build.log

build.log (text/plain), 16.19 KB, created by Martin Mokrejš on 2011-01-08 10:37:32 UTC

[32;01m * [39;49;00mPackage:    sci-biology/blossoc-1.4.0
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail]
[32;01m * [39;49;00mUSE:        amd64 elibc_glibc kernel_linux multilib userland_GNU
[32;01m * [39;49;00mFEATURES:   nostrip sandbox splitdebug
>>> 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 ...
 [32;01m*[0m Applying blossoc-1.4.0-gcc43.patch ...
[A[222C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0' ...
 [32;01m*[0m Running aclocal -I m4 ...
[A[222C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[222C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[222C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[222C [34;01m[ [32;01mok[34;01m ][0m
>>> 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=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64
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 x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
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 x86_64-pc-linux-gnu-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-g++... gcc3
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3
checking for sin in -lm... yes
checking build system type... x86_64-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 the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
checking the name of the Boost::UnitTestFramework library... 
configure: Could not link against boost_unit_test_framework-mgw-s !
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 -j5 
make  all-am
make[1]: Entering directory `/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT tree.o -MD -MP -MF .deps/tree.Tpo -c -o tree.o tree.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT tree_builder.o -MD -MP -MF .deps/tree_builder.Tpo -c -o tree_builder.o tree_builder.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT matrix_utils.o -MD -MP -MF .deps/matrix_utils.Tpo -c -o matrix_utils.o matrix_utils.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT incompatibility.o -MD -MP -MF .deps/incompatibility.Tpo -c -o incompatibility.o incompatibility.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT compatible_cache.o -MD -MP -MF .deps/compatible_cache.Tpo -c -o compatible_cache.o compatible_cache.cc
mv -f .deps/tree.Tpo .deps/tree.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT pph.o -MD -MP -MF .deps/pph.Tpo -c -o pph.o pph.cc
mv -f .deps/incompatibility.Tpo .deps/incompatibility.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT score.o -MD -MP -MF .deps/score.Tpo -c -o score.o score.cc
mv -f .deps/matrix_utils.Tpo .deps/matrix_utils.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT case_control_score.o -MD -MP -MF .deps/case_control_score.Tpo -c -o case_control_score.o case_control_score.cc
mv -f .deps/compatible_cache.Tpo .deps/compatible_cache.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT qt_score.o -MD -MP -MF .deps/qt_score.Tpo -c -o qt_score.o qt_score.cc
mv -f .deps/tree_builder.Tpo .deps/tree_builder.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT genotype_score.o -MD -MP -MF .deps/genotype_score.Tpo -c -o genotype_score.o genotype_score.cc
pph.cc: In function 'void<unnamed>::main_ENT()':
pph.cc:1674: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'int<unnamed>::compute_free(int)':
pph.cc:1818: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'int<unnamed>::compute_locked(int)':
pph.cc:1839: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'void<unnamed>::outputENTsol()':
pph.cc:1868: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'int<unnamed>::traverse(<unnamed>::CComp*, int, int, double, double*, int)':
pph.cc:2053: warning: unused variable 'error'
pph.cc: In function 'void<unnamed>::merge_cc(<unnamed>::CComp*, <unnamed>::CComp*)':
pph.cc:2390: warning: comparison between signed and unsigned integer expressions
pph.cc:2396: warning: comparison between signed and unsigned integer expressions
pph.cc: In function '<unnamed>::CComp*<unnamed>::get_cc(<unnamed>::Gen*, <unnamed>::CComp*)':
pph.cc:2412: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'void<unnamed>::read_genotypes()':
pph.cc:2535: warning: comparison between signed and unsigned integer expressions
pph.cc:2542: warning: comparison between signed and unsigned integer expressions
pph.cc:2547: warning: comparison between signed and unsigned integer expressions
pph.cc:2553: warning: comparison between signed and unsigned integer expressions
pph.cc:2555: warning: comparison between signed and unsigned integer expressions
pph.cc:2563: warning: comparison between signed and unsigned integer expressions
pph.cc:2576: warning: comparison between signed and unsigned integer expressions
pph.cc: In function 'int<unnamed>::traverse(<unnamed>::CComp*, int, int, double, double*, int)':
pph.cc:2060: warning: 'old1_id' may be used uninitialized in this function
pph.cc:2060: warning: 'old2_id' may be used uninitialized in this function
pph.cc:2060: warning: 'h1_id' may be used uninitialized in this function
pph.cc:2060: warning: 'h2_id' may be used uninitialized in this function
pph.cc:2061: warning: 'sav_cov' may be used uninitialized in this function
mv -f .deps/score.Tpo .deps/score.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT io.o -MD -MP -MF .deps/io.Tpo -c -o io.o io.cc
