>>> 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::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::compute_free(int)': pph.cc:1817: warning: comparison between signed and unsigned integer expressions pph.cc: In function 'int::compute_locked(int)': pph.cc:1838: warning: comparison between signed and unsigned integer expressions pph.cc: In function 'void::outputENTsol()': pph.cc:1867: warning: comparison between signed and unsigned integer expressions pph.cc: In function 'int::traverse(::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::fill_template(::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::merge_cc(::CComp*, ::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 '::CComp*::get_cc(::Gen*, ::CComp*)': pph.cc:2411: warning: comparison between signed and unsigned integer expressions pph.cc: In function 'void::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'