phyml →
2:20141029+dfsg-1 →
armhf → 2015-09-15 01:11:34
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on testbuildd.raspbian.org
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║ phyml 2:20141029+dfsg-1 (armhf) 15 Sep 2015 00:54 ║
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Package: phyml
Version: 2:20141029+dfsg-1
Source Version: 2:20141029+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/phyml-ApdYYf/phyml-20141029+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/phyml-ApdYYf' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-4408312b-a6aa-4b95-8686-7a0c08426e50' 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 [8329 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.2 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
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Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
NOTICE: 'phyml' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/phyml.git
Need to get 860 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main phyml 2:20141029+dfsg-1 (dsc) [2031 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main phyml 2:20141029+dfsg-1 (tar) [848 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main phyml 2:20141029+dfsg-1 (diff) [10.2 kB]
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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-gLqX6B/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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Ign file: ./ Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
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), autotools-dev, dh-autoreconf, pkg-config, libhmsbeagle-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), autotools-dev, dh-autoreconf, pkg-config, libhmsbeagle-dev
dpkg-deb: building package 'sbuild-build-depends-phyml-dummy' in '/«BUILDDIR»/resolver-GF9tEv/apt_archive/sbuild-build-depends-phyml-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
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Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install phyml 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 autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf file gettext gettext-base groff-base intltool-debian
libasprintf0v5 libcroco3 libffi6 libglib2.0-0 libhmsbeagle-dev
libhmsbeagle1v5 libmagic1 libpipeline1 libsigsegv2 libtool libunistring0
libxml2 m4 man-db pkg-config po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois
vacation dh-make gettext-doc groff libtool-doc automaken gfortran
fortran95-compiler gcj-jdk less www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data
shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf file gettext gettext-base groff-base intltool-debian
libasprintf0v5 libcroco3 libffi6 libglib2.0-0 libhmsbeagle-dev
libhmsbeagle1v5 libmagic1 libpipeline1 libsigsegv2 libtool libunistring0
libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-phyml-dummy
0 upgraded, 29 newly installed, 0 to remove and 1 not upgraded.
Need to get 10.9 MB/10.9 MB of archives.
After this operation, 32.2 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]
Get:9 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libsigsegv2 armhf 2.10-4 [28.2 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.5.1-1 [118 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main m4 armhf 1.4.17-4 [238 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main autoconf all 2.69-9 [338 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main autotools-dev all 20140911.1 [70.5 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main automake all 1:1.15-3 [735 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main autopoint all 0.19.5.1-1 [426 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.5.1-1 [1386 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150811 [817 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libtool all 2.4.2-1.11 [190 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main dh-autoreconf all 10 [15.2 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libhmsbeagle1v5 armhf 2.1.2+20150609-1.1 [48.0 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libhmsbeagle-dev armhf 2.1.2+20150609-1.1 [149 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main pkg-config armhf 0.28-1 [55.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 11953 files and directories currently installed.)
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Unpacking sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Setting up groff-base (1.22.3-1) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-1) ...
Setting up man-db (2.7.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0v5:armhf (0.19.5.1-1) ...
Setting up libmagic1:armhf (1:5.22+15-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
Setting up libffi6:armhf (3.2.1-3) ...
Setting up libglib2.0-0:armhf (2.44.1-1.1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-3) ...
Setting up libsigsegv2:armhf (2.10-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up file (1:5.22+15-2) ...
Setting up gettext-base (0.19.5.1-1) ...
Setting up m4 (1.4.17-4) ...
Setting up autoconf (2.69-9) ...
Setting up autotools-dev (20140911.1) ...
Setting up automake (1:1.15-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.5.1-1) ...
Setting up gettext (0.19.5.1-1) ...
Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150811) ...
Setting up libtool (2.4.2-1.11) ...
Setting up dh-autoreconf (10) ...
Setting up libhmsbeagle1v5 (2.1.2+20150609-1.1) ...
Setting up libhmsbeagle-dev (2.1.2+20150609-1.1) ...
Setting up pkg-config (0.28-1) ...
