phyml →
3:3.2.0+dfsg-2 →
armhf → 2016-04-22 11:23:24
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-04
+==============================================================================+
| phyml 3:3.2.0+dfsg-2 (armhf) 22 Apr 2016 10:51 |
+==============================================================================+
Package: phyml
Version: 3:3.2.0+dfsg-2
Source Version: 3:3.2.0+dfsg-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/phyml-vZdyPM/phyml-3.2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phyml-vZdyPM' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-9c11225f-1123-4014-b80a-50fddc5ed996' with '<<CHROOT>>'
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| Update chroot |
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Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8918 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
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| Fetch source files |
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Check APT
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Download source files with APT
------------------------------
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NOTICE: 'phyml' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/cgit/debian-med/phyml.git
Please use:
git clone https://anonscm.debian.org/cgit/debian-med/phyml.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1081 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main phyml 3:3.2.0+dfsg-2 (dsc) [2073 B]
Get:2 http://172.17.0.1/private stretch-staging/main phyml 3:3.2.0+dfsg-2 (tar) [1068 kB]
Get:3 http://172.17.0.1/private stretch-staging/main phyml 3:3.2.0+dfsg-2 (diff) [10.4 kB]
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Check dependencies
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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-7tuP8h/apt_archive/sbuild-build-depends-core-dummy.deb'.
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| Install core build dependencies (apt-based resolver) |
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Installing build dependencies
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 18 not upgraded.
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Merged Build-Depends: debhelper (>= 9), autotools-dev, dh-autoreconf, pkg-config, libhmsbeagle-dev, libopenmpi-dev
Filtered Build-Depends: debhelper (>= 9), autotools-dev, dh-autoreconf, pkg-config, libhmsbeagle-dev, libopenmpi-dev
dpkg-deb: building package 'sbuild-build-depends-phyml-dummy' in '/<<BUILDDIR>>/resolver-wID3c4/apt_archive/sbuild-build-depends-phyml-dummy.deb'.
OK
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Get:5 file:/<<BUILDDIR>>/resolver-wID3c4/apt_archive ./ Packages [569 B]
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| Install phyml 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 debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libhmsbeagle-dev
libhmsbeagle1v5 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu55
libltdl-dev libltdl7 libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi1.10 libpipeline1 libsigsegv2 libtool libunistring0 libxml2 m4
man-db openmpi-common pkg-config po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libhwloc-contrib-plugins libtool-doc opennmpi-doc gfortran
| fortran95-compiler gcj-jdk less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libhwloc-plugins 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 gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libhmsbeagle-dev
libhmsbeagle1v5 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu55
libltdl-dev libltdl7 libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi1.10 libpipeline1 libsigsegv2 libtool libunistring0 libxml2 m4
man-db openmpi-common pkg-config po-debconf sbuild-build-depends-phyml-dummy
0 upgraded, 45 newly installed, 0 to remove and 18 not upgraded.
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Get:1 file:/<<BUILDDIR>>/resolver-wID3c4/apt_archive ./ sbuild-build-depends-phyml-dummy 0.invalid.0 [804 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
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Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
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Get:13 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
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Get:30 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 5.3.1-14 [153 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libhmsbeagle1v5 armhf 2.1.2+20150609-1.1 [48.0 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libhmsbeagle-dev armhf 2.1.2+20150609-1.1 [149 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.6-0.1 [42.8 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libltdl-dev armhf 2.4.6-0.1 [159 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libnl-3-200 armhf 3.2.27-1 [53.4 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libnl-route-3-200 armhf 3.2.27-1 [111 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf pkg-config armhf 0.29-3 [59.0 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libhwloc5 armhf 1.11.2-3 [80.8 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libhwloc-dev armhf 1.11.2-3 [133 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libibverbs1 armhf 1.2.0-1 [31.7 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libibverbs-dev armhf 1.2.0-1 [88.2 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libopenmpi1.10 armhf 1.10.2-8+rpi1 [1781 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf openmpi-common all 1.10.2-8+rpi1 [141 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libopenmpi-dev armhf 1.10.2-8+rpi1 [625 kB]
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Not building database; man-db/auto-update is not 'true'.
