mrbayes →
3.2.5+dfsg-1 →
armhf → 2015-07-04 06:52:35
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ mrbayes 3.2.5+dfsg-1 (armhf) 04 Jul 2015 06:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: mrbayes
Version: 3.2.5+dfsg-1
Source Version: 3.2.5+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/mrbayes-Xqp3Db/mrbayes-3.2.5+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/mrbayes-Xqp3Db' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-42d7421b-1dfc-4799-b665-9c4a519dfa41' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8047 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9892 kB]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Download source files with APT
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NOTICE: 'mrbayes' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/mrbayes/trunk/
Need to get 2648 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main mrbayes 3.2.5+dfsg-1 (dsc) [2405 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main mrbayes 3.2.5+dfsg-1 (tar) [2640 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main mrbayes 3.2.5+dfsg-1 (diff) [6336 B]
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-H0bGYN/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 77 not upgraded.
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Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libreadline-dev, mpi-default-dev, libhmsbeagle-dev (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2), autoconf, automake
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), 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-M0NDMN/apt_archive/sbuild-build-depends-mrbayes-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install mrbayes build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
autoconf automake autotools-dev bsdmainutils debhelper file gcc-5-base
gettext gettext-base groff-base intltool-debian libasprintf0c2 libcr0
libcroco3 libffi6 libgfortran3 libglib2.0-0 libhmsbeagle-dev libhmsbeagle1
libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libltdl-dev libltdl7
libmagic1 libncurses5 libncursesw5 libopenmpi-dev libopenmpi1.6 libpipeline1
libreadline-dev libreadline6-dev libsigsegv2 libtinfo-dev libtinfo5
libunistring0 libxml2 m4 man-db mpi-default-dev openmpi-common po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois
vacation dh-make gettext-doc groff blcr-dkms libhwloc-contrib-plugins
libtool-doc readline-doc less www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs libhwloc-plugins libgpm2
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autotools-dev bsdmainutils debhelper file gcc-5-base
gettext gettext-base groff-base intltool-debian libasprintf0c2 libcr0
libcroco3 libffi6 libgfortran3 libglib2.0-0 libhmsbeagle-dev libhmsbeagle1
libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libltdl-dev libltdl7
libmagic1 libopenmpi-dev libopenmpi1.6 libpipeline1 libreadline-dev
libreadline6-dev libsigsegv2 libtinfo-dev libunistring0 libxml2 m4 man-db
mpi-default-dev openmpi-common po-debconf sbuild-build-depends-mrbayes-dummy
The following packages will be upgraded:
libncurses5 libncursesw5 libtinfo5
3 upgraded, 41 newly installed, 0 to remove and 74 not upgraded.
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Get:16 http://172.17.0.1/private/ stretch-staging/main libhmsbeagle1 armhf 2.1.2-1 [48.4 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libltdl7 armhf 2.4.2-1.11 [42.5 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libsigsegv2 armhf 2.10-4 [28.2 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libhwloc5 armhf 1.11.0-1 [73.5 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main m4 armhf 1.4.17-4 [238 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main autoconf all 2.69-8 [340 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main autotools-dev all 20140911.1 [70.5 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main automake all 1:1.14.1-4 [725 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150628 [817 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libcr0 armhf 0.8.5-2.2 [30.0 kB]
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Get:33 http://172.17.0.1/private/ stretch-staging/main libltdl-dev armhf 2.4.2-1.11 [155 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libtinfo-dev armhf 5.9+20150516-2 [66.0 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libreadline6-dev armhf 6.3-8 [105 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libreadline-dev armhf 6.3-8 [994 B]
Get:37 http://172.17.0.1/private/ stretch-staging/main libhwloc-dev armhf 1.11.0-1 [131 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libibverbs1 armhf 1.1.8-1.1 [28.5 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libibverbs-dev armhf 1.1.8-1.1 [82.6 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libopenmpi1.6 armhf 1.6.5-10+rpi1 [1240 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main openmpi-common all 1.6.5-10+rpi1 [111 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main libopenmpi-dev armhf 1.6.5-10+rpi1 [447 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main mpi-default-dev armhf 1.0.2+nmu2 [3984 B]
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Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.7.0.2-5) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.19.4-1) ...
Setting up libmagic1:armhf (1:5.22+15-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.44.1-1.1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-3) ...
Setting up gcc-5-base:armhf (5.1.1-12+rpi1) ...
