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molpopgen / fwdpp

fwdpp is a C++ template library for implementing efficient forward-time population genetic simulations
http://fwdpp.readthedocs.io
GNU General Public License v3.0
27 stars 11 forks source link

fwdpp fails internal test for yosemite macOs #52

Closed tmozgach closed 7 years ago

tmozgach commented 7 years ago

Hello, I updated the version 0.5.6 in formulae of fwdpp for the homebrew and Jenkins fails tests for macOs version yosemite

See log.


failed: brew install --verbose --build-bottle homebrew/science/fwdpp
Stacktrace

        ==> Installing fwdpp from homebrew/science
==> Using the sandbox
/usr/bin/sandbox-exec -f /tmp/homebrew20170802-6187-1of7l0u.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/build.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-science/fwdpp.rb --build-bottle --verbose
==> Downloading https://github.com/molpopgen/fwdpp/archive/0.5.6.tar.gz
Already downloaded: /Users/brew/Library/Caches/Homebrew/fwdpp-0.5.6.tar.gz
==> Verifying fwdpp-0.5.6.tar.gz checksum
tar xzf /Users/brew/Library/Caches/Homebrew/fwdpp-0.5.6.tar.gz
==> ./configure --prefix=/usr/local/Cellar/fwdpp/0.5.6
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/private/tmp/fwdpp-20170802-6189-wwfykr/fwdpp-0.5.6/missing: Unknown `--is-lightweight' option
Try `/private/tmp/fwdpp-20170802-6189-wwfykr/fwdpp-0.5.6/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of clang... gcc3
checking for an ANSI C-conforming const... yes
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking dependency style of clang++... gcc3
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether clang++ supports C++11 features by default... no
checking whether clang++ supports C++11 features with -std=c++11... yes
checking how to run the C++ preprocessor... clang++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 Sequence/SimData.hpp usability... yes
checking Sequence/SimData.hpp presence... yes
checking for Sequence/SimData.hpp... yes
checking gsl/gsl_rng.h usability... yes
checking gsl/gsl_rng.h presence... yes
checking for gsl/gsl_rng.h... yes
checking gsl/gsl_randist.h usability... yes
checking gsl/gsl_randist.h presence... yes
checking for gsl/gsl_randist.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking boost/test/unit_test.hpp usability... yes
checking boost/test/unit_test.hpp presence... yes
checking for boost/test/unit_test.hpp... yes
checking for gzungetc in -lz... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
checking for main in -lsequence... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating fwdpp/version.hpp
config.status: creating fwdpp/Makefile
config.status: creating fwdpp/internal/Makefile
config.status: creating fwdpp/tags/Makefile
config.status: creating fwdpp/sugar/Makefile
config.status: creating fwdpp/sugar/poptypes/Makefile
config.status: creating fwdpp/sugar/gsl/Makefile
config.status: creating fwdpp/sugar/sampling/Makefile
config.status: creating fwdpp/experimental/Makefile
config.status: creating fwdpp/extensions/Makefile
config.status: creating examples/Makefile
config.status: creating testsuite/Makefile
config.status: creating experimental_examples/Makefile
config.status: creating src/Makefile
config.status: creating doc/fwdpp.doxygen
config.status: creating config.h
config.status: executing depfiles commands
==> make
make  all-recursive
Making all in fwdpp
Making all in internal
make[3]: Nothing to be done for `all'.
Making all in tags
make[3]: Nothing to be done for `all'.
Making all in sugar
Making all in gsl
make[4]: Nothing to be done for `all'.
Making all in poptypes
make[4]: Nothing to be done for `all'.
Making all in sampling
make[4]: Nothing to be done for `all'.
make[4]: Nothing to be done for `all-am'.
Making all in experimental
make[3]: Nothing to be done for `all'.
Making all in extensions
make[3]: Nothing to be done for `all'.
make[3]: Nothing to be done for `all-am'.
Making all in examples
depbase=`echo diploid_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT diploid_ind.o -MD -MP -MF $depbase.Tpo -c -o diploid_ind.o diploid_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo diploid_binaryIO_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT diploid_binaryIO_ind.o -MD -MP -MF $depbase.Tpo -c -o diploid_binaryIO_ind.o diploid_binaryIO_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo diploid_gzbinaryIO_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT diploid_gzbinaryIO_ind.o -MD -MP -MF $depbase.Tpo -c -o diploid_gzbinaryIO_ind.o diploid_gzbinaryIO_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo diploid_fixed_sh_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT diploid_fixed_sh_ind.o -MD -MP -MF $depbase.Tpo -c -o diploid_fixed_sh_ind.o diploid_fixed_sh_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo migsel_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT migsel_ind.o -MD -MP -MF $depbase.Tpo -c -o migsel_ind.o migsel_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo migsel_split_ind_list.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT migsel_split_ind_list.o -MD -MP -MF $depbase.Tpo -c -o migsel_split_ind_list.o migsel_split_ind_list.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo bneck_selection_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT bneck_selection_ind.o -MD -MP -MF $depbase.Tpo -c -o bneck_selection_ind.o bneck_selection_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo diploid_ind_2locus.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT diploid_ind_2locus.o -MD -MP -MF $depbase.Tpo -c -o diploid_ind_2locus.o diploid_ind_2locus.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo K_linked_regions_multilocus.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT K_linked_regions_multilocus.o -MD -MP -MF $depbase.Tpo -c -o K_linked_regions_multilocus.o K_linked_regions_multilocus.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo K_linked_regions_extensions.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT K_linked_regions_extensions.o -MD -MP -MF $depbase.Tpo -c -o K_linked_regions_extensions.o K_linked_regions_extensions.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo HOC_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT HOC_ind.o -MD -MP -MF $depbase.Tpo -c -o HOC_ind.o HOC_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