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libglib2.0-0:armhf (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtool (2.4.6-0.1) ...
Setting up libgfortran3:armhf (5.3.1-14) ...
Setting up libhmsbeagle1v5 (2.1.2+20150609-1.1) ...
Setting up libhmsbeagle-dev (2.1.2+20150609-1.1) ...
Setting up libltdl7:armhf (2.4.6-0.1) ...
Setting up libltdl-dev:armhf (2.4.6-0.1) ...
Setting up libnl-3-200:armhf (3.2.27-1) ...
Setting up libnl-route-3-200:armhf (3.2.27-1) ...
Setting up pkg-config (0.29-3) ...
Setting up libhwloc5:armhf (1.11.2-3) ...
Setting up libhwloc-dev:armhf (1.11.2-3) ...
Setting up libibverbs1 (1.2.0-1) ...
Setting up libibverbs-dev (1.2.0-1) ...
Setting up libopenmpi1.10 (1.10.2-8+rpi1) ...
Setting up openmpi-common (1.10.2-8+rpi1) ...
Setting up libopenmpi-dev (1.10.2-8+rpi1) ...
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-5) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-14 gcc-5_5.3.1-14 libc6-dev_2.22-5 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.114 apt_1.2.10 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-14 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.120-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.43~WIP.2016.03.15-2 e2fsprogs_1.43~WIP.2016.03.15-2 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-14 gcc_4:5.3.1-1+rpi1 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_4.9.3-12 gcc-5_5.3.1-14 gcc-5-base_5.3.1-14 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-5 gpgv_1.4.20-5 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-5 hostname_3.17 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10-4 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.2.10 libarchive-zip-perl_1.57-1 libasan1_4.9.3-12 libasan2_5.3.1-14 libatomic1_5.3.1-14 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-6 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-5 libc-dev-bin_2.22-5 libc6_2.22-5 libc6-dev_2.22-5 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-14 libcomerr2_1.43~WIP.2016.03.15-2 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.208 libdevmapper1.02.1_2:1.02.120-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.4 libgcc-4.9-dev_4.9.3-12 libgcc-5-dev_5.3.1-14 libgcc1_1:5.3.1-14 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libgfortran3_5.3.1-14 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-14 libgpg-error0_1.21-2 libhmsbeagle-dev_2.1.2+20150609-1.1 libhmsbeagle1v5_2.1.2+20150609-1.1 libhwloc-dev_1.11.2-3 libhwloc5_1.11.2-3 libibverbs-dev_1.2.0-1 libibverbs1_1.2.0-1 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1.1 libltdl-dev_2.4.6-0.1 libltdl7_2.4.6-0.1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160319-1 libncursesw5_6.0+20160319-1 libnl-3-200_3.2.27-1 libnl-route-3-200_3.2.27-1 libopenmpi-dev_1.10.2-8+rpi1 libopenmpi1.10_1.10.2-8+rpi1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3.1 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.3.0-1 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-5 libslang2_2.3.0-2.3 libsmartcols1_2.27.1-6 libss2_1.43~WIP.2016.03.15-2 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 libsystemd0_229-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160319-1 libtool_2.4.6-0.1 libubsan0_5.3.1-14 libudev1_229-4 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.05-1 mawk_1.3.3-17 mount_2.27.1-6 multiarch-support_2.22-5 nano_2.5.3-2 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 openmpi-common_1.10.2-8+rpi1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 pkg-config_0.29-3 po-debconf_1.0.19 procps_2:3.3.11-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-4 systemd-sysv_229-4 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016c-0+deb8u1 udev_229-4 util-linux_2.27.1-6 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 Mon Mar 14 11:55:52 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./phyml_3.2.0+dfsg-2.dsc
dpkg-source: info: extracting phyml in phyml-3.2.0+dfsg
dpkg-source: info: unpacking phyml_3.2.0+dfsg.orig.tar.gz
dpkg-source: info: unpacking phyml_3.2.0+dfsg-2.debian.tar.xz
dpkg-source: info: applying sse_only_if_supported.patch
dpkg-source: info: applying no-stdc++.patch
dpkg-source: info: applying no-configure-ac-date
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-9c11225f-1123-4014-b80a-50fddc5ed996
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package phyml
dpkg-buildpackage: source version 3:3.2.0+dfsg-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build phyml-3.2.0+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# save pdf from cleaning
mv doc/phyml-manual.pdf .