Setting up libgfortran3:armhf (5.1.1-12+rpi1) ...
Setting up libhmsbeagle1 (2.1.2-1) ...
Setting up libltdl7:armhf (2.4.2-1.11) ...
Setting up libsigsegv2:armhf (2.10-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libhwloc5:armhf (1.11.0-1) ...
Setting up file (1:5.22+15-2) ...
Setting up gettext-base (0.19.4-1) ...
Setting up m4 (1.4.17-4) ...
Setting up autoconf (2.69-8) ...
Setting up autotools-dev (20140911.1) ...
Setting up automake (1:1.14.1-4) ...
update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.4-1) ...
Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150628) ...
Setting up libcr0 (0.8.5-2.2) ...
Setting up libhmsbeagle-dev (2.1.2-1) ...
Setting up libltdl-dev:armhf (2.4.2-1.11) ...
Setting up libtinfo-dev:armhf (5.9+20150516-2) ...
Setting up libreadline6-dev:armhf (6.3-8) ...
Setting up libreadline-dev:armhf (6.3-8) ...
Setting up libhwloc-dev:armhf (1.11.0-1) ...
Setting up libibverbs1 (1.1.8-1.1) ...
Setting up libibverbs-dev (1.1.8-1.1) ...
Setting up libopenmpi1.6 (1.6.5-10+rpi1) ...
Setting up openmpi-common (1.6.5-10+rpi1) ...
Setting up libopenmpi-dev (1.6.5-10+rpi1) ...
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Setting up mpi-default-dev (1.0.2+nmu2) ...
Setting up sbuild-build-depends-mrbayes-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-18) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 autoconf_2.69-8 automake_1:1.14.1-4 autotools-dev_20140911.1 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150628 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gcc-5-base_5.1.1-12+rpi1 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-10 libasprintf0c2_0.19.4-1 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcr0_0.8.5-2.2 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libfakeroot_1.20.2-1 libffi6_3.1-2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran3_5.1.1-12+rpi1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-6+rpi1 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libhmsbeagle-dev_2.1.2-1 libhmsbeagle1_2.1.2-1 libhwloc-dev_1.11.0-1 libhwloc5_1.11.0-1 libibverbs-dev_1.1.8-1.1 libibverbs1_1.1.8-1.1 libisl10_0.12.2-2 libklibc_2.0.4-2+rpi1 libkmod2_18-3 liblocale-gettext-perl_1.05-8+b1 libltdl-dev_2.4.2-1.11 libltdl7_2.4.2-1.11 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20150516-2 libncursesw5_5.9+20150516-2 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libopenmpi-dev_1.6.5-10+rpi1 libopenmpi1.6_1.6.5-10+rpi1 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libreadline-dev_6.3-8 libreadline6_6.3-8 libreadline6-dev_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libsigsegv2_2.10-4 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libss2_1.42.12-1.1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-17 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo-dev_5.9+20150516-2 libtinfo5_5.9+20150516-2 libubsan0_4.9.2-10 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 m4_1.4.17-4 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-6 mountall_2.54 mpi-default-dev_1.0.2+nmu2 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 openmpi-common_1.6.5-10+rpi1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mrbayes-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 udev_215-17 util-linux_2.25.2-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Jun 29 07:02:40 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./mrbayes_3.2.5+dfsg-1.dsc
dpkg-source: info: extracting mrbayes in mrbayes-3.2.5+dfsg
dpkg-source: info: unpacking mrbayes_3.2.5+dfsg.orig.tar.xz
dpkg-source: info: unpacking mrbayes_3.2.5+dfsg-1.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
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-42d7421b-1dfc-4799-b665-9c4a519dfa41
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package mrbayes
dpkg-buildpackage: source version 3.2.5+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build mrbayes-3.2.5+dfsg
dpkg-buildpackage: 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-3.2.5+dfsg'
( cd src ; /usr/bin/make -f Makefile.in distclean )
make[2]: Entering directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg/src'
rm -f *.o *~ mb
rm -rf Makefile config.log config.status config.h *.cache
make[2]: Leaving directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg/src'
rm -f src/configure
rm -f mb mb-mpi src/mb
make[1]: Leaving directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg'
dh_clean -O--sourcedirectory=src
debian/rules build-arch
dh build-arch --sourcedirectory=src
dh_testdir -a -O--sourcedirectory=src
debian/rules override_dh_auto_configure
make[1]: Entering directory '/«BUILDDIR»/mrbayes-3.2.5+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-3.2.5+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg'
# build mb-mpi (from initial config)
LIBS="-Wl,--as-needed" dh_auto_build
make -j1
make[2]: Entering directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg/src'
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o command.o command.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o model.o model.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o likelihood.o likelihood.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o best.o best.c
mpicc -g -O2 -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-3.2.5+dfsg/src'
mv src/mb ./mb-mpi
# Now - build mb
( cd src ; make clean )
make[2]: Entering directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg/src'
rm -f *.o *~ mb
make[2]: Leaving directory '/«BUILDDIR»/mrbayes-3.2.5+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-3.2.5+dfsg/src'
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o command.o command.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o model.o model.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o likelihood.o likelihood.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o best.o best.c
gcc -g -O2 -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-3.2.5+dfsg/src'
mv src/mb .