clang++  -g -O2 -std=c++11   -o diploid_ind diploid_ind.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o diploid_binaryIO_ind diploid_binaryIO_ind.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o diploid_gzbinaryIO_ind diploid_gzbinaryIO_ind.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o diploid_fixed_sh_ind diploid_fixed_sh_ind.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o migsel_ind migsel_ind.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o migsel_split_ind_list migsel_split_ind_list.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o bneck_selection_ind bneck_selection_ind.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o diploid_ind_2locus diploid_ind_2locus.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o HOC_ind HOC_ind.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o K_linked_regions_multilocus K_linked_regions_multilocus.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o K_linked_regions_extensions K_linked_regions_extensions.o  -lgsl -lgslcblas -lz  -lsequence
Making all in testsuite
make[2]: Nothing to be done for `all'.
Making all in experimental_examples
depbase=`echo sex_limited_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT sex_limited_ind.o -MD -MP -MF $depbase.Tpo -c -o sex_limited_ind.o sex_limited_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo diploid_fixed_sh_ind.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..  -Wall -W -I. -DNDEBUG -std=c++11  -g -O2 -std=c++11 -MT diploid_fixed_sh_ind.o -MD -MP -MF $depbase.Tpo -c -o diploid_fixed_sh_ind.o diploid_fixed_sh_ind.cc &&\
    mv -f $depbase.Tpo $depbase.Po
clang++  -g -O2 -std=c++11   -o sex_limited_ind sex_limited_ind.o  -lgsl -lgslcblas -lz  -lsequence
clang++  -g -O2 -std=c++11   -o diploid_fixed_sh_ind diploid_fixed_sh_ind.o  -lgsl -lgslcblas -lz  -lsequence
Making all in src
depbase=`echo fwdppConfig.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11 -I.. -g -O2 -std=c++11 -MT fwdppConfig.o -MD -MP -MF $depbase.Tpo -c -o fwdppConfig.o fwdppConfig.cc &&\
    mv -f $depbase.Tpo $depbase.Po
clang++ -I.. -g -O2 -std=c++11   -o fwdppConfig fwdppConfig.o  
make[2]: Nothing to be done for `all-am'.
==> make check
Making check in fwdpp
Making check in internal
make[2]: Nothing to be done for `check'.
Making check in tags
make[2]: Nothing to be done for `check'.
Making check in sugar
Making check in gsl
make[3]: Nothing to be done for `check'.
Making check in poptypes
make[3]: Nothing to be done for `check'.
Making check in sampling
make[3]: Nothing to be done for `check'.
make[3]: Nothing to be done for `check-am'.
Making check in experimental
make[2]: Nothing to be done for `check'.
Making check in extensions
make[2]: Nothing to be done for `check'.
make[2]: Nothing to be done for `check-am'.
Making check in examples
make[1]: Nothing to be done for `check'.
Making check in testsuite
make  unit/fwdpp_unit_tests unit/extensions_unit_tests unit/sugar_unit_tests integration/sugar_integration_tests integration/extensions_integration_tests
depbase=`echo unit/fwdpp_unit_tests.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/fwdpp_unit_tests.o -MD -MP -MF $depbase.Tpo -c -o unit/fwdpp_unit_tests.o unit/fwdpp_unit_tests.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/mutateTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/mutateTest.o -MD -MP -MF $depbase.Tpo -c -o unit/mutateTest.o unit/mutateTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/gameteTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/gameteTest.o -MD -MP -MF $depbase.Tpo -c -o unit/gameteTest.o unit/gameteTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/utilTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/utilTest.o -MD -MP -MF $depbase.Tpo -c -o unit/utilTest.o unit/utilTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/type_traitsTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/type_traitsTest.o -MD -MP -MF $depbase.Tpo -c -o unit/type_traitsTest.o unit/type_traitsTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/recombinationTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/recombinationTest.o -MD -MP -MF $depbase.Tpo -c -o unit/recombinationTest.o unit/recombinationTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/demographyTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/demographyTest.o -MD -MP -MF $depbase.Tpo -c -o unit/demographyTest.o unit/demographyTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/siteDepFitnessTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/siteDepFitnessTest.o -MD -MP -MF $depbase.Tpo -c -o unit/siteDepFitnessTest.o unit/siteDepFitnessTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/serializationTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/serializationTest.o -MD -MP -MF $depbase.Tpo -c -o unit/serializationTest.o unit/serializationTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/ms_samplingTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/ms_samplingTest.o -MD -MP -MF $depbase.Tpo -c -o unit/ms_samplingTest.o unit/ms_samplingTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/mlocusCrossoverTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/mlocusCrossoverTest.o -MD -MP -MF $depbase.Tpo -c -o unit/mlocusCrossoverTest.o unit/mlocusCrossoverTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/gamete_cleanerTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/gamete_cleanerTest.o -MD -MP -MF $depbase.Tpo -c -o unit/gamete_cleanerTest.o unit/gamete_cleanerTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/extensions_unit_test.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/extensions_unit_test.o -MD -MP -MF $depbase.Tpo -c -o unit/extensions_unit_test.o unit/extensions_unit_test.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/extensions_regionsTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/extensions_regionsTest.o -MD -MP -MF $depbase.Tpo -c -o unit/extensions_regionsTest.o unit/extensions_regionsTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/extensions_callbacksTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/extensions_callbacksTest.o -MD -MP -MF $depbase.Tpo -c -o unit/extensions_callbacksTest.o unit/extensions_callbacksTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/sugar_unit_tests.