mrbayes →
3.2.5+dfsg-2 →
armhf → 2015-09-13 06:46:50
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-03
╔══════════════════════════════════════════════════════════════════════════════╗
║ mrbayes 3.2.5+dfsg-2 (armhf) 13 Sep 2015 06:17 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: mrbayes
Version: 3.2.5+dfsg-2
Source Version: 3.2.5+dfsg-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/mrbayes-wITNI1/mrbayes-3.2.5+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/mrbayes-wITNI1' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-9d93f419-1674-4deb-9bcb-23ef2ed05268' 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 [8326 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.2 MB]
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┌──────────────────────────────────────────────────────────────────────────────┐
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Check 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-2 (dsc) [2405 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main mrbayes 3.2.5+dfsg-2 (tar) [2640 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main mrbayes 3.2.5+dfsg-2 (diff) [6380 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-TRrL8H/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ 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
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 0 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-rWSVTY/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 gettext
gettext-base groff-base intltool-debian libasprintf0v5 libcr0 libcroco3
libffi6 libgfortran3 libglib2.0-0 libhmsbeagle-dev libhmsbeagle1v5
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
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 xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autotools-dev bsdmainutils debhelper file gettext
gettext-base groff-base intltool-debian libasprintf0v5 libcr0 libcroco3
libffi6 libgfortran3 libglib2.0-0 libhmsbeagle-dev libhmsbeagle1v5
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
0 upgraded, 40 newly installed, 0 to remove and 0 not upgraded.
Need to get 12.9 MB/12.9 MB of archives.
After this operation, 43.0 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.2-1 [973 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0v5 armhf 0.19.5.1-1 [32.0 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
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Get:11 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.2.1-16+rpi1 [154 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libltdl7 armhf 2.4.2-1.11 [42.5 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libsigsegv2 armhf 2.10-4 [28.2 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libhwloc5 armhf 1.11.0-1 [73.5 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.5.1-1 [118 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main m4 armhf 1.4.17-4 [238 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main autoconf all 2.69-9 [338 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main autotools-dev all 20140911.1 [70.5 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main automake all 1:1.15-3 [735 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.5.1-1 [1386 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150811 [817 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libcr0 armhf 0.8.5-2.2 [30.0 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libhmsbeagle1v5 armhf 2.1.2+20150609-1.1 [48.0 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libhmsbeagle-dev armhf 2.1.2+20150609-1.1 [149 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libltdl-dev armhf 2.4.2-1.11 [155 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main libtinfo-dev armhf 6.0+20150810-1 [65.8 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libreadline6-dev armhf 6.3-8+b3 [105 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libreadline-dev armhf 6.3-8+b3 [958 B]
Get:33 http://172.17.0.1/private/ stretch-staging/main libhwloc-dev armhf 1.11.0-1 [131 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libibverbs1 armhf 1.1.8-1.1 [28.5 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libibverbs-dev armhf 1.1.8-1.1 [82.6 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libopenmpi1.6 armhf 1.6.5-10+rpi1 [1240 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main openmpi-common all 1.6.5-10+rpi1 [111 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libopenmpi-dev armhf 1.6.5-10+rpi1 [447 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main mpi-default-dev armhf 1.0.2+nmu2 [3984 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-4.9_4.9.3-4 