mrbayes →
3.2.6+dfsg-2 →
armhf → 2017-07-26 08:37:29
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| mrbayes 3.2.6+dfsg-2 (armhf) Wed, 26 Jul 2017 07:57:42 +0000 |
+==============================================================================+
Package: mrbayes
Version: 3.2.6+dfsg-2
Source Version: 3.2.6+dfsg-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-6cfab707-c868-4efd-b535-03155670c7c0' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [11.9 MB]
Fetched 22.0 MB in 25s (868 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: 'mrbayes' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/mrbayes.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/mrbayes.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2653 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main mrbayes 3.2.6+dfsg-2 (dsc) [2381 B]
Get:2 http://172.17.0.1/private buster-staging/main mrbayes 3.2.6+dfsg-2 (tar) [2644 kB]
Get:3 http://172.17.0.1/private buster-staging/main mrbayes 3.2.6+dfsg-2 (diff) [6716 B]
Fetched 2653 kB in 0s (5436 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mrbayes-JJVdht/mrbayes-3.2.6+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mrbayes-JJVdht' 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-soNqTD/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-soNqTD/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-soNqTD/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-soNqTD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (3090 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 NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 49 not upgraded.
Need to get 774 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 774 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12681 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 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), libreadline-dev, mpi-default-dev, libhmsbeagle-dev (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2), autoconf, automake
Filtered Build-Depends: debhelper (>= 9), libreadline-dev, mpi-default-dev, libhmsbeagle-dev (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2), autoconf, automake
dpkg-deb: building package 'sbuild-build-depends-mrbayes-dummy' in '/<<BUILDDIR>>/resolver-soNqTD/apt_archive/sbuild-build-depends-mrbayes-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-mrbayes-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-soNqTD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ Sources [546 B]
Get:5 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ Packages [627 B]
Fetched 2506 B in 0s (3385 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install mrbayes build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-6 debhelper
dh-autoreconf dh-strip-nondeterminism file g++-6 gcc-6 gcc-6-base gcc-7-base
gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan3
libatomic1 libbsd0 libcc1-0 libclang-common-4.0-dev libclc-amdgcn libclc-dev
libclc-r600 libcroco3 libdrm-amdgpu1 libdrm-freedreno1 libdrm-nouveau2
libdrm-radeon1 libedit2 libelf1 libexpat1 libffi6
libfile-stripnondeterminism-perl libgcc-6-dev libgcc1 libgfortran3
libglib2.0-0 libgomp1 libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev
libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu57 libllvm3.9
libllvm4.0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libncurses5
libncursesw5 libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi2
libpciaccess0 libpipeline1 libreadline-dev libsensors4 libsigsegv2
libstdc++-6-dev libstdc++6 libtimedate-perl libtinfo-dev libtinfo5 libtool
libubsan0 libunistring2 libxml2 m4 man-db mesa-opencl-icd mpi-default-dev
ocl-icd-libopencl1 openmpi-common po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-6-locales dh-make gcc-6-doc libstdc++6-6-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan3-dbg liblsan0-dbg
libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg
gettext-doc libasprintf-dev libgettextpo-dev groff libhwloc-contrib-plugins
libtool-doc openmpi-doc pciutils readline-doc lm-sensors libstdc++-6-doc
gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 openmpi-bin xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gcc-7-base gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0
libclang-common-4.0-dev libclc-amdgcn libclc-dev libclc-r600 libcroco3
libdrm-amdgpu1 libdrm-freedreno1 libdrm-nouveau2 libdrm-radeon1 libedit2
libelf1 libexpat1 libffi6 libfile-stripnondeterminism-perl libgfortran3
libglib2.0-0 libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins
libhwloc5 libibverbs-dev libibverbs1 libicu57 libllvm3.9 libllvm4.0
libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200
libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libreadline-dev
libsensors4 libsigsegv2 libtimedate-perl libtinfo-dev libtool libunistring2
libxml2 m4 man-db mesa-opencl-icd mpi-default-dev ocl-icd-libopencl1
openmpi-common po-debconf sbuild-build-depends-mrbayes-dummy
The following packages will be upgraded:
cpp-6 g++-6 gcc-6 gcc-6-base libasan3 libatomic1 libcc1-0 libgcc-6-dev
libgcc1 libgomp1 libncurses5 libncursesw5 libstdc++-6-dev libstdc++6
libtinfo5 libubsan0
16 upgraded, 68 newly installed, 0 to remove and 33 not upgraded.