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/sugar_unit_tests.o -MD -MP -MF $depbase.Tpo -c -o unit/sugar_unit_tests.o unit/sugar_unit_tests.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/sugar_GSLrngTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/sugar_GSLrngTest.o -MD -MP -MF $depbase.Tpo -c -o unit/sugar_GSLrngTest.o unit/sugar_GSLrngTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/sugar_samplingTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/sugar_samplingTest.o -MD -MP -MF $depbase.Tpo -c -o unit/sugar_samplingTest.o unit/sugar_samplingTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/sugar_add_mutationTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/sugar_add_mutationTest.o -MD -MP -MF $depbase.Tpo -c -o unit/sugar_add_mutationTest.o unit/sugar_add_mutationTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/sugar_change_neutralTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/sugar_change_neutralTest.o -MD -MP -MF $depbase.Tpo -c -o unit/sugar_change_neutralTest.o unit/sugar_change_neutralTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/sugar_generalmutTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/sugar_generalmutTest.o -MD -MP -MF $depbase.Tpo -c -o unit/sugar_generalmutTest.o unit/sugar_generalmutTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo unit/sugar_generalmut_vecTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT unit/sugar_generalmut_vecTest.o -MD -MP -MF $depbase.Tpo -c -o unit/sugar_generalmut_vecTest.o unit/sugar_generalmut_vecTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/sugar_integration_tests.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/sugar_integration_tests.o -MD -MP -MF $depbase.Tpo -c -o integration/sugar_integration_tests.o integration/sugar_integration_tests.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/sugar_metapop_custom_diploidTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/sugar_metapop_custom_diploidTest.o -MD -MP -MF $depbase.Tpo -c -o integration/sugar_metapop_custom_diploidTest.o integration/sugar_metapop_custom_diploidTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/sugar_metapopTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/sugar_metapopTest.o -MD -MP -MF $depbase.Tpo -c -o integration/sugar_metapopTest.o integration/sugar_metapopTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/sugar_multilocusTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/sugar_multilocusTest.o -MD -MP -MF $depbase.Tpo -c -o integration/sugar_multilocusTest.o integration/sugar_multilocusTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/sugar_singlepop_custom_diploidTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/sugar_singlepop_custom_diploidTest.o -MD -MP -MF $depbase.Tpo -c -o integration/sugar_singlepop_custom_diploidTest.o integration/sugar_singlepop_custom_diploidTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/sugar_singlepopTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/sugar_singlepopTest.o -MD -MP -MF $depbase.Tpo -c -o integration/sugar_singlepopTest.o integration/sugar_singlepopTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/sugar_matrixTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/sugar_matrixTest.o -MD -MP -MF $depbase.Tpo -c -o integration/sugar_matrixTest.o integration/sugar_matrixTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/extensions_integration_tests.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/extensions_integration_tests.o -MD -MP -MF $depbase.Tpo -c -o integration/extensions_integration_tests.o integration/extensions_integration_tests.cc &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo integration/extensions_regionsIntegrationTest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    clang++ -DHAVE_CONFIG_H -I. -I..   -std=c++11  -g -O2 -std=c++11 -MT integration/extensions_regionsIntegrationTest.o -MD -MP -MF $depbase.Tpo -c -o integration/extensions_regionsIntegrationTest.o integration/extensions_regionsIntegrationTest.cc &&\
    mv -f $depbase.Tpo $depbase.Po
clang++  -g -O2 -std=c++11   -o unit/fwdpp_unit_tests unit/fwdpp_unit_tests.o unit/mutateTest.o unit/gameteTest.o unit/utilTest.o unit/type_traitsTest.o unit/recombinationTest.o unit/demographyTest.o unit/siteDepFitnessTest.o unit/serializationTest.o unit/ms_samplingTest.o unit/mlocusCrossoverTest.o unit/gamete_cleanerTest.o  -lgsl -lgslcblas -lz 
clang++  -g -O2 -std=c++11   -o unit/extensions_unit_tests unit/extensions_unit_test.o unit/extensions_regionsTest.o unit/extensions_callbacksTest.o  -lgsl -lgslcblas -lz 
clang++  -g -O2 -std=c++11   -o unit/sugar_unit_tests unit/sugar_unit_tests.o unit/sugar_GSLrngTest.o unit/sugar_samplingTest.o unit/sugar_add_mutationTest.o unit/sugar_change_neutralTest.o unit/sugar_generalmutTest.o unit/sugar_generalmut_vecTest.o  -lgsl -lgslcblas -lz 
clang++  -g -O2 -std=c++11   -o integration/sugar_integration_tests integration/sugar_integration_tests.o integration/sugar_metapop_custom_diploidTest.o integration/sugar_metapopTest.o integration/sugar_multilocusTest.o integration/sugar_singlepop_custom_diploidTest.o integration/sugar_singlepopTest.o integration/sugar_matrixTest.o  -lgsl -lgslcblas -lz 
clang++  -g -O2 -std=c++11   -o integration/extensions_integration_tests integration/extensions_integration_tests.o integration/extensions_regionsIntegrationTest.o  -lgsl -lgslcblas -lz 
make  check-TESTS
PASS: unit/extensions_unit_tests
FAIL: unit/fwdpp_unit_tests
PASS: unit/sugar_unit_tests
PASS: integration/extensions_integration_tests
PASS: integration/sugar_integration_tests
============================================================================
Testsuite summary for fwdpp 0.5.6
============================================================================
# TOTAL: 5
# PASS:  4
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0
============================================================================
See testsuite/test-suite.log
Please report to https://github.com/molpopgen/fwdpp
============================================================================
make[3]: *** [test-suite.log] Error 1
make[2]: *** [check-TESTS] Error 2
make[1]: *** [check-am] Error 2
make: *** [check-recursive] Error 1