dh_auto_clean
mv phyml-manual.pdf doc
# remove temporary bin dir for phyml (see above hack)
rm -rf debian/bin
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
dh_update_autotools_config -a
debian/rules override_dh_autoreconf
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_autoreconf --as-needed
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
libtoolize: and rerunning libtoolize and aclocal.
libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
configure.ac:17: installing './compile'
configure.ac:15: installing './config.guess'
configure.ac:15: installing './config.sub'
configure.ac:5: installing './install-sh'
configure.ac:5: installing './missing'
src/Makefile.am: installing './depcomp'
patching file ./ltmain.sh
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# According to README you need different configure options to get different executables
# Here we hack in a full build process for phyml executable
dh_auto_configure -- --enable-beagle
./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 --enable-beagle
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether 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 whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... none
checking dependency style of gcc... (cached) none
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking for log in -lm... yes
checking 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 sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for BEAGLE... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -- LDFLAGS="-Wl,-z,relro"
make -j1 LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make all-recursive
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making all in src
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
.: Building [phyml-beagle]. Version 3:3.2.0+dfsg-2 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o main.o main.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o utilities.o utilities.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o optimiz.o optimiz.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o lk.o lk.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o bionj.o bionj.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o models.o models.c
models.c: In function 'General_Dist':
models.c:1171:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0)
^
models.c: In function 'GTR_Dist':
models.c:1273:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0) {Free(pi); return -1.;}
^
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o free.o free.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o help.o help.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o simu.o simu.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o eigen.o eigen.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o pars.o pars.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o alrt.o alrt.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o interface.o interface.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o cl.o cl.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o spr.o spr.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o draw.o draw.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o stats.o stats.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o rates.o rates.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o mcmc.o mcmc.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o times.o times.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o tiporder.o tiporder.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o mg.o mg.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o m4.o m4.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o io.o io.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o make.o make.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o nexus.o nexus.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o init.o init.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o xml.o xml.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o mixt.o mixt.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o beagle_utils.o beagle_utils.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -Wl,-z,relro -o phyml-beagle main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o beagle_utils.o -lm -lhmsbeagle -lm
libtool: link: gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -Wl,-z -Wl,relro -o phyml-beagle main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o beagle_utils.o -ldl -lhmsbeagle -lm
Done.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# move phyml binary to temporary dir inside debian/
mkdir -p /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin
mv src/phyml-beagle /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin/phyml
mv doc/phyml-manual.pdf .
/usr/bin/make distclean
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making distclean in src
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
rm -f phyml-beagle
test -z "" || rm -f
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
rm -f *.tab.c
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
rm -rf ./.deps
rm -f Makefile
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
Making distclean in doc
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/doc'
test -z "phyml-manual.pdf phyml-manual.log phyml-manual.idx phyml-manual.out phyml-manual.toc phyml-manual.aux phyml-manual.ilg phyml-manual.ind phyml-manual.dvi " || rm -f phyml-manual.pdf phyml-manual.log phyml-manual.idx phyml-manual.out phyml-manual.toc phyml-manual.aux phyml-manual.ilg phyml-manual.ind phyml-manual.dvi
rm -rf .libs _libs
rm -f *.lo
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f Makefile
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/doc'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
rm -rf .libs _libs
rm -f *.lo
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f config.h stamp-h1
rm -f libtool config.lt
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
rm -f cscope.out cscope.in.out cscope.po.out cscope.files
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
mv phyml-manual.pdf doc
dh_auto_configure -- --enable-mpi
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --enable-mpi
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether 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 whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... none
checking dependency style of gcc... (cached) none
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking for log in -lm... yes
checking 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 sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -- LDFLAGS="-Wl,-z,relro"
make -j1 LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make all-recursive
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making all in src
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
.: Building [phyml-mpi]. Version 3:3.2.0+dfsg-2 :.
