Multiple platform build/check report for BioC 3.8 - BUILD BIN report for CoGAPS on merida1

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### Running command:
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###   rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CoGAPS_3.2.40.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CoGAPS.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CoGAPS.buildbin-libdir CoGAPS_3.2.40.tar.gz'
>>>>>>> 

* installing *source* package ‘CoGAPS’ ...
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 how to run the C++ preprocessor... clang++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ accepts -g... (cached) yes
checking for C++ compiler vendor... clang
checking for a sed that does not truncate output... /usr/bin/sed
checking for C++ compiler version... 4.0.0
checking for OpenMP flag of C++ compiler... unknown
building on clang compiler version 4.0.0
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c Cogaps.cpp -o Cogaps.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c GapsParameters.cpp -o GapsParameters.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c GapsResult.cpp -o GapsResult.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:17:
In file included from include/boost/date_time/posix_time/posix_time.hpp:24:
In file included from include/boost/date_time/posix_time/time_formatters.hpp:12:
In file included from include/boost/date_time/gregorian/gregorian.hpp:31:
In file included from include/boost/date_time/gregorian/gregorian_io.hpp:16:
In file included from include/boost/date_time/date_facet.hpp:23:
In file included from include/boost/date_time/period_parser.hpp:14:
In file included from include/boost/date_time/string_parse_tree.hpp:13:
In file included from include/boost/lexical_cast.hpp:32:
In file included from include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from include/boost/container/container_fwd.hpp:61:
include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c GapsStatistics.cpp -o GapsStatistics.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c test-runner.cpp -o test-runner.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c data_structures/HashSets.cpp -o data_structures/HashSets.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c data_structures/Matrix.cpp -o data_structures/Matrix.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c data_structures/Vector.cpp -o data_structures/Vector.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c file_parser/FileParser.cpp -o file_parser/FileParser.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c file_parser/GctParser.cpp -o file_parser/GctParser.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c math/Math.cpp -o math/Math.o
In file included from math/Math.cpp:4:
In file included from include/boost/math/distributions/exponential.hpp:10:
In file included from include/boost/math/constants/constants.hpp:13:
In file included from include/boost/math/tools/convert_from_string.hpp:15:
In file included from include/boost/lexical_cast.hpp:32:
In file included from include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from include/boost/container/container_fwd.hpp:61:
include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c math/MatrixMath.cpp -o math/MatrixMath.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c math/Random.cpp -o math/Random.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -march=native  -fPIC  -Wall -g -O2  -c math/VectorMath.cpp -o math/VectorMath.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CoGAPS.so Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/AtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CsvParser.o file_parser/FileParser.o file_parser/GctParser.o file_parser/TsvParser.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseStoragePolicy.o gibbs_sampler/SparseStoragePolicy.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.8-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CoGAPS)


>>>>>>> 
>>>>>>> FIXING LINKS FOR CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "CoGAPS.buildbin-libdir/CoGAPS/libs//CoGAPS.so"
BUILD BIN report for CoGAPS on merida1

Summary

Command output
