Elana J. Fertig
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CoGAPS |
| Branch: RELEASE_3_7 |
| Last Commit: 9d82c1f |
| Last Changed Date: 2018-07-26 15:59:34 -0400 (Thu, 26 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:48:43 -0400 (Wed, 17 Oct 2018).
| Package 287/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CoGAPS 3.0.2 Elana J. Fertig
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
| Package: CoGAPS |
| Version: 3.0.2 |
| Command: rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CoGAPS_3.0.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CoGAPS.buildbin-libdir |
| StartedAt: 2018-10-17 01:07:58 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:10:35 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 157.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CoGAPS_3.0.2.tgz |
| PackageFileSize: 1.344 MiB |
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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_3.0.2.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_3.0.2.tar.gz'
>>>>>>>
* installing *source* package ‘CoGAPS’ ...
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Algorithms.cpp -o Algorithms.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c AtomicSupport.cpp -o AtomicSupport.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Cogaps.cpp -o Cogaps.o
In file included from Cogaps.cpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/date_facet.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/period_parser.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/string_parse_tree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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 {
^
In file included from Cogaps.cpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/text_oarchive.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/basic_text_oarchive.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/detail/common_oarchive.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/detail/interface_oarchive.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/detail/oserializer.hpp:40:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/serialization/extended_type_info_typeid.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/serialization/static_warning.hpp:67:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/mpl/print.hpp:52:19: warning: in-class initialization of non-static data member is a C++11 extension [-Wc++11-extensions]
const int m_x = 1 / (sizeof(T) - sizeof(T));
^
2 warnings generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c GibbsSampler.cpp -o GibbsSampler.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Matrix.cpp -o Matrix.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Random.cpp -o Random.o
In file included from Random.cpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/distributions/normal.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/erf.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -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 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -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 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testAlgorithms.cpp -o cpp_tests/testAlgorithms.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testAtomicSupport.cpp -o cpp_tests/testAtomicSupport.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testGibbsSampler.cpp -o cpp_tests/testGibbsSampler.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testMatrix.cpp -o cpp_tests/testMatrix.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testRandom.cpp -o cpp_tests/testRandom.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testSerialization.cpp -o cpp_tests/testSerialization.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 Algorithms.o AtomicSupport.o Cogaps.o GibbsSampler.o Matrix.o Random.o RcppExports.o test-runner.o cpp_tests/testAlgorithms.o cpp_tests/testAtomicSupport.o cpp_tests/testGibbsSampler.o cpp_tests/testMatrix.o cpp_tests/testRandom.o cpp_tests/testSerialization.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-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"