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o main.o main.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o utilities.o utilities.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o optimiz.o optimiz.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o lk.o lk.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o bionj.o bionj.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o models.o models.c
models.c: In function 'General_Dist':
models.c:1171:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0)
^
models.c: In function 'GTR_Dist':
models.c:1273:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0) {Free(pi); return -1.;}
^
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o free.o free.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o help.o help.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o simu.o simu.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o eigen.o eigen.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o pars.o pars.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o alrt.o alrt.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o interface.o interface.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o cl.o cl.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o spr.o spr.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o draw.o draw.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o stats.o stats.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o rates.o rates.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mcmc.o mcmc.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o times.o times.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o tiporder.o tiporder.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mg.o mg.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o m4.o m4.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o io.o io.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o make.o make.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o nexus.o nexus.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o init.o init.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o xml.o xml.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mixt.o mixt.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mpi_boot.o mpi_boot.c
/bin/bash ../libtool --tag=CC --mode=link mpicc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -Wl,-z,relro -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o mpi_boot.o -lm -lm
libtool: link: mpicc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -Wl,-z -Wl,relro -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o mpi_boot.o -lm
Done.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# move phyml binary to temporary dir inside debian/
# mkdir -p /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin
mv src/phyml-mpi /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin/phyml-mpi
mv doc/phyml-manual.pdf .
/usr/bin/make distclean
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making distclean in src
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
rm -f phyml-mpi
test -z "" || rm -f
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
rm -f *.tab.c
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
rm -rf ./.deps
rm -f Makefile
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
Making distclean in doc
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/doc'
test -z "phyml-manual.pdf phyml-manual.log phyml-manual.idx phyml-manual.out phyml-manual.toc phyml-manual.aux phyml-manual.ilg phyml-manual.ind phyml-manual.dvi " || rm -f phyml-manual.pdf phyml-manual.log phyml-manual.idx phyml-manual.out phyml-manual.toc phyml-manual.aux phyml-manual.ilg phyml-manual.ind phyml-manual.dvi
rm -rf .libs _libs
rm -f *.lo
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f Makefile
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/doc'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
rm -rf .libs _libs
rm -f *.lo
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f config.h stamp-h1
rm -f libtool config.lt
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
rm -f cscope.out cscope.in.out cscope.po.out cscope.files
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
mv phyml-manual.pdf doc
dh_auto_configure -- --enable-phytime
./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 --enable-phytime
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether 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 whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... none
checking dependency style of gcc... (cached) none
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking for log in -lm... yes
checking 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 sys/types.h... yes
checking for sys/stat.h... yes
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checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
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checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
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configure: WARNING: Documentation will not be built!
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
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checking if gcc supports -fno-rtti -fno-exceptions... no
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checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
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checking whether to build shared libraries... yes
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checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -- LDFLAGS="-Wl,-z,relro" CPPFLAGS="-DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2"
make -j1 LDFLAGS=-Wl,-z,relro "CPPFLAGS=-DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2"
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make all-recursive
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making all in src
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
.: Building [phytime]. Version 3:3.2.0+dfsg-2 :.
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o main.o main.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o utilities.o utilities.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o optimiz.o optimiz.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o lk.o lk.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o bionj.o bionj.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o models.o models.c
models.c: In function 'General_Dist':
models.c:1171:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0)
^
models.c: In function 'GTR_Dist':
models.c:1273:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0) {Free(pi); return -1.;}
^
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o free.o free.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o help.o help.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o simu.o simu.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o eigen.o eigen.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o pars.o pars.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o alrt.o alrt.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o interface.o interface.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o cl.o cl.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o spr.o spr.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o times.o times.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o m4.o m4.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o draw.o draw.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o rates.o rates.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mcmc.o mcmc.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o stats.o stats.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mg.o mg.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o tiporder.o tiporder.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o io.o io.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o make.o make.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mixt.o mixt.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o init.o init.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o nexus.o nexus.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o xml.o xml.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o phyrex.o phyrex.c
phyrex.c: In function 'PHYREX_Main_Simulate':
phyrex.c:137:7: warning: variable 'n_otus' set but not used [-Wunused-but-set-variable]
int n_otus, n_sites;
^
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -Wl,-z,relro -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o xml.o phyrex.o -lm -lm
libtool: link: gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -Wl,-z -Wl,relro -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o xml.o phyrex.o -lm
Done.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_auto_test -a
make -j1 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
.: Building [phytime]. Version 3:3.2.0+dfsg-2 :.