==> Formula
Tap: homebrew/science
Path: /usr/local/Homebrew/Library/Taps/homebrew/homebrew-science/fwdpp.rb
==> Configuration
HOMEBREW_VERSION: 1.3.0-15-g2ad03b8
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 2ad03b8eb30ca69bf4b45c1cfc1ca619e49b9a04
Last commit: 28 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core/
Core tap HEAD: 9165540c6cb317ab724a26c41299bc72ae1e65c3
Core tap last commit: 7 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local/Homebrew
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: quad-core 64-bit nehalem
Homebrew Ruby: 2.0.0-p481
Clang: 7.0 build 700
Git: 2.5.4 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: 1.8.0_131
macOS: 10.10.5-x86_64
Xcode: 7.2.1
CLT: 7.2.0.0.1.1447826929
X11: 2.7.11 => /opt/X11
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
SDKROOT: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /usr/local
CMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
MACOSX_DEPLOYMENT_TARGET: 10.10
PKG_CONFIG_PATH: /usr/local/opt/gsl/lib/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Homebrew/Library/Homebrew/os/mac/pkgconfig/10.10
ACLOCAL_PATH: /usr/local/share/aclocal
PATH: /usr/local/Homebrew/Library/Homebrew/shims/super:/usr/local/opt/gsl/bin:/usr/local/opt/libsequence/bin:/usr/bin:/bin:/usr/sbin:/sbin

