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BUILD BIN report for COHCAP on merida2

This page was generated on 2018-10-17 08:52:20 -0400 (Wed, 17 Oct 2018).

Package 290/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COHCAP 1.26.0
Charles Warden
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/COHCAP
Branch: RELEASE_3_7
Last Commit: b15be80
Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: COHCAP
Version: 1.26.0
Command: rm -rf COHCAP.buildbin-libdir && mkdir COHCAP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COHCAP_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R COHCAP.buildbin-libdir
StartedAt: 2018-10-17 01:08:07 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:08:52 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 45.0 seconds
RetCode: 0
Status:  OK 
PackageFile: COHCAP_1.26.0.tgz
PackageFileSize: 377.8 KiB

Command output

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###
### Running command:
###
###   rm -rf COHCAP.buildbin-libdir && mkdir COHCAP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COHCAP_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R COHCAP.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.26.0.tar.gz'
>>>>>>> 

* installing *source* package ‘COHCAP’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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  -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 Rcpp_BH_ANOVA.cpp -o Rcpp_BH_ANOVA.o
In file included from Rcpp_BH_ANOVA.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/distributions/fisher_f.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/beta.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  -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 Rcpp_BH_ttest.cpp -o Rcpp_BH_ttest.o
In file included from Rcpp_BH_ttest.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/distributions/students_t.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/beta.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++ -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 COHCAP.so RcppExports.o Rcpp_BH_ANOVA.o Rcpp_BH_ttest.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/COHCAP.buildbin-libdir/COHCAP/libs
** R
** 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 (COHCAP)


>>>>>>> 
>>>>>>> FIXING LINKS FOR COHCAP.buildbin-libdir/COHCAP/libs//COHCAP.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" "COHCAP.buildbin-libdir/COHCAP/libs//COHCAP.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "COHCAP.buildbin-libdir/COHCAP/libs//COHCAP.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" "COHCAP.buildbin-libdir/COHCAP/libs//COHCAP.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "COHCAP.buildbin-libdir/COHCAP/libs//COHCAP.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "COHCAP.buildbin-libdir/COHCAP/libs//COHCAP.so"