Setting up sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-19) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ 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++-5_5.2.1-16+rpi1 gcc-5_5.2.1-16+rpi1 libc6-dev_2.19-19 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: adduser_3.113+nmu3 apt_1.0.10.2 autoconf_2.69-9 automake_1:1.15-3 autopoint_0.19.5.1-1 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-5_5.2.1-16+rpi1 dash_0.5.7-4 debconf_1.5.57 debconf-i18n_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debianutils_4.5.1 dh-autoreconf_10 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++-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-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-pkg4.16_1.0.10.2 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 libcomerr2_1.42.13-1 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-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 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 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.05-9 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 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 libprocps4_2:3.3.10-2 libreadline6_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 libsmartcols1_2.26.2-9 libss2_1.42.13-1 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 libtinfo5_6.0+20150810-1 libtool_2.4.2-1.11 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 multiarch-support_2.19-19 ncurses-base_6.0+20150810-1 ncurses-bin_6.0+20150810-1 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 pkg-config_0.28-1 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-phyml-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 Thu Aug 27 15:20:09 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./phyml_20141029+dfsg-1.dsc
dpkg-source: info: extracting phyml in phyml-20141029+dfsg
dpkg-source: info: unpacking phyml_20141029+dfsg.orig.tar.xz
dpkg-source: info: unpacking phyml_20141029+dfsg-1.debian.tar.xz
dpkg-source: info: applying sse_only_if_supported.patch
dpkg-source: info: applying no-stdc++.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=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-4408312b-a6aa-4b95-8686-7a0c08426e50
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package phyml
dpkg-buildpackage: source version 2:20141029+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build phyml-20141029+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-20141029+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-20141029+dfsg'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
debian/rules override_dh_autoreconf
make[1]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
dh_autoreconf --as-needed
libtoolize: putting auxiliary files in `.'.
libtoolize: copying file `./ltmain.sh'
libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.ac and
libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
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-20141029+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/phyml-20141029+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 whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
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 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-20141029+dfsg'
make all-recursive
make[3]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
Making all in src
make[4]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
.: Building [phyml-beagle]. Version 20150915 :.
gcc -I. -I.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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.. -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-20141029+dfsg/src'
make[4]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[4]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[3]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[2]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
# move phyml binary to temporary dir inside debian/
mkdir -p /«BUILDDIR»/phyml-20141029+dfsg/debian/bin
mv src/phyml-beagle /«BUILDDIR»/phyml-20141029+dfsg/debian/bin/phyml
mv doc/phyml-manual.pdf .
/usr/bin/make distclean
make[2]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
Making distclean in src
make[3]: Entering directory '/«BUILDDIR»/phyml-20141029+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-20141029+dfsg/src'
Making distclean in doc
make[3]: Entering directory '/«BUILDDIR»/phyml-20141029+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-20141029+dfsg/doc'
make[3]: Entering directory '/«BUILDDIR»/phyml-20141029+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-20141029+dfsg'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/«BUILDDIR»/phyml-20141029+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
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 whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
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 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-20141029+dfsg'
make all-recursive
make[3]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
Making all in src
make[4]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
.: Building [phytime]. Version 20150915 :.
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o main.o main.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o utilities.o utilities.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o optimiz.o optimiz.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o lk.o lk.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o bionj.o bionj.c
gcc -I. -I.. -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.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o free.o free.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o help.o help.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o simu.o simu.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o eigen.o eigen.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o pars.o pars.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o alrt.o alrt.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o interface.o interface.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o cl.o cl.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o spr.o spr.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o times.o times.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o m4.o m4.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o draw.o draw.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o rates.o rates.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mcmc.o mcmc.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o stats.o stats.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mg.o mg.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o tiporder.o tiporder.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o io.o io.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o make.o make.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mixt.o mixt.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o init.o init.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o nexus.o nexus.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o xml.o xml.c
/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 -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 -lm
Done.
make[4]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
make[4]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[4]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[3]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[2]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[1]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
dh_auto_test -a
make -j1 check
make[1]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
Making check in src
make[2]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
.: Building [phytime]. Version 20150915 :.
Done.
make[2]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
make[2]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[2]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[1]: Leaving directory '/«BUILDDIR»/phyml-20141029+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-20141029+dfsg'
dh_auto_install
make -j1 install DESTDIR=/«BUILDDIR»/phyml-20141029\+dfsg/debian/phyml AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
Making install in src
make[3]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
.: Building [phytime]. Version 20150915 :.
