Build log

snpfile-2.0.1:20090702-035919.log (text/plain), 29.87 KB, created by Diego Elio Pettenò (RETIRED) on 2009-07-02 11:15:02 UTC

>>> Unpacking source...
>>> Unpacking snpfile-2.0.1.tar.gz to /var/tmp/portage/sci-biology/snpfile-2.0.1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/snpfile-2.0.1/work
>>> Compiling source in /var/tmp/portage/sci-biology/snpfile-2.0.1/work/snpfile-2.0.1 ...
 * econf: updating snpfile-2.0.1/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating snpfile-2.0.1/config.guess with /usr/share/gnuconfig/config.guess
./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
configure: loading site script /usr/share/config.site
configure: loading site script /usr/share/crossdev/include/site/linux
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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-ranlib... i686-pc-linux-gnu-ranlib
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 ANSI C... none needed
checking dependency style of i686-pc-linux-gnu-gcc... gcc3
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 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 !
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.hh
config.status: executing depfiles commands
make -j14 
make  all-am
make[1]: Entering directory `/var/tmp/portage/sci-biology/snpfile-2.0.1/work/snpfile-2.0.1'
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT matrix.o -MD -MP -MF ".deps/matrix.Tpo" -c -o matrix.o matrix.cc; \
	then mv -f ".deps/matrix.Tpo" ".deps/matrix.Po"; else rm -f ".deps/matrix.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT file_matrix.o -MD -MP -MF ".deps/file_matrix.Tpo" -c -o file_matrix.o file_matrix.cc; \
	then mv -f ".deps/file_matrix.Tpo" ".deps/file_matrix.Po"; else rm -f ".deps/file_matrix.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT array_matrix.o -MD -MP -MF ".deps/array_matrix.Tpo" -c -o array_matrix.o array_matrix.cc; \
	then mv -f ".deps/array_matrix.Tpo" ".deps/array_matrix.Po"; else rm -f ".deps/array_matrix.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT byte_order_handler.o -MD -MP -MF ".deps/byte_order_handler.Tpo" -c -o byte_order_handler.o byte_order_handler.cc; \
	then mv -f ".deps/byte_order_handler.Tpo" ".deps/byte_order_handler.Po"; else rm -f ".deps/byte_order_handler.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT metadata.o -MD -MP -MF ".deps/metadata.Tpo" -c -o metadata.o metadata.cc; \
	then mv -f ".deps/metadata.Tpo" ".deps/metadata.Po"; else rm -f ".deps/metadata.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile.o -MD -MP -MF ".deps/snpfile.Tpo" -c -o snpfile.o snpfile.cc; \
	then mv -f ".deps/snpfile.Tpo" ".deps/snpfile.Po"; else rm -f ".deps/snpfile.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT text2snpfile.o -MD -MP -MF ".deps/text2snpfile.Tpo" -c -o text2snpfile.o text2snpfile.cc; \
	then mv -f ".deps/text2snpfile.Tpo" ".deps/text2snpfile.Po"; else rm -f ".deps/text2snpfile.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile2text.o -MD -MP -MF ".deps/snpfile2text.Tpo" -c -o snpfile2text.o snpfile2text.cc; \
	then mv -f ".deps/snpfile2text.Tpo" ".deps/snpfile2text.Po"; else rm -f ".deps/snpfile2text.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile2fastPHASE.o -MD -MP -MF ".deps/snpfile2fastPHASE.Tpo" -c -o snpfile2fastPHASE.o snpfile2fastPHASE.cc; \
	then mv -f ".deps/snpfile2fastPHASE.Tpo" ".deps/snpfile2fastPHASE.Po"; else rm -f ".deps/snpfile2fastPHASE.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT fastPHASE2snpfile.o -MD -MP -MF ".deps/fastPHASE2snpfile.Tpo" -c -o fastPHASE2snpfile.o fastPHASE2snpfile.cc; \
	then mv -f ".deps/fastPHASE2snpfile.Tpo" ".deps/fastPHASE2snpfile.Po"; else rm -f ".deps/fastPHASE2snpfile.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile2haploview.o -MD -MP -MF ".deps/snpfile2haploview.Tpo" -c -o snpfile2haploview.o snpfile2haploview.cc; \
	then mv -f ".deps/snpfile2haploview.Tpo" ".deps/snpfile2haploview.Po"; else rm -f ".deps/snpfile2haploview.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT beagle_phase_snpfile.o -MD -MP -MF ".deps/beagle_phase_snpfile.Tpo" -c -o beagle_phase_snpfile.o beagle_phase_snpfile.cc; \
	then mv -f ".deps/beagle_phase_snpfile.Tpo" ".deps/beagle_phase_snpfile.Po"; else rm -f ".deps/beagle_phase_snpfile.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT genotype_count.o -MD -MP -MF ".deps/genotype_count.Tpo" -c -o genotype_count.o genotype_count.cc; \
	then mv -f ".deps/genotype_count.Tpo" ".deps/genotype_count.Po"; else rm -f ".deps/genotype_count.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile_phenotypes.o -MD -MP -MF ".deps/snpfile_phenotypes.Tpo" -c -o snpfile_phenotypes.o snpfile_phenotypes.cc; \
	then mv -f ".deps/snpfile_phenotypes.Tpo" ".deps/snpfile_phenotypes.Po"; else rm -f ".deps/snpfile_phenotypes.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile_markers.o -MD -MP -MF ".deps/snpfile_markers.Tpo" -c -o snpfile_markers.o snpfile_markers.cc; \
	then mv -f ".deps/snpfile_markers.Tpo" ".deps/snpfile_markers.Po"; else rm -f ".deps/snpfile_markers.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile_metadata_info.o -MD -MP -MF ".deps/snpfile_metadata_info.Tpo" -c -o snpfile_metadata_info.o snpfile_metadata_info.cc; \
	then mv -f ".deps/snpfile_metadata_info.Tpo" ".deps/snpfile_metadata_info.Po"; else rm -f ".deps/snpfile_metadata_info.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile_set_metadata.o -MD -MP -MF ".deps/snpfile_set_metadata.Tpo" -c -o snpfile_set_metadata.o snpfile_set_metadata.cc; \
	then mv -f ".deps/snpfile_set_metadata.Tpo" ".deps/snpfile_set_metadata.Po"; else rm -f ".deps/snpfile_set_metadata.Tpo"; exit 1; fi
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.    -Wall -pthread -I/usr/include -g -O2  -O2 -pipe -MT snpfile_get_metadata.o -MD -MP -MF ".deps/snpfile_get_metadata.Tpo" -c -o snpfile_get_metadata.o snpfile_get_metadata.cc; \
	then mv -f ".deps/snpfile_get_metadata.Tpo" ".deps/snpfile_get_metadata.Po"; else rm -f ".deps/snpfile_get_metadata.Tpo"; exit 1; fi
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from genotype_count.cc:29:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from genotype_count.cc:29:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from genotype_count.cc:29:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [genotype_count.o] Error 1
make[1]: *** Waiting for unfinished jobs....