Need to get 106 MB of archives.
After this operation, 378 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-soNqTD/apt_archive ./ sbuild-build-depends-mrbayes-dummy 0.invalid.0 [832 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.1.0-9+rpi1 [180 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:7.1.0-9+rpi1 [38.6 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 7.1.0-9+rpi1 [334 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libncurses5 armhf 6.0+20170715-2 [73.7 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libtinfo5 armhf 6.0+20170715-2 [296 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libncursesw5 armhf 6.0+20170715-2 [93.5 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 7.1.0-9+rpi1 [63.1 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 7.1.0-9+rpi1 [6732 B]
Get:15 http://172.17.0.1/private buster-staging/main armhf libasan3 armhf 6.4.0-1+rpi1 [267 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.1.0-9+rpi1 [100 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf g++-6 armhf 6.4.0-1+rpi1 [5553 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libstdc++-6-dev armhf 6.4.0-1+rpi1 [1450 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf gcc-6 armhf 6.4.0-1+rpi1 [5429 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libgcc-6-dev armhf 6.4.0-1+rpi1 [511 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 7.1.0-9+rpi1 [30.3 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf cpp-6 armhf 6.4.0-1+rpi1 [5112 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf gcc-6-base armhf 6.4.0-1+rpi1 [181 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20170329-1 [69.0 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libffi6 armhf 3.2.1-6 [18.7 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.52.3-1 [2576 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libunistring2 armhf 0.9.7-2 [351 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libllvm4.0 armhf 1:4.0.1-1+rpi1 [10.6 MB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libclang-common-4.0-dev armhf 1:4.0.1-1+rpi1 [1027 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libclc-dev all 0.2.0+git20170330-2 [24.9 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libclc-amdgcn all 0.2.0+git20170330-2 [20.4 MB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libclc-r600 all 0.2.0+git20170330-2 [14.4 MB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libdrm-amdgpu1 armhf 2.4.81-2+rpi1 [26.0 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libdrm-freedreno1 armhf 2.4.81-2+rpi1 [24.4 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libdrm-nouveau2 armhf 2.4.81-2+rpi1 [24.0 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libdrm-radeon1 armhf 2.4.81-2+rpi1 [28.2 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.168-1 [154 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.2-2 [66.3 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libgfortran3 armhf 6.4.0-1+rpi1 [166 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf ocl-icd-libopencl1 armhf 2.2.11-1 [35.5 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libllvm3.9 armhf 1:3.9.1-10+rpi1 [9681 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libsensors4 armhf 1:3.4.0-4 [50.5 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf mesa-opencl-icd armhf 13.0.6-1+b5 [5939 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libhmsbeagle1v5 armhf 2.1.2+20160831-5+b8 [89.8 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libhmsbeagle-dev armhf 2.1.2+20160831-5+b8 [154 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-2 [386 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2 [159 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.2.27-2 [53.7 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.2.27-2 [113 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.13.4-1 [47.4 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libtinfo-dev armhf 6.0+20170715-2 [66.6 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-3 [109 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.5-1+rpi1 [83.2 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.5-1+rpi1 [136 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.5-1+rpi1 [14.9 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 1.2.1-2 [35.4 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 1.2.1-2 [104 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libopenmpi2 armhf 2.1.1-6+rpi1 [1750 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 2.1.1-6+rpi1 [154 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 2.1.1-6+rpi1 [1019 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf mpi-default-dev armhf 1.8 [4846 B]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up libltdl-dev:armhf (2.4.6-2) ...
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No schema files found: doing nothing.
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Setting up gcc-6 (6.4.0-1+rpi1) ...
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Setting up automake (1:1.15.1-2) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
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Setting up debhelper (10.2.5) ...
Setting up sbuild-build-depends-mrbayes-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-12) ...