make[1]: Leaving directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg'
dh_auto_test -a -O--sourcedirectory=src
fakeroot debian/rules binary-arch
dh binary-arch --sourcedirectory=src
dh_testroot -a -O--sourcedirectory=src
dh_prep -a -O--sourcedirectory=src
debian/rules override_dh_auto_install
make[1]: Entering directory '/«BUILDDIR»/mrbayes-3.2.5+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-3.2.5+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
debian/rules override_dh_compress
make[1]: Entering directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg'
dh_fixperms -a -O--sourcedirectory=src
debian/rules override_dh_strip
make[1]: Entering directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg'
dh_strip --dbg-package=mrbayes-dbg
make[1]: Leaving directory '/«BUILDDIR»/mrbayes-3.2.5+dfsg'
dh_makeshlibs -a -O--sourcedirectory=src
dh_shlibdeps -a -O--sourcedirectory=src
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi was not linked against libdl.so.2 (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 libhwloc.so.5 (it uses none of the library's symbols)
dh_installdeb -a -O--sourcedirectory=src
dh_gencontrol -a -O--sourcedirectory=src
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a -O--sourcedirectory=src
dh_builddeb -a -O--sourcedirectory=src
dpkg-deb: building package `mrbayes-mpi' in `../mrbayes-mpi_3.2.5+dfsg-1_armhf.deb'.
dpkg-deb: building package `mrbayes' in `../mrbayes_3.2.5+dfsg-1_armhf.deb'.
dpkg-deb: building package `mrbayes-dbg' in `../mrbayes-dbg_3.2.5+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mrbayes_3.2.5+dfsg-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build mrbayes-3.2.5+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150704-0652
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
mrbayes_3.2.5+dfsg-1_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Mon, 29 Jun 2015 08:56:47 +0200
Source: mrbayes
Binary: mrbayes mrbayes-mpi mrbayes-dbg mrbayes-doc
Architecture: armhf
Version: 3.2.5+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
mrbayes - Bayesian Inference of Phylogeny
mrbayes-dbg - Bayesian Inference of Phylogeny - debug symbols
mrbayes-doc - Bayesian Inference of Phylogeny - manual
mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version
Changes:
mrbayes (3.2.5+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Restore old get-orig-source script that works again now
Checksums-Sha1:
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61481453508849c3aef4a7f0d5d23751fd1b8fe4 1599056 mrbayes-dbg_3.2.5+dfsg-1_armhf.deb
Checksums-Sha256:
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Files:
e60df49b8931bd62fb5716c4c05670a0 478986 science optional mrbayes_3.2.5+dfsg-1_armhf.deb
024006d79d41ee951ec40c3009e8156c 488958 science optional mrbayes-mpi_3.2.5+dfsg-1_armhf.deb
02e1cad6e6d8af0c654c61e459a1ec42 1599056 debug extra mrbayes-dbg_3.2.5+dfsg-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
mrbayes_3.2.5+dfsg-1_armhf.deb
──────────────────────────────
new debian package, version 2.0.
size 478986 bytes: control archive=897 bytes.