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from snpfile_phenotypes.cc:27:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from snpfile_phenotypes.cc:27:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from snpfile_phenotypes.cc:27:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [snpfile_phenotypes.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from snpfile_metadata_info.cc:31:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from snpfile_metadata_info.cc:31:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from snpfile_metadata_info.cc:31:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from snpfile2fastPHASE.cc:29:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from snpfile2fastPHASE.cc:29:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from snpfile2fastPHASE.cc:29:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [snpfile2fastPHASE.o] Error 1
make[1]: *** [snpfile_metadata_info.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from snpfile_markers.cc:27:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from snpfile_markers.cc:27:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from snpfile_markers.cc:27:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [snpfile_markers.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from text2snpfile.cc:29:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from text2snpfile.cc:29:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from text2snpfile.cc:29:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [text2snpfile.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from file_matrix.cc:30:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from file_matrix.cc:30:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from file_matrix.cc:30:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from fastPHASE2snpfile.cc:29:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from fastPHASE2snpfile.cc:29:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from fastPHASE2snpfile.cc:29:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [file_matrix.o] Error 1
make[1]: *** [fastPHASE2snpfile.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from beagle_phase_snpfile.cc:29:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from beagle_phase_snpfile.cc:29:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from beagle_phase_snpfile.cc:29:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [beagle_phase_snpfile.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from snpfile2text.cc:30:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from snpfile2text.cc:30:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from snpfile2text.cc:30:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [snpfile2text.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from snpfile2haploview.cc:30:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from snpfile2haploview.cc:30:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from snpfile2haploview.cc:30:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [snpfile2haploview.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from snpfile_set_metadata.cc:35:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from snpfile_set_metadata.cc:35:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from snpfile_set_metadata.cc:35:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [snpfile_set_metadata.o] Error 1
In file included from archives.hh:35,
                 from metadata_access.hh:32,
                 from snpfile_get_metadata.cc:31:
input_archive.hh: In member function 'void BiRC::SNPFile::InputArchive::loadIntegral(T&)':
input_archive.hh:81: error: 'uint64_t' was not declared in this scope
input_archive.hh:81: error: expected ';' before 'tmp'
input_archive.hh:82: error: 'tmp' was not declared in this scope
In file included from archives.hh:36,
                 from metadata_access.hh:32,
                 from snpfile_get_metadata.cc:31:
output_archive.hh: In member function 'void BiRC::SNPFile::OutputArchive::saveIntegral(T)':
output_archive.hh:80: error: 'uint64_t' was not declared in this scope
output_archive.hh:80: error: expected ';' before 'tmp'
output_archive.hh:81: error: 'tmp' was not declared in this scope
In file included from metadata_access.hh:33,
                 from snpfile_get_metadata.cc:31:
type_trait.hh: At global scope:
type_trait.hh:119: error: 'uint8_t' was not declared in this scope
type_trait.hh:119: error: template argument 1 is invalid
type_trait.hh:120: error: 'uint16_t' was not declared in this scope
type_trait.hh:120: error: template argument 1 is invalid
type_trait.hh:121: error: 'uint32_t' was not declared in this scope
type_trait.hh:121: error: template argument 1 is invalid
type_trait.hh:122: error: 'uint64_t' was not declared in this scope
type_trait.hh:122: error: template argument 1 is invalid
make[1]: *** [snpfile_get_metadata.o] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-biology/snpfile-2.0.1/work/snpfile-2.0.1'
make: *** [all] Error 2
 [31;01m*[0m 
 [31;01m*[0m ERROR: sci-biology/snpfile-2.0.1 failed.
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line   49:  Called src_compile
 [31;01m*[0m             environment, line 2353:  Called _eapi0_src_compile
 [31;01m*[0m               ebuild.sh, line  600:  Called _eapi2_src_compile
 [31;01m*[0m               ebuild.sh, line  634:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		emake || die "emake failed"
 [31;01m*[0m  The die message:
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the topmost build error, and the call stack if relevant.
 [31;01m*[0m A complete build log is located at '/var/log/portage/sci-biology/snpfile-2.0.1:20090702-035919.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/snpfile-2.0.1/temp/environment'.
 [31;01m*[0m