g++-5_5.2.1-16+rpi1 gcc-4.9_4.9.3-4 gcc-5_5.2.1-16+rpi1 libc6-dev_2.19-19 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.10.2 autoconf_2.69-9 automake_1:1.15-3 autotools-dev_20140911.1 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.26.2-9 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-4.9_4.9.3-4 cpp-5_5.2.1-16+rpi1 dash_0.5.7-4 debconf_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:5.2.1-4+rpi2 g++-4.9_4.9.3-4 g++-5_5.2.1-16+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-4 gcc-4.9_4.9.3-4 gcc-4.9-base_4.9.3-4 gcc-5_5.2.1-16+rpi1 gcc-5-base_5.2.1-16+rpi1 gettext_0.19.5.1-1 gettext-base_0.19.5.1-1 gnupg_1.4.19-5 gpgv_1.4.19-5 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.16 init_1.23 init-system-helpers_1.23 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.9.2-3 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libasan1_4.9.3-4 libasan2_5.2.1-16+rpi1 libasprintf0v5_0.19.5.1-1 libatomic1_5.2.1-16+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-1 libaudit1_1:2.4.4-1 libblkid1_2.26.2-9 libbz2-1.0_1.0.6-8 libc-bin_2.19-19 libc-dev-bin_2.19-19 libc6_2.19-19 libc6-dev_2.19-19 libcap2_1:2.24-11 libcap2-bin_1:2.24-11 libcc1-0_5.2.1-16+rpi1 libcloog-isl4_0.18.3-1 libcomerr2_1.42.13-1 libcr0_0.8.5-2.2 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.8.20-1 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.104-1 libdpkg-perl_1.18.2 libdrm2_2.4.64-1 libfakeroot_1.20.2-1 libfdisk1_2.26.2-9 libffi6_3.2.1-3 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.3-4 libgcc-5-dev_5.2.1-16+rpi1 libgcc1_1:5.2.1-16+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran3_5.2.1-16+rpi1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-7+rpi1 libgomp1_5.2.1-16+rpi1 libgpg-error0_1.19-2 libhmsbeagle-dev_2.1.2+20150609-1.1 libhmsbeagle1v5_2.1.2+20150609-1.1 libhwloc-dev_1.11.0-1 libhwloc5_1.11.0-1 libibverbs-dev_1.1.8-1.1 libibverbs1_1.1.8-1.1 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.05-9 libltdl-dev_2.4.2-1.11 libltdl7_2.4.2-1.11 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.22+15-2 libmount1_2.26.2-9 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20150810-1 libncursesw5_6.0+20150810-1 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_2:8.35-7.1 libpipeline1_1.4.1-1 libpng12-0_1.2.50-2+b2 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libreadline-dev_6.3-8+b3 libreadline6_6.3-8+b3 libreadline6-dev_6.3-8+b3 libseccomp2_2.2.3-2 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+b1 libsmartcols1_2.26.2-9 libss2_1.42.13-1 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 libsystemd0_225-1 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20150810-1 libtinfo5_6.0+20150810-1 libubsan0_5.2.1-16+rpi1 libudev1_225-1 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.26.2-9 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 m4_1.4.17-4 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.2-1 mawk_1.3.3-17 mount_2.26.2-9 mountall_2.54 mpi-default-dev_1.0.2+nmu2 multiarch-support_2.19-19 ncurses-base_6.0+20150810-1 ncurses-bin_6.0+20150810-1 openmpi-common_1.6.5-10+rpi1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.10-2 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_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_225-1 systemd-sysv_225-1 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-1 tzdata_2015f-1 udev_225-1 util-linux_2.26.2-9 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Sep 5 13:56:55 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-2.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-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
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=root
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-9d93f419-1674-4deb-9bcb-23ef2ed05268
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package mrbayes
dpkg-buildpackage: source version 3.2.5+dfsg-2
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' in '../mrbayes_3.2.5+dfsg-2_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.5+dfsg-2_armhf.deb'.
dpkg-deb: building package 'mrbayes-dbg' in '../mrbayes-dbg_3.2.5+dfsg-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mrbayes_3.2.5+dfsg-2_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 20150913-0644
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
mrbayes_3.2.5+dfsg-2_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Sat, 05 Sep 2015 15:53:40 +0200
Source: mrbayes
Binary: mrbayes mrbayes-mpi mrbayes-dbg mrbayes-doc
Architecture: armhf
Version: 3.2.5+dfsg-2
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
Closes: 798070
Changes:
mrbayes (3.2.5+dfsg-2) unstable; urgency=medium
.