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_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1+rpi1 gcc-6_6.4.0-1+rpi1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4.6 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.9+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4 cpp-6_6.4.0-1+rpi1 dash_0.5.8-2.4 debconf_1.5.61 debhelper_10.2.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20161106-2 g++_4:6.3.0-4 g++-6_6.4.0-1+rpi1 gcc_4:6.3.0-4 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.4.0-1+rpi1 gcc-6-base_6.4.0-1+rpi1 gcc-7-base_7.1.0-9+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.48 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-3 libapt-pkg5.0_1.4.6 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1+rpi1 libassuan0_2.4.3-2 libatomic1_7.1.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libblkid1_2.29.2-1 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9+rpi1 libclang-common-4.0-dev_1:4.0.1-1+rpi1 libclc-amdgcn_0.2.0+git20170330-2 libclc-dev_0.2.0+git20170330-2 libclc-r600_0.2.0+git20170330-2 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.18-1 libdebconfclient0_0.228 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm-amdgpu1_2.4.81-2+rpi1 libdrm-freedreno1_2.4.81-2+rpi1 libdrm-nouveau2_2.4.81-2+rpi1 libdrm-radeon1_2.4.81-2+rpi1 libdrm2_2.4.74-1 libedit2_3.1-20170329-1 libelf1_0.168-1 libexpat1_2.2.2-2 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1+rpi1 libgcc1_1:7.1.0-9+rpi1 libgcrypt20_1.7.7-2 libgdbm3_1.8.3-14 libgfortran3_6.4.0-1+rpi1 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgomp1_7.1.0-9+rpi1 libgpg-error0_1.26-2 libhmsbeagle-dev_2.1.2+20160831-5+b8 libhmsbeagle1v5_2.1.2+20160831-5+b8 libhwloc-dev_1.11.5-1+rpi1 libhwloc-plugins_1.11.5-1+rpi1 libhwloc5_1.11.5-1+rpi1 libibverbs-dev_1.2.1-2 libibverbs1_1.2.1-2 libicu57_57.1-6 libidn11_1.33-1 libip4tc0_1.6.0+snapshot20161117-6 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 libllvm3.9_1:3.9.1-10+rpi1 libllvm4.0_1:4.0.1-1+rpi1 liblocale-gettext-perl_1.07-3+b1 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnpth0_1.3-1 libopenmpi-dev_2.1.1-6+rpi1 libopenmpi2_2.1.1-6+rpi1 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpciaccess0_0.13.4-1 libpcre3_2:8.39-3 libperl5.24_5.24.1-4 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.29-3 libprocps6_2:3.3.12-3 libreadline-dev_7.0-3 libreadline7_7.0-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsensors4_1:3.4.0-4 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 libsystemd0_233-9 libtext-charwidth-perl_0.04-7+b7 libtext-iconv-perl_1.7-5+b8 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20170715-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-9+rpi1 libudev1_233-9 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-3 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mesa-opencl-icd_13.0.6-1+b5 mount_2.29.2-1 mountall_2.54 mpi-default-dev_1.8 multiarch-support_2.24-12 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 ocl-icd-libopencl1_2.2.11-1 openmpi-common_2.1.1-6+rpi1 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.24.1-4 perl-base_5.24.1-4 perl-modules-5.24_5.24.1-4 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mrbayes-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_233-9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2017b-2 udev_233-9 util-linux_2.29.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Jul 21 04:39:37 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./mrbayes_3.2.6+dfsg-2.dsc
dpkg-source: info: extracting mrbayes in /<<BUILDDIR>>/mrbayes-3.2.6+dfsg
dpkg-source: info: unpacking mrbayes_3.2.6+dfsg.orig.tar.xz
dpkg-source: info: unpacking mrbayes_3.2.6+dfsg-2.debian.tar.xz
dpkg-source: info: applying as-needed.patch
dpkg-source: info: applying ldlibs.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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-6cfab707-c868-4efd-b535-03155670c7c0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package mrbayes
dpkg-buildpackage: info: source version 3.2.6+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build mrbayes-3.2.6+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --sourcedirectory=src
dh_testdir -O--sourcedirectory=src
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
( cd src ; /usr/bin/make -f Makefile.in distclean )
make[2]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg/src'
rm -f *.o *~ mb
rm -rf Makefile config.log config.status config.h *.cache
make[2]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg/src'
rm -f src/configure
rm -f mb mb-mpi src/mb
make[1]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
dh_clean -O--sourcedirectory=src
debian/rules build-arch
dh build-arch --sourcedirectory=src
dh_testdir -a -O--sourcedirectory=src
dh_update_autotools_config -a -O--sourcedirectory=src
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
#Configure for MPI at first
( cd src ; autoconf )
dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
configure: NOTICE: Because the variable $CFLAGS is defined in your shell, the
default MrBayes flags will be overridden. To ensure optimal performance, please check
that your $CFLAGS variable is set correctly. Alternatively, unset the $CFLAGS
variable in your shell in order to use the default MrBayes compiler options.
