build.log

sci-biology:blossoc-1.4.0:20091112-140408.log (text/plain), 8.71 KB, created by Sebastian Luther (few) on 2009-11-12 20:39:33 UTC

>>> Unpacking source...
>>> Unpacking blossoc-1.4.0.tar.gz to /var/tmp/portage/sci-biology/blossoc-1.4.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/blossoc-1.4.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0 ...
 * Running eautoreconf in '/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0' ...
 * Running aclocal -I m4 ...
  [ ok ]
 * Running autoconf ...
  [ ok ]
 * Running autoheader ...
  [ ok ]
 * Running automake --add-missing --copy ...
  [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0 ...
 * econf: updating blossoc-1.4.0/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating blossoc-1.4.0/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib
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... gawk
checking whether make sets $(MAKE)... yes
checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++
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 i686-pc-linux-gnu-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of i686-pc-linux-gnu-g++... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... yes
checking whether i686-pc-linux-gnu-gcc accepts -g... yes
checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking dependency style of i686-pc-linux-gnu-gcc... gcc3
checking for sin in -lm... yes
checking build system type... i686-pc-linux-gnu
checking for boostlib >= 1.33.1... yes
checking whether the Boost::Filesystem library is available... yes
checking for main in -lboost_filesystem... yes
checking whether the Boost::Program_Options library is available... yes
checking for main in -lboost_program_options... yes
checking whether the Boost::Thread library is available... yes
checking for main in -lboost_thread... yes
checking whether the Boost::IOStreams library is available... yes
checking for main in -lboost_iostreams... yes
checking whether the Boost::Serialization library is available... yes
checking for main in -lboost_serialization... yes
checking for main in -lboost_wserialization... yes
checking whether the Boost::Signals library is available... yes
checking for main in -lboost_signals... yes
checking whether the Boost::Date_Time library is available... yes
checking for main in -lboost_date_time... yes
checking whether the Boost::Regex library is available... yes
checking for main in -lboost_regex... yes
checking whether the Boost::UnitTestFramework library is available... yes
checking the name of the Boost::UnitTestFramework library... 
checking for cblas_dsdot in -lgslcblas... yes
checking for gsl_cdf_chisq_Q in -lgsl... yes
checking for main in -lsnpfile... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.hh
config.status: executing depfiles commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0 ...
make -j2 
cd . && /bin/sh /var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0/missing --run autoheader
rm -f stamp-h1
touch config.hh.in
cd . && /bin/sh ./config.status config.hh
config.status: creating config.hh
config.status: config.hh is unchanged
make  all-am
make[1]: Entering directory `/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0'
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -march=native -pipe -MT tree.o -MD -MP -MF .deps/tree.Tpo -c -o tree.o tree.cc
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -march=native -pipe -MT tree_builder.o -MD -MP -MF .deps/tree_builder.Tpo -c -o tree_builder.o tree_builder.cc
mv -f .deps/tree.Tpo .deps/tree.Po
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -march=native -pipe -MT matrix_utils.o -MD -MP -MF .deps/matrix_utils.Tpo -c -o matrix_utils.o matrix_utils.cc
mv -f .deps/tree_builder.Tpo .deps/tree_builder.Po
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -march=native -pipe -MT incompatibility.o -MD -MP -MF .deps/incompatibility.Tpo -c -o incompatibility.o incompatibility.cc
mv -f .deps/matrix_utils.Tpo .deps/matrix_utils.Po
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -march=native -pipe -MT compatible_cache.o -MD -MP -MF .deps/compatible_cache.Tpo -c -o compatible_cache.o compatible_cache.cc
mv -f .deps/incompatibility.Tpo .deps/incompatibility.Po
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -march=native -pipe -MT pph.o -MD -MP -MF .deps/pph.Tpo -c -o pph.o pph.cc
mv -f .deps/compatible_cache.Tpo .deps/compatible_cache.Po
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -march=native -pipe -MT score.o -MD -MP -MF .deps/score.Tpo -c -o score.o score.cc
pph.cc: In function 'void<unnamed>::main_ENT()':
pph.cc:1673: warning: comparison between signed and unsigned integer expressions
pph.cc:1696: error: 'stderr' was not declared in this scope
pph.cc:1696: error: 'fprintf' was not declared in this scope
pph.cc: In function 'int<unnamed>::compute_free(int)':
pph.cc:1817: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'int<unnamed>::compute_locked(int)':
pph.cc:1838: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'void<unnamed>::outputENTsol()':
pph.cc:1867: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'int<unnamed>::traverse(<unnamed>::CComp*, int, int, double, double*, int)':
pph.cc:2047: error: 'stderr' was not declared in this scope
pph.cc:2047: error: 'fprintf' was not declared in this scope
pph.cc:2052: warning: unused variable 'error'
pph.cc: In function 'bool<unnamed>::fill_template(<unnamed>::Gen*)':
pph.cc:2378: error: 'stderr' was not declared in this scope
pph.cc:2378: error: 'fprintf' was not declared in this scope
pph.cc: In function 'void<unnamed>::merge_cc(<unnamed>::CComp*, <unnamed>::CComp*)':
pph.cc:2389: warning: comparison between signed and unsigned integer expressions
pph.cc:2395: warning: comparison between signed and unsigned integer expressions
pph.cc: In function '<unnamed>::CComp*<unnamed>::get_cc(<unnamed>::Gen*, <unnamed>::CComp*)':
pph.cc:2411: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'void<unnamed>::read_genotypes()':
pph.cc:2534: warning: comparison between signed and unsigned integer expressions
pph.cc:2541: warning: comparison between signed and unsigned integer expressions
pph.cc:2546: warning: comparison between signed and unsigned integer expressions
pph.cc:2552: warning: comparison between signed and unsigned integer expressions
pph.cc:2554: warning: comparison between signed and unsigned integer expressions
pph.cc:2562: warning: comparison between signed and unsigned integer expressions
pph.cc:2575: warning: comparison between signed and unsigned integer expressions
pph.cc:2581: error: 'stderr' was not declared in this scope
pph.cc:2581: error: 'fprintf' was not declared in this scope
make[1]: *** [pph.o] Fehler 1
make[1]: *** Warte auf noch nicht beendete Prozesse...
mv -f .deps/score.Tpo .deps/score.Po
make[1]: Leaving directory `/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0'
make: *** [all] Fehler 2
 * ERROR: sci-biology/blossoc-1.4.0 failed:
 *   emake failed
 * 
 * Call stack:
 *     ebuild.sh, line   49:  Called src_compile
 *   environment, line 2759:  Called _eapi2_src_compile
 *     ebuild.sh, line  629:  Called die
 * The specific snippet of code:
 *   		emake || die "emake failed"
 * 
 * If you need support, post the output of 'emerge --info =sci-biology/blossoc-1.4.0',
 * the complete build log and the output of 'emerge -pqv =sci-biology/blossoc-1.4.0'.
 * The complete build log is located at '/var/log/portage/sci-biology:blossoc-1.4.0:20091112-140408.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/blossoc-1.4.0/temp/environment'.
 * S: '/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0'