* Avoid hardcoded shared library dependency
Closes: #798070
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Files:
430af305170ce312ed865e75b8aa4070 1596214 debug extra mrbayes-dbg_3.2.5+dfsg-2_armhf.deb
954409749f842031f3614cd697edddce 490438 science optional mrbayes-mpi_3.2.5+dfsg-2_armhf.deb
1659bce1f07de2281cdb3500c36a5f26 479082 science optional mrbayes_3.2.5+dfsg-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
mrbayes-dbg_3.2.5+dfsg-2_armhf.deb
──────────────────────────────────
new debian package, version 2.0.
size 1596214 bytes: control archive=989 bytes.
1190 bytes, 23 lines control
362 bytes, 4 lines md5sums
Package: mrbayes-dbg
Source: mrbayes
Version: 3.2.5+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1720
Depends: mrbayes (= 3.2.5+dfsg-2) | mrbayes-mpi (= 3.2.5+dfsg-2)
Breaks: mrbayes (>> 3.2.5+dfsg-2), mrbayes (<< 3.2.5+dfsg-2), mrbayes-mpi (>> 3.2.5+dfsg-2), mrbayes-mpi (<< 3.2.5+dfsg-2)
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 2015-09-13 06:43 ./
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/lib/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/lib/debug/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/lib/debug/.build-id/f4/
-rw-r--r-- root/root 865368 2015-09-13 06:43 ./usr/lib/debug/.build-id/f4/22971fb39db4cd907fff17884b92b333fe20cd.debug
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/lib/debug/.build-id/fe/
-rw-r--r-- root/root 879492 2015-09-13 06:43 ./usr/lib/debug/.build-id/fe/88290b33494b8d69e162130a5f7087a23047e6.debug
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/doc/mrbayes-dbg/
-rw-r--r-- root/root 1818 2015-09-05 13:53 ./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
mrbayes-mpi_3.2.5+dfsg-2_armhf.deb
──────────────────────────────────
new debian package, version 2.0.
size 490438 bytes: control archive=969 bytes.
1023 bytes, 21 lines control
399 bytes, 6 lines md5sums
Package: mrbayes-mpi
Source: mrbayes
Version: 3.2.5+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1409
Depends: libc6 (>= 2.7), libhmsbeagle1v5, 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 2015-09-13 06:43 ./
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/bin/
-rwxr-xr-x root/root 162 2013-09-12 08:57 ./usr/bin/mb-mpi
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/lib/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/lib/mrbayes-mpi/
-rwxr-xr-x root/root 1423632 2015-09-13 06:43 ./usr/lib/mrbayes-mpi/mb-mpi
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./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 1818 2015-09-05 13:53 ./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 2015-09-13 06:43 ./usr/share/man/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/man/man1/
-rw-r--r-- root/root 226 2015-09-13 06:43 ./usr/share/man/man1/mb-mpi.1.gz
mrbayes_3.2.5+dfsg-2_armhf.deb
──────────────────────────────
new debian package, version 2.0.
size 479082 bytes: control archive=842 bytes.
844 bytes, 18 lines control
318 bytes, 5 lines md5sums
Package: mrbayes
Version: 3.2.5+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1382
Depends: libc6 (>= 2.7), libhmsbeagle1v5, 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 2015-09-13 06:43 ./
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/bin/
-rwxr-xr-x root/root 1399008 2015-09-13 06:43 ./usr/bin/mb
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./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 1818 2015-09-05 13:53 ./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 2015-09-13 06:43 ./usr/share/man/
drwxr-xr-x root/root 0 2015-09-13 06:43 ./usr/share/man/man1/
-rw-r--r-- root/root 206 2015-09-13 06:43 ./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: 33484
Build-Time: 1307
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 259
Job: mrbayes_3.2.5+dfsg-2
Machine Architecture: armhf
Package: mrbayes
Package-Time: 1631
Source-Version: 3.2.5+dfsg-2
Space: 33484
Status: successful
Version: 3.2.5+dfsg-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20150913-0644
Build needed 00:27:11, 33484k disc space