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for exp in -lm... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for mpicc... yes
checking for SSE support... no
checking for /usr/include/libhmsbeagle/libhmsbeagle/beagle.h... no
checking for /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h... yes
checking for /usr/include/libhmsbeagle/libhmsbeagle/platform.h... no
checking for /usr/include/libhmsbeagle-1/libhmsbeagle/platform.h... yes
checking for /usr/lib... yes
checking for readline in -lreadline... yes
checking for rl_completion_matches function... yes
checking for 32 or 64 bits cpu... 32
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
make[1]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
# build mb-mpi (from initial config)
LIBS="-Wl,--as-needed" dh_auto_build
make -j1
make[2]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg/src'
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o command.o command.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o model.o model.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o likelihood.o likelihood.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o best.o best.c
mpicc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -o mb bayes.o command.o model.o mcmc.o likelihood.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm
make[2]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg/src'
mv src/mb ./mb-mpi
# Now - build mb
( cd src ; make clean )
make[2]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg/src'
rm -f *.o *~ mb
make[2]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg/src'
dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=no --enable-debug=yes
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
configure: NOTICE: Because the variable $CFLAGS is defined in your shell, the
default MrBayes flags will be overridden. To ensure optimal performance, please check
that your $CFLAGS variable is set correctly. Alternatively, unset the $CFLAGS
variable in your shell in order to use the default MrBayes compiler options.
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for exp in -lm... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for SSE support... no
checking for /usr/include/libhmsbeagle/libhmsbeagle/beagle.h... no
checking for /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h... yes
checking for /usr/include/libhmsbeagle/libhmsbeagle/platform.h... no
checking for /usr/include/libhmsbeagle-1/libhmsbeagle/platform.h... yes
checking for /usr/lib... yes
checking for readline in -lreadline... yes
checking for rl_completion_matches function... yes
checking for 32 or 64 bits cpu... 32
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
LIBS="-Wl,--as-needed" dh_auto_build
make -j1
make[2]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg/src'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o command.o command.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o model.o model.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o likelihood.o likelihood.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o best.o best.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -o mb bayes.o command.o model.o mcmc.o likelihood.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm
make[2]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg/src'
mv src/mb .
make[1]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
dh_auto_test -a -O--sourcedirectory=src
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --sourcedirectory=src
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--sourcedirectory=src
dh_prep -a -O--sourcedirectory=src
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
echo "Do not try to install to /usr/local/bin"
Do not try to install to /usr/local/bin
make[1]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
dh_install -a -O--sourcedirectory=src
dh_installdocs -a -O--sourcedirectory=src
dh_installchangelogs -a -O--sourcedirectory=src
dh_installman -a -O--sourcedirectory=src
dh_perl -a -O--sourcedirectory=src
dh_link -a -O--sourcedirectory=src
dh_strip_nondeterminism -a -O--sourcedirectory=src
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<BUILDDIR>>/mrbayes-3.2.6+dfsg'
dh_fixperms -a -O--sourcedirectory=src
dh_strip -a -O--sourcedirectory=src
dh_makeshlibs -a -O--sourcedirectory=src
dh_shlibdeps -a -O--sourcedirectory=src
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes/usr/bin/mb was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a -O--sourcedirectory=src
dh_gencontrol -a -O--sourcedirectory=src
dh_md5sums -a -O--sourcedirectory=src
dh_builddeb -a -O--sourcedirectory=src
dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.6+dfsg-2_armhf.deb'.
dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.6+dfsg-2_armhf.deb'.
dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.6+dfsg-2_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.6+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mrbayes_3.2.6+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build mrbayes-3.2.6+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-07-26T08:33:31Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mrbayes_3.2.6+dfsg-2_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 19 Jul 2017 23:40:13 -0400
Source: mrbayes
Binary: mrbayes mrbayes-mpi mrbayes-doc
Architecture: armhf
Version: 3.2.6+dfsg-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nadiya Sitdykova <rovenskasa@gmail.com>
Description:
mrbayes - Bayesian Inference of Phylogeny
mrbayes-doc - Bayesian Inference of Phylogeny - manual
mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version
Changes:
mrbayes (3.2.6+dfsg-2) unstable; urgency=medium
.