Done.
make[4]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
/bin/mkdir -p '/«BUILDDIR»/phyml-20141029+dfsg/debian/phyml/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c phytime '/«BUILDDIR»/phyml-20141029+dfsg/debian/phyml/usr/bin'
libtool: install: /usr/bin/install -c phytime /«BUILDDIR»/phyml-20141029+dfsg/debian/phyml/usr/bin/phytime
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
make[3]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg/src'
make[3]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[4]: Entering directory '/«BUILDDIR»/phyml-20141029+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-20141029+dfsg'
make[3]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
make[2]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
# install phyml binary we have kept safe above
mv /«BUILDDIR»/phyml-20141029+dfsg/debian/bin/* /«BUILDDIR»/phyml-20141029+dfsg/debian/phyml/usr/bin
make[1]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
debian/rules override_dh_installdocs
make[1]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
dh_installdocs
mv /«BUILDDIR»/phyml-20141029+dfsg/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /«BUILDDIR»/phyml-20141029+dfsg/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf
make[1]: Leaving directory '/«BUILDDIR»/phyml-20141029+dfsg'
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
debian/rules override_dh_compress
make[1]: Entering directory '/«BUILDDIR»/phyml-20141029+dfsg'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/«BUILDDIR»/phyml-20141029+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
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'phyml' in '../phyml_20141029+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../phyml_20141029+dfsg-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build phyml-20141029+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150915-0111
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
phyml_20141029+dfsg-1_armhf.changes:
────────────────────────────────────
Format: 1.8
Date: Thu, 27 Aug 2015 17:18:17 +0200
Source: phyml
Binary: phyml
Architecture: armhf
Version: 2:20141029+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Changes:
phyml (2:20141029+dfsg-1) unstable; urgency=medium
.
* d/watch: Source is now on Github
* Upstream confirmed that the development version should be fairly stable
and most probably suitable for Debian
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* Remove executable binary from archive (as well as LaTeX remainings once
we are starting to remove files)
* Move to git
* Build-Depends: pkg-config, libhmsbeagle-dev
* debian/rules:
- hack around removal of PDF manual
- enable building with libhmsbeagle-dev
* DEP5
Checksums-Sha1:
6997e757d042c45d2506d62c1e662e993fb5565c 899122 phyml_20141029+dfsg-1_armhf.deb
Checksums-Sha256:
54f569815118c09de13f942c384f9678508d9174041cd52dc955419abb314413 899122 phyml_20141029+dfsg-1_armhf.deb
Files:
bcd8d4027773718fedffdd298775f187 899122 science optional phyml_20141029+dfsg-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
phyml_20141029+dfsg-1_armhf.deb
───────────────────────────────
new debian package, version 2.0.
size 899122 bytes: control archive=1413 bytes.
1658 bytes, 31 lines control
631 bytes, 10 lines md5sums
Package: phyml
Version: 2:20141029+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2510
Depends: libc6 (>= 2.7), libhmsbeagle1v5
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 2015-09-15 01:11 ./
drwxr-xr-x root/root 0 2015-09-15 01:11 ./usr/
drwxr-xr-x root/root 0 2015-09-15 01:11 ./usr/bin/
-rwxr-xr-x root/root 1070884 2015-09-15 01:11 ./usr/bin/phyml
-rwxr-xr-x root/root 1074920 2015-09-15 01:11 ./usr/bin/phytime
drwxr-xr-x root/root 0 2015-09-15 01:11 ./usr/share/
drwxr-xr-x root/root 0 2015-09-15 01:11 ./usr/share/doc-base/
-rw-r--r-- root/root 202 2015-08-27 15:18 ./usr/share/doc-base/phyml
drwxr-xr-x root/root 0 2015-09-15 01:11 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-15 01:11 ./usr/share/doc/phyml/
-rw-r--r-- root/root 2056 2015-08-27 15:18 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root 1784 2015-08-27 15:18 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root 5458 2014-09-15 02:18 ./usr/share/doc/phyml/changelog.gz
-rw-r--r-- root/root 2025 2015-08-27 15:18 ./usr/share/doc/phyml/copyright
-rw-r--r-- root/root 392421 2014-10-29 03:35 ./usr/share/doc/phyml/phyml_manual.pdf
drwxr-xr-x root/root 0 2015-09-15 01:11 ./usr/share/man/
drwxr-xr-x root/root 0 2015-09-15 01:11 ./usr/share/man/man1/
-rw-r--r-- root/root 2898 2015-09-15 01:11 ./usr/share/man/man1/phyml.1.gz
-rw-r--r-- root/root 2306 2015-09-15 01:11 ./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: 13000
Build-Time: 781
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 184
Job: phyml_2:20141029+dfsg-1
Machine Architecture: armhf
Package: phyml
Package-Time: 1024
Source-Version: 2:20141029+dfsg-1
Space: 13000
Status: successful
Version: 2:20141029+dfsg-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150915-0111
Build needed 00:17:04, 13000k disc space