Done.
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_auto_install
make -j1 install DESTDIR=/<<BUILDDIR>>/phyml-3.2.0\+dfsg/debian/phyml AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making install in src
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
.: Building [phytime]. Version 3:3.2.0+dfsg-2 :.
Done.
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
/bin/mkdir -p '/<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c phytime '/<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/bin'
libtool: install: /usr/bin/install -c phytime /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/bin/phytime
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# install phyml binary we have kept safe above
mv /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin/* /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/bin
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
debian/rules override_dh_installdocs
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_installdocs
mv /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyml/usr/bin/phyml was not linked against libdl.so.2 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
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
dh_builddeb -a
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.2.0+dfsg-2_armhf.deb'.
dpkg-deb: building package 'phyml' in '../phyml_3.2.0+dfsg-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../phyml_3.2.0+dfsg-2_armhf.changes
dpkg-genchanges: warning: package phyml-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build phyml-3.2.0+dfsg
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160422-1117
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phyml_3.2.0+dfsg-2_armhf.changes:
---------------------------------
Format: 1.8
Date: Mon, 14 Mar 2016 12:52:14 +0100
Source: phyml
Binary: phyml
Architecture: armhf
Version: 3:3.2.0+dfsg-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Changes:
phyml (3:3.2.0+dfsg-2) unstable; urgency=medium
.
[ Kevin Murray ]
* Fix VCS link in d/control
* Patch for reproduible build (configure.ac date)
* Bump standards version to 3.9.7
.
[ Andreas Tille ]
* Enable MPI version of phyml
Checksums-Sha1:
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30e01d4b457f378e1814eccd1916bb0affe69c3b 1012932 phyml_3.2.0+dfsg-2_armhf.deb
Checksums-Sha256:
d57f5e89b538a7ce351a1b41afe035c94cdfaa14f159cb28675f2ff2ab186337 56606 phyml-dbgsym_3.2.0+dfsg-2_armhf.deb
0108e89e32c59240c412d9aeb719a11418d9c37f519401085bfbf1a770ec50de 1012932 phyml_3.2.0+dfsg-2_armhf.deb
Files:
3996af8e9129287c1c727666a9f6fc44 56606 debug extra phyml-dbgsym_3.2.0+dfsg-2_armhf.deb
2e81f93dbb369bf2c6b9e515d8a0df0a 1012932 science optional phyml_3.2.0+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phyml-dbgsym_3.2.0+dfsg-2_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 56606 bytes: control archive=614 bytes.
502 bytes, 13 lines control
318 bytes, 3 lines md5sums
Package: phyml-dbgsym
Source: phyml
Version: 3:3.2.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 270
Depends: phyml (= 3:3.2.0+dfsg-2)
Section: debug
Priority: extra
Homepage: http://www.atgc-montpellier.fr/phyml
Description: Debug symbols for phyml
Auto-Built-Package: debug-symbols
Build-Ids: 06ebe849e65043df6a1ec2282c172f3b4549623f 8296d07163bc6b5f059f45e8ea837a296d96108e b97536623fdb8586cc7c8a75fd833d72ae624035
drwxr-xr-x root/root 0 2016-04-22 11:17 ./
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/lib/
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/lib/debug/.build-id/06/
-rw-r--r-- root/root 84172 2016-04-22 11:17 ./usr/lib/debug/.build-id/06/ebe849e65043df6a1ec2282c172f3b4549623f.debug
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/lib/debug/.build-id/82/
-rw-r--r-- root/root 93964 2016-04-22 11:17 ./usr/lib/debug/.build-id/82/96d07163bc6b5f059f45e8ea837a296d96108e.debug
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/lib/debug/.build-id/b9/
-rw-r--r-- root/root 84884 2016-04-22 11:17 ./usr/lib/debug/.build-id/b9/7536623fdb8586cc7c8a75fd833d72ae624035.debug
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/share/
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-04-22 11:17 ./usr/share/doc/phyml-dbgsym -> phyml
phyml_3.2.0+dfsg-2_armhf.deb
----------------------------
new debian package, version 2.0.