* Team upload.
.
[ Nadiya Sitdykova ]
* Add autopkgtest test-suite
* Add tests for mb-mpi
* Add missing ssh dependency for mb-mpi
.
[ Steffen Moeller ]
* [debian/upstream/metadata] added refs to registries
.
[ Andreas Tille ]
* cme fix dpkg-control
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Files:
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45a2f5c03c76e04881aec42f76a621af 855046 debug extra mrbayes-mpi-dbgsym_3.2.6+dfsg-2_armhf.deb
75ee3b19de31e59b25b1b3973244663a 488566 science optional mrbayes-mpi_3.2.6+dfsg-2_armhf.deb
1d6d1f208dbdd9d5f7d48ecf93ed81e7 6261 science optional mrbayes_3.2.6+dfsg-2_armhf.buildinfo
dec6c51deb2761df4608702f3e998a1b 582890 science optional mrbayes_3.2.6+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mrbayes-dbgsym_3.2.6+dfsg-2_armhf.deb
-------------------------------------
new debian package, version 2.0.
size 833756 bytes: control archive=483 bytes.
416 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: mrbayes-dbgsym
Source: mrbayes
Version: 3.2.6+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 889
Depends: mrbayes (= 3.2.6+dfsg-2)
Section: debug
Priority: extra
Homepage: http://mrbayes.csit.fsu.edu/
Description: Debug symbols for mrbayes
Build-Ids: e29f37a828536a04e1ca8202a978e5c360dde37e
drwxr-xr-x root/root 0 2017-07-20 03:40 ./
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/debug/.build-id/e2/
-rw-r--r-- root/root 900016 2017-07-20 03:40 ./usr/lib/debug/.build-id/e2/9f37a828536a04e1ca8202a978e5c360dde37e.debug
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-07-20 03:40 ./usr/share/doc/mrbayes-dbgsym -> mrbayes
mrbayes-mpi-dbgsym_3.2.6+dfsg-2_armhf.deb
-----------------------------------------
new debian package, version 2.0.
size 855046 bytes: control archive=486 bytes.
428 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: mrbayes-mpi-dbgsym
Source: mrbayes
Version: 3.2.6+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 911
Depends: mrbayes-mpi (= 3.2.6+dfsg-2)
Section: debug
Priority: extra
Homepage: http://mrbayes.csit.fsu.edu/
Description: Debug symbols for mrbayes-mpi
Build-Ids: 1746a445aaaf29bf3e98d7adc8105d7274e1dc26
drwxr-xr-x root/root 0 2017-07-20 03:40 ./
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/debug/.build-id/17/
-rw-r--r-- root/root 922176 2017-07-20 03:40 ./usr/lib/debug/.build-id/17/46a445aaaf29bf3e98d7adc8105d7274e1dc26.debug
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-07-20 03:40 ./usr/share/doc/mrbayes-mpi-dbgsym -> mrbayes-mpi
mrbayes-mpi_3.2.6+dfsg-2_armhf.deb
----------------------------------
new debian package, version 2.0.
size 488566 bytes: control archive=957 bytes.
1003 bytes, 21 lines control
399 bytes, 6 lines md5sums
Package: mrbayes-mpi
Source: mrbayes
Version: 3.2.6+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1397
Depends: libc6 (>= 2.7), libhmsbeagle1v5, libopenmpi2, libreadline7 (>= 6.0), mpi-default-bin, ssh
Suggests: mpi-default, mrbayes-doc
Section: science
Priority: optional
Homepage: http://mrbayes.csit.fsu.edu/
Description: Bayesian Inference of Phylogeny - mpi version
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
conditioned on the observations. The conditioning is accomplished using
Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
.
