Automatic build of phyml_200900706-2 on fabrice-desktop by sbuild/amd64 0.57.7 Build started at 20090803-2250 ****************************************************************************** phyml_200900706-2.dsc exists in .; copying to chroot ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 7), automake, autoconf Checking for already installed source dependencies... debhelper: missing Using default version 7.3.8ubuntu1 automake: missing autoconf: missing Checking for source dependency conflicts... Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libselinux1 libxml2 m4 man-db po-debconf Suggested packages: autoconf2.13 autobook autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation dh-make cvs gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libxml2 m4 man-db po-debconf The following packages will be upgraded: libselinux1 1 upgraded, 18 newly installed, 0 to remove and 96 not upgraded. Need to get 9582kB of archives. After this operation, 31.0MB of additional disk space will be used. 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Kernel: Linux 2.6.28-14-generic amd64 (x86_64) Toolchain package versions: libc6-dev_2.9-4ubuntu6 linux-libc-dev_2.6.30-1.1 g++-4.4_4.4.0-0ubuntu5 gcc-4.4_4.4.0-0ubuntu5 binutils_2.19.51.20090423-0ubuntu2 libstdc++6_4.4.0-0ubuntu5 libstdc++6-4.4-dev_4.4.0-0ubuntu5 ------------------------------------------------------------------------------ dpkg-buildpackage: set CFLAGS to default value: -g -O2 dpkg-buildpackage: set CPPFLAGS to default value: dpkg-buildpackage: set LDFLAGS to default value: -Wl,-Bsymbolic-functions dpkg-buildpackage: set FFLAGS to default value: -g -O2 dpkg-buildpackage: set CXXFLAGS to default value: -g -O2 dpkg-buildpackage: source package phyml dpkg-buildpackage: source version 1:200900706-2 dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean dh_clean debian/rules build cd src ; aclocal ; autoconf -f ; automake -f ; ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src/missing: Unknown `--run' option Try `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src/missing --help' for more information configure: WARNING: `missing' script is too old or missing 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 build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 for style of include used by make... GNU checking dependency style of gcc... gcc3 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 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: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands dh_testdir /usr/bin/make -C src CFLAGS="-Wall -g -O2" make[1]: Entering directory `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src' cd . && autoheader rm -f stamp-h1 touch config.h.in /usr/bin/make all-am make[2]: Entering directory `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src' :: Building PhyML version v3.0_exporté :: sed -e 's/#define VERSION.*/#define VERSION \"v3.0_exporté\"/' utilities.h > new_utilities.h cp new_utilities.h utilities.h gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c main.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c utilities.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c optimiz.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c lk.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c bionj.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c models.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c free.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c options.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c simu.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c eigen.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c pars.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c alrt.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c interface.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c cl.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c spr.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c draw.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c mpi_boot.c gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -c numeric.c gcc -lm -O3 -fomit-frame-pointer -funroll-loops -Wall -Wl,-Bsymbolic-functions -lm main.o utilities.o optimiz.o lk.o bionj.o models.o free.o options.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o mpi_boot.o numeric.o -o phyml Done. cd . && /bin/bash ./config.status config.h config.status: creating config.h make[2]: Leaving directory `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src' make[1]: Leaving directory `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src' touch build-stamp /usr/bin/fakeroot debian/rules binary dh_testdir dh_testroot dh_prep dh_installdirs /usr/bin/make -C src prefix=`pwd`/debian/`dh_listpackages`/usr install make[1]: Entering directory `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src' :: Building PhyML version v3.0_exporté :: sed -e 's/#define VERSION.