size 1012932 bytes: control archive=1451 bytes.
1671 bytes, 31 lines control
683 bytes, 11 lines md5sums
Package: phyml
Version: 3:3.2.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3746
Depends: libc6 (>= 2.7), libhmsbeagle1v5, libopenmpi1.10
Section: science
Priority: optional
Homepage: http://www.atgc-montpellier.fr/phyml
Description: Phylogenetic estimation using Maximum Likelihood
PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide
range of options that were designed to facilitate standard phylogenetic
analyses. The main strengths of PhyML lies in the large number of
substitution models coupled to various options to search the space of
phylogenetic tree topologies, going from very fast and efficient methods
to slower but generally more accurate approaches. It also implements
two methods to evaluate branch supports in a sound statistical framework
(the non-parametric bootstrap and the approximate likelihood ratio test).
.
PhyML was designed to process moderate to large data sets. In theory,
alignments with up to 4,000 sequences 2,000,000 character-long can
be analyzed. In practice however, the amount of memory required to process
a data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided
that they are short. Also, PhyML can handle long sequences provided that
they are not numerous. With most standard personal computers, the “comfort
zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
character long.
.
This package also includes PhyTime.
drwxr-xr-x root/root 0 2016-04-22 11:17 ./
drwxr-xr-x root/root 0 2016-04-22 11:16 ./usr/
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/bin/
-rwxr-xr-x root/root 1091460 2016-04-22 11:17 ./usr/bin/phyml
-rwxr-xr-x root/root 1103732 2016-04-22 11:17 ./usr/bin/phyml-mpi
-rwxr-xr-x root/root 1201996 2016-04-22 11:17 ./usr/bin/phytime
drwxr-xr-x root/root 0 2016-04-22 11:16 ./usr/share/
drwxr-xr-x root/root 0 2016-04-22 11:16 ./usr/share/doc-base/
-rw-r--r-- root/root 202 2016-03-14 11:52 ./usr/share/doc-base/phyml
drwxr-xr-x root/root 0 2016-04-22 11:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/share/doc/phyml/
-rw-r--r-- root/root 1922 2016-03-14 11:52 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root 1933 2016-03-14 11:52 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root 5458 2015-12-17 10:01 ./usr/share/doc/phyml/changelog.gz
-rw-r--r-- root/root 2025 2016-03-14 11:52 ./usr/share/doc/phyml/copyright
-rw-r--r-- root/root 407931 2015-12-17 10:01 ./usr/share/doc/phyml/phyml_manual.pdf
drwxr-xr-x root/root 0 2016-04-22 11:16 ./usr/share/man/
drwxr-xr-x root/root 0 2016-04-22 11:17 ./usr/share/man/man1/
-rw-r--r-- root/root 2898 2016-04-22 11:16 ./usr/share/man/man1/phyml.1.gz
-rw-r--r-- root/root 2306 2016-04-22 11:16 ./usr/share/man/man1/phytime.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 15264
Build-Time: 1247
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 262
Job: phyml_3:3.2.0+dfsg-2
Machine Architecture: armhf
Package: phyml
Package-Time: 1561
Source-Version: 3:3.2.0+dfsg-2
Space: 15264
Status: successful
Version: 3:3.2.0+dfsg-2
--------------------------------------------------------------------------------
Finished at 20160422-1117
Build needed 00:26:01, 15264k disc space