This package offers a binary compiled for parallel computation with MPI.
drwxr-xr-x root/root 0 2017-07-20 03:40 ./
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/bin/
-rwxr-xr-x root/root 162 2017-07-20 03:40 ./usr/bin/mb-mpi
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/lib/mrbayes-mpi/
-rwxr-xr-x root/root 1411528 2017-07-20 03:40 ./usr/lib/mrbayes-mpi/mb-mpi
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/doc/mrbayes-mpi/
-rw-r--r-- root/root 348 2017-07-20 03:40 ./usr/share/doc/mrbayes-mpi/README.Debian
-rw-r--r-- root/root 2027 2017-07-20 03:40 ./usr/share/doc/mrbayes-mpi/changelog.Debian.gz
-rw-r--r-- root/root 1482 2017-07-20 03:40 ./usr/share/doc/mrbayes-mpi/copyright
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/man/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/man/man1/
-rw-r--r-- root/root 226 2017-07-20 03:40 ./usr/share/man/man1/mb-mpi.1.gz
mrbayes_3.2.6+dfsg-2_armhf.deb
------------------------------
new debian package, version 2.0.
size 582890 bytes: control archive=1157 bytes.
844 bytes, 18 lines control
1105 bytes, 15 lines md5sums
Package: mrbayes
Version: 3.2.6+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1478
Depends: libc6 (>= 2.7), libhmsbeagle1v5, libreadline7 (>= 6.0)
Suggests: mrbayes-doc
Section: science
Priority: optional
Homepage: http://mrbayes.csit.fsu.edu/
Description: Bayesian Inference of Phylogeny
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
conditioned on the observations. The conditioning is accomplished using
Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
drwxr-xr-x root/root 0 2017-07-20 03:40 ./
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/bin/
-rwxr-xr-x root/root 1386912 2017-07-20 03:40 ./usr/bin/mb
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/doc/mrbayes/
-rw-r--r-- root/root 311 2017-07-20 03:40 ./usr/share/doc/mrbayes/README.Debian
-rw-r--r-- root/root 262 2017-07-20 03:40 ./usr/share/doc/mrbayes/README.test
-rw-r--r-- root/root 2027 2017-07-20 03:40 ./usr/share/doc/mrbayes/changelog.Debian.gz
-rw-r--r-- root/root 1482 2017-07-20 03:40 ./usr/share/doc/mrbayes/copyright
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/doc/mrbayes/examples/
-rw-r--r-- root/root 3041 2015-04-07 17:23 ./usr/share/doc/mrbayes/examples/avian_ovomucoids.nex.gz
-rw-r--r-- root/root 1689 2015-01-27 12:31 ./usr/share/doc/mrbayes/examples/codon.nex
-rw-r--r-- root/root 15939 2015-01-27 12:31 ./usr/share/doc/mrbayes/examples/cynmix.nex.gz
-rw-r--r-- root/root 8740 2015-01-27 12:31 ./usr/share/doc/mrbayes/examples/finch.nex.gz
-rw-r--r-- root/root 60092 2015-04-07 17:23 ./usr/share/doc/mrbayes/examples/hymfossil.nex.gz
-rw-r--r-- root/root 2932 2015-01-27 12:31 ./usr/share/doc/mrbayes/examples/primates.nex.gz
-rw-r--r-- root/root 2563 2014-11-21 11:58 ./usr/share/doc/mrbayes/examples/replicase.nex.gz
-rw-r--r-- root/root 9885 2015-04-07 17:23 ./usr/share/doc/mrbayes/examples/sceloporus.nex.gz
-rw-r--r-- root/root 405 2017-07-20 03:40 ./usr/share/doc/mrbayes/run-unit-test
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/man/
drwxr-xr-x root/root 0 2017-07-20 03:40 ./usr/share/man/man1/
-rw-r--r-- root/root 206 2017-07-20 03:40 ./usr/share/man/man1/mb.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 34076
Build-Time: 1428
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 674
Job: mrbayes_3.2.6+dfsg-2
Machine Architecture: armhf
Package: mrbayes
Package-Time: 2149
Source-Version: 3.2.6+dfsg-2
Space: 34076
Status: successful
Version: 3.2.6+dfsg-2
--------------------------------------------------------------------------------
Finished at 2017-07-26T08:33:31Z
Build needed 00:35:49, 34076k disc space