*/#define VERSION \"v3.0_exporté\"/' utilities.h > new_utilities.h cp new_utilities.h utilities.h gcc -DUNIX -DPHYML -DDEBUG -O3 -fomit-frame-pointer -funroll-loops -Wall -Wall -g -O2 -O3 -fomit-frame-pointer -funroll-loops -Wall -c utilities.c gcc -lm -O3 -fomit-frame-pointer -funroll-loops -Wall -Wl,-Bsymbolic-functions -lm main.o utilities.o optimiz.o lk.o bionj.o models.o free.o options.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o mpi_boot.o numeric.o -o phyml Done. make[2]: Entering directory `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src' :: Building PhyML version v3.0_exporté :: sed -e 's/#define VERSION.*/#define VERSION \"v3.0_exporté\"/' utilities.h > new_utilities.h cp new_utilities.h utilities.h gcc -lm -O3 -fomit-frame-pointer -funroll-loops -Wall -Wl,-Bsymbolic-functions -lm main.o utilities.o optimiz.o lk.o bionj.o models.o free.o options.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o mpi_boot.o numeric.o -o phyml Done. test -z "/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/debian/phyml/usr/bin" || /bin/mkdir -p "/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/debian/phyml/usr/bin" /usr/bin/install -c 'phyml' '/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/debian/phyml/usr/bin/phyml' make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src' make[1]: Leaving directory `/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml-200900706-2/src' dh binary-arch dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installcatalogs -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_bugfiles -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `phyml' in `../phyml_200900706-2_amd64.deb'. dpkg-genchanges -b -mFabrice Coutadeur >../phyml_200900706-2_amd64.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20090803-2252 phyml_200900706-2_amd64.changes: Format: 1.8 Date: Wed, 15 Jul 2009 09:35:40 +0900 Source: phyml Binary: phyml Architecture: amd64 Version: 1:200900706-2 Distribution: unstable Urgency: low Maintainer: Fabrice Coutadeur Changed-By: Charles Plessy Description: phyml - Phylogenetic estimation using Maximum Likelihood Closes: 536967 Changes: phyml (1:200900706-2) unstable; urgency=low . * Disable parallel building, that was incorrectly supported and induced build failures by race condidtion (Closes: #536967). Checksums-Sha1: 3f7ea3309f164d480585789cb4ec42b8b1903265 564462 phyml_200900706-2_amd64.deb Checksums-Sha256: 7a654ac3b2dce32d00f505e74ebe2bd0dbf9c94352bc357a43bc4d79bb37b646 564462 phyml_200900706-2_amd64.deb Files: 1c77963dd556b5616fd4fe57409a8fbd 564462 science optional phyml_200900706-2_amd64.deb /var/lib/schroot/mount/karmic-b1105329-c36b-4fc1-8aae-9ca138ed1062/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml_200900706-2_amd64.deb: new debian package, version 2.0. size 564462 bytes: control archive= 1227 bytes. 1596 bytes, 29 lines control 319 bytes, 5 lines md5sums Package: phyml Version: 1:200900706-2 Architecture: amd64 Maintainer: Debian-Med Packaging Team Installed-Size: 968 Depends: libc6 (>= 2.4) 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. /var/lib/schroot/mount/karmic-b1105329-c36b-4fc1-8aae-9ca138ed1062/build/fabrice-phyml_200900706-2-amd64-UtpCPa/phyml_200900706-2_amd64.deb: drwxr-xr-x root/root 0 2009-08-03 22:52 ./ drwxr-xr-x root/root 0 2009-08-03 22:52 ./usr/ drwxr-xr-x root/root 0 2009-08-03 22:52 ./usr/share/ drwxr-xr-x root/root 0 2009-08-03 22:52 ./usr/share/doc/ drwxr-xr-x root/root 0 2009-08-03 22:52 ./usr/share/doc/phyml/ -rw-r--r-- root/root 236901 2009-04-30 23:46 ./usr/share/doc/phyml/phyml_manual.pdf.gz -rw-r--r-- root/root 3770 2009-08-03 22:51 ./usr/share/doc/phyml/copyright -rw-r--r-- root/root 634 2009-08-03 22:51 ./usr/share/doc/phyml/changelog.Debian.gz drwxr-xr-x root/root 0 2009-08-03 22:52 ./usr/share/doc-base/ -rw-r--r-- root/root 205 2009-08-03 22:51 ./usr/share/doc-base/phyml drwxr-xr-x root/root 0 2009-08-03 22:52 ./usr/bin/ -rwxr-xr-x root/root 698680 2009-08-03 22:52 ./usr/bin/phyml ****************************************************************************** Built successfully Purging /var/lib/schroot/mount/karmic-b1105329-c36b-4fc1-8aae-9ca138ed1062/build/fabrice-phyml_200900706-2-amd64-UtpCPa ------------------------------------------------------------------------------ Not removing build depends: cloned chroot in use ****************************************************************************** Finished at 20090803-2252 Build needed 00:01:36, 8512k disk space