842 bytes, 18 lines control
318 bytes, 5 lines md5sums
Package: mrbayes
Version: 3.2.5+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1375
Depends: libc6 (>= 2.7), libhmsbeagle1, libreadline6 (>= 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 2015-07-04 06:51 ./
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/bin/
-rwxr-xr-x root/root 1403112 2015-07-04 06:51 ./usr/bin/mb
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/doc/mrbayes/
-rw-r--r-- root/root 311 2013-09-12 08:57 ./usr/share/doc/mrbayes/README.Debian
-rw-r--r-- root/root 1771 2015-06-29 06:56 ./usr/share/doc/mrbayes/changelog.Debian.gz
-rw-r--r-- root/root 1482 2013-09-12 08:57 ./usr/share/doc/mrbayes/copyright
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/man/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/man/man1/
-rw-r--r-- root/root 206 2015-07-04 06:51 ./usr/share/man/man1/mb.1.gz
mrbayes-mpi_3.2.5+dfsg-1_armhf.deb
──────────────────────────────────
new debian package, version 2.0.
size 488958 bytes: control archive=1033 bytes.
1021 bytes, 21 lines control
399 bytes, 6 lines md5sums
Package: mrbayes-mpi
Source: mrbayes
Version: 3.2.5+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1399
Depends: libc6 (>= 2.7), libhmsbeagle1, libhwloc5 (>= 1.11.0), libopenmpi1.6, libreadline6 (>= 6.0), mpi-default-bin
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 2015-07-04 06:52 ./
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/bin/
-rwxr-xr-x root/root 162 2013-09-12 08:57 ./usr/bin/mb-mpi
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/lib/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/lib/mrbayes-mpi/
-rwxr-xr-x root/root 1427736 2015-07-04 06:51 ./usr/lib/mrbayes-mpi/mb-mpi
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/doc/mrbayes-mpi/
-rw-r--r-- root/root 348 2013-09-12 08:57 ./usr/share/doc/mrbayes-mpi/README.Debian
-rw-r--r-- root/root 1771 2015-06-29 06:56 ./usr/share/doc/mrbayes-mpi/changelog.Debian.gz
-rw-r--r-- root/root 1482 2013-09-12 08:57 ./usr/share/doc/mrbayes-mpi/copyright
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/man/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/man/man1/
-rw-r--r-- root/root 226 2015-07-04 06:51 ./usr/share/man/man1/mb-mpi.1.gz
mrbayes-dbg_3.2.5+dfsg-1_armhf.deb
──────────────────────────────────
new debian package, version 2.0.
size 1599056 bytes: control archive=1056 bytes.
1190 bytes, 23 lines control
362 bytes, 4 lines md5sums
Package: mrbayes-dbg
Source: mrbayes
Version: 3.2.5+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1706
Depends: mrbayes (= 3.2.5+dfsg-1) | mrbayes-mpi (= 3.2.5+dfsg-1)
Breaks: mrbayes (>> 3.2.5+dfsg-1), mrbayes (<< 3.2.5+dfsg-1), mrbayes-mpi (>> 3.2.5+dfsg-1), mrbayes-mpi (<< 3.2.5+dfsg-1)
Section: debug
Priority: extra
Homepage: http://mrbayes.csit.fsu.edu/
Description: Bayesian Inference of Phylogeny - debug symbols
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.
.
The package provides the debug symbols that are otherwise stripped from
the binaries to reduce the footprint of the package. This package can be
installed to help debugging of problems when running mrbayes.
drwxr-xr-x root/root 0 2015-07-04 06:52 ./
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/lib/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/lib/debug/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 864532 2015-07-04 06:51 ./usr/lib/debug/.build-id/bf/c99392583e3d17600a170f74e981277a85861e.debug
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/lib/debug/.build-id/f0/
-rw-r--r-- root/root 877932 2015-07-04 06:51 ./usr/lib/debug/.build-id/f0/79b4b948fdc97fd53d94d3503fe8a06bf403c0.debug
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-07-04 06:51 ./usr/share/doc/mrbayes-dbg/
-rw-r--r-- root/root 1771 2015-06-29 06:56 ./usr/share/doc/mrbayes-dbg/changelog.Debian.gz
-rw-r--r-- root/root 1482 2013-09-12 08:57 ./usr/share/doc/mrbayes-dbg/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 33500
Build-Time: 1448
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 292
Job: mrbayes_3.2.5+dfsg-1
Machine Architecture: armhf
Package: mrbayes
Package-Time: 1800
Source-Version: 3.2.5+dfsg-1
Space: 33500
Status: successful
Version: 3.2.5+dfsg-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150704-0652
Build needed 00:30:00, 33500k disc space