mv -f .deps/qt_score.Tpo .deps/qt_score.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT blossoc.o -MD -MP -MF .deps/blossoc.Tpo -c -o blossoc.o blossoc.cc
mv -f .deps/genotype_score.Tpo .deps/genotype_score.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT snpfile_blossoc.o -MD -MP -MF .deps/snpfile_blossoc.Tpo -c -o snpfile_blossoc.o snpfile_blossoc.cc
mv -f .deps/pph.Tpo .deps/pph.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT regions.o -MD -MP -MF .deps/regions.Tpo -c -o regions.o regions.cc
mv -f .deps/case_control_score.Tpo .deps/case_control_score.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT blossoc_trees.o -MD -MP -MF .deps/blossoc_trees.Tpo -c -o blossoc_trees.o blossoc_trees.cc
mv -f .deps/io.Tpo .deps/io.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT interactions.o -MD -MP -MF .deps/interactions.Tpo -c -o interactions.o interactions.cc
mv -f .deps/regions.Tpo .deps/regions.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT low_mem_interactions.o -MD -MP -MF .deps/low_mem_interactions.Tpo -c -o low_mem_interactions.o low_mem_interactions.cc
mv -f .deps/blossoc.Tpo .deps/blossoc.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT snpfile_interactions.o -MD -MP -MF .deps/snpfile_interactions.Tpo -c -o snpfile_interactions.o snpfile_interactions.cc
mv -f .deps/blossoc_trees.Tpo .deps/blossoc_trees.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT fast_snpfile_interactions.o -MD -MP -MF .deps/fast_snpfile_interactions.Tpo -c -o fast_snpfile_interactions.o fast_snpfile_interactions.cc
mv -f .deps/snpfile_blossoc.Tpo .deps/snpfile_blossoc.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT matrix_test.o -MD -MP -MF .deps/matrix_test.Tpo -c -o matrix_test.o matrix_test.cc
mv -f .deps/matrix_test.Tpo .deps/matrix_test.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT incompatibility_test.o -MD -MP -MF .deps/incompatibility_test.Tpo -c -o incompatibility_test.o incompatibility_test.cc
mv -f .deps/incompatibility_test.Tpo .deps/incompatibility_test.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT tree_test.o -MD -MP -MF .deps/tree_test.Tpo -c -o tree_test.o tree_test.cc
mv -f .deps/interactions.Tpo .deps/interactions.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT tree_builder_test.o -MD -MP -MF .deps/tree_builder_test.Tpo -c -o tree_builder_test.o tree_builder_test.cc
mv -f .deps/tree_test.Tpo .deps/tree_test.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT score_test.o -MD -MP -MF .deps/score_test.Tpo -c -o score_test.o score_test.cc
score_test.cc:78:2: warning: #warning This test is disabled. Enable it again!
mv -f .deps/low_mem_interactions.Tpo .deps/low_mem_interactions.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT io_test.o -MD -MP -MF .deps/io_test.Tpo -c -o io_test.o io_test.cc
mv -f .deps/score_test.Tpo .deps/score_test.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT incompatible_regress_test.o -MD -MP -MF .deps/incompatible_regress_test.Tpo -c -o incompatible_regress_test.o incompatible_regress_test.cc
mv -f .deps/io_test.Tpo .deps/io_test.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.    -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona -MT genotype_score_test.o -MD -MP -MF .deps/genotype_score_test.Tpo -c -o genotype_score_test.o genotype_score_test.cc
mv -f .deps/tree_builder_test.Tpo .deps/tree_builder_test.Po
x86_64-pc-linux-gnu-g++ -Wall -pthread -I/usr/include -g -O0  -O2 -pipe -march=nocona  -Wl,-O1 -Wl,--as-needed -o blossoc tree.o tree_builder.o matrix_utils.o incompatibility.o compatible_cache.o pph.o score.o case_control_score.o qt_score.o genotype_score.o io.o blossoc.o -lboost_program_options -lsnpfile -lgsl -lgslcblas -lm 
/usr/lib/libboost_signals-1_42.so.1.42.0: undefined reference to `std::_List_node_base::_M_reverse()@GLIBCXX_3.4.14'
/usr/lib/libboost_signals-1_42.so.1.42.0: undefined reference to `std::_List_node_base::_M_unhook()@GLIBCXX_3.4.14'
/usr/lib/libboost_signals-1_42.so.1.42.0: undefined reference to `std::_List_node_base::_M_transfer(std::_List_node_base*, std::_List_node_base*)@GLIBCXX_3.4.14'
/usr/lib/libboost_signals-1_42.so.1.42.0: undefined reference to `std::_List_node_base::_M_hook(std::_List_node_base*)@GLIBCXX_3.4.14'
collect2: ld returned 1 exit status
make[1]: *** [blossoc] Error 1
make[1]: *** Waiting for unfinished jobs....
mv -f .deps/incompatible_regress_test.Tpo .deps/incompatible_regress_test.Po
mv -f .deps/genotype_score_test.Tpo .deps/genotype_score_test.Po
mv -f .deps/snpfile_interactions.Tpo .deps/snpfile_interactions.Po
mv -f .deps/fast_snpfile_interactions.Tpo .deps/fast_snpfile_interactions.Po
make[1]: Leaving directory `/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0'
make: *** [all] Error 2
emake failed
 [31;01m*[0m ERROR: sci-biology/blossoc-1.4.0 failed:
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line   56:  Called src_compile
 [31;01m*[0m   environment, line 2896:  Called _eapi2_src_compile
 [31;01m*[0m     ebuild.sh, line  657:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		emake || die "emake failed"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-biology/blossoc-1.4.0',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-biology/blossoc-1.4.0'.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/blossoc-1.4.0/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/blossoc-1.4.0/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0'