf3e0540fc113f5490a 41916 debug optional phyml-dbgsym_3.3.20200621-2_armhf.deb
47395f6d5febdd8c9e9f461693c0a35a 6605 science optional phyml_3.3.20200621-2_armhf.buildinfo
c2eca8d3fcf8ff27577bfdb745220eba 1537564 science optional phyml_3.3.20200621-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phyml-dbgsym_3.3.20200621-2_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 41916 bytes: control archive=656 bytes.
462 bytes, 12 lines control
318 bytes, 3 lines md5sums
Package: phyml-dbgsym
Source: phyml
Version: 3:3.3.20200621-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 293
Depends: phyml (= 3:3.3.20200621-2)
Section: debug
Priority: optional
Description: debug symbols for phyml
Build-Ids: 7e0fd6a35baf2f0dc98cbec801569dffdc9570ef 93e4016404d36245f7e66abe68b1c4314e5bffe1 c536213b8162762e8059aae14657ea3a20c09043
drwxr-xr-x root/root 0 2021-10-06 15:30 ./
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/debug/.build-id/7e/
-rw-r--r-- root/root 94976 2021-10-06 15:30 ./usr/lib/debug/.build-id/7e/0fd6a35baf2f0dc98cbec801569dffdc9570ef.debug
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/debug/.build-id/93/
-rw-r--r-- root/root 95764 2021-10-06 15:30 ./usr/lib/debug/.build-id/93/e4016404d36245f7e66abe68b1c4314e5bffe1.debug
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/debug/.build-id/c5/
-rw-r--r-- root/root 95764 2021-10-06 15:30 ./usr/lib/debug/.build-id/c5/36213b8162762e8059aae14657ea3a20c09043.debug
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-06 15:30 ./usr/share/doc/phyml-dbgsym -> phyml
phyml_3.3.20200621-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 1537564 bytes: control archive=1912 bytes.
1678 bytes, 31 lines control
1779 bytes, 25 lines md5sums
Package: phyml
Version: 3:3.3.20200621-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5006
Depends: libc6 (>= 2.29), libopenmpi3 (>= 4.1.1), 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 2021-10-06 15:30 ./
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/bin/
-rwxr-xr-x root/root 579 2021-10-06 15:30 ./usr/bin/phyml
-rwxr-xr-x root/root 1271632 2021-10-06 15:30 ./usr/bin/phyml-mpi
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/phyml/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/lib/phyml/bin/
-rwxr-xr-x root/root 1263108 2021-10-06 15:30 ./usr/lib/phyml/bin/phyml
-rwxr-xr-x root/root 1271300 2021-10-06 15:30 ./usr/lib/phyml/bin/phyml-mpi
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/doc-base/
-rw-r--r-- root/root 202 2021-10-06 15:30 ./usr/share/doc-base/phyml.phyml
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/doc/phyml/
-rw-r--r-- root/root 2446 2021-10-06 15:30 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root 3370 2021-10-06 15:30 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root 1490 2021-10-06 15:30 ./usr/share/doc/phyml/copyright
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/doc/phyml/examples/
-rw-r--r-- root/root 20905 2021-10-06 15:30 ./usr/share/doc/phyml/examples/example.nex
drwxr-xr-x root/root 0 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/
-rw-r--r-- root/root 1900 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/X1.mat
-rw-r--r-- root/root 1899 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/X2.mat
-rw-r--r-- root/root 1893 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/X3.mat
-rw-r--r-- root/root 1895 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/X4.mat
-rw-r--r-- root/root 1994 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/lg4x.xml
-rw-r--r-- root/root 2175 2020-07-14 09:31 ./usr/share/doc/phyml/examples/nexus_example.nxs
-rwxr-xr-x root/root 60771 2020-07-14 09:31 ./usr/share/doc/phyml/examples/nucleic
drwxr-xr-x root/root 0 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phyrex/
-rw-r--r-- root/root 9115 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phyrex/flu.xml
-rw-r--r-- root/root 70310 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phyrex/h1n1.nxs
-rw-r--r-- root/root 1784 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phyrex/usa_coord.txt
drwxr-xr-x root/root 0 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phytime/
-rw-r--r-- root/root 2248 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phytime/dating_example.xml
-rw-r--r-- root/root 100171 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phytime/seq.txt
-rwxr-xr-x root/root 25990 2020-07-14 09:31 ./usr/share/doc/phyml/examples/proteic
-rw-r--r-- root/root 976126 2020-07-14 09:31 ./usr/share/doc/phyml/phyml_manual.pdf
-rw-r--r-- root/root 1257 2021-10-06 15:30 ./usr/share/doc/phyml/run-unit-test
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-06 15:30 ./usr/share/man/man1/
-rw-r--r-- root/root 2899 2021-10-06 15:30 ./usr/share/man/man1/phyml.1.gz
+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 18040
Build-Time: 408
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 475
Job: phyml_3:3.3.20200621-2
Machine Architecture: armhf
Package: phyml
Package-Time: 933
Source-Version: 3:3.3.20200621-2
Space: 18040
Status: successful
Version: 3:3.3.20200621-2
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Finished at 2021-10-09T07:02:53Z
Build needed 00:15:33, 18040k disc space