Error: homebrew/science/fwdpp 0.5.6 did not build
Logs:
     /Users/brew/Jenkins/workspace/Homebrew Science Pull Requests/version/yosemite/logs/fwdpp/00.options.out
     /Users/brew/Jenkins/workspace/Homebrew Science Pull Requests/version/yosemite/logs/fwdpp/01.configure
     /Users/brew/Jenkins/workspace/Homebrew Science Pull Requests/version/yosemite/logs/fwdpp/01.configure.cc
     /Users/brew/Jenkins/workspace/Homebrew Science Pull Requests/version/yosemite/logs/fwdpp/02.make
     /Users/brew/Jenkins/workspace/Homebrew Science Pull Requests/version/yosemite/logs/fwdpp/02.make.cc
     /Users/brew/Jenkins/workspace/Homebrew Science Pull Requests/version/yosemite/logs/fwdpp/03.make
     /Users/brew/Jenkins/workspace/Homebrew Science Pull Requests/version/yosemite/logs/fwdpp/03.make.cc
     /Users/brew/Jenkins/workspace/Homebrew Science Pull Requests/version/yosemite/logs/fwdpp/config.log
READ THIS: https://docs.brew.sh/Troubleshooting.html
molpopgen commented 7 years ago

This is not the correct log. Please supply the log from the unit tests and report all versions of all dependencies.

10.10 is getting a bit old--this could be a won't fix.

tmozgach commented 7 years ago

I see. https://jenkins.brew.sh/job/Homebrew%20Science%20Pull%20Requests/1054/version=yosemite/testReport/junit/brew-test-bot/yosemite/install_homebrew_science_fwdpp/

molpopgen commented 7 years ago

Right, that is the same log that you copy/pasted above. It is telling you to look in testsuite/test-suite.log for the details of the failure.

I've submitted a branch of fwdpp asking Travis to build using xcode 6.4, but that'll happen with GCC pulled in via anaconda/conda-forge. I don't build with clang because it is too annoying to deal with installing the dependencies for the unit test suite.

molpopgen commented 7 years ago

@tmozgach the unit tests pass on Travis/Yosemite using gcc: https://travis-ci.org/molpopgen/fwdpp/builds/261420814

I don't test with clang because I pull dependencies in using bioconda, and they're built with gcc. However, unit tests have been passing with clang for years.

I am guessing there's an ABI incompatibility lurking somewhere. In other words, I suspect some dependency is compiled with GCC and uses cpp11. That is a recipe for incompatibility.