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BUILD BIN report for netReg on celaya2

This page was generated on 2019-10-16 12:59:53 -0400 (Wed, 16 Oct 2019).

Package 1099/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netReg 1.8.0
Simon Dirmeier
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/netReg
Branch: RELEASE_3_9
Last Commit: 03e580f
Last Changed Date: 2019-05-02 11:54:06 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: netReg
Version: 1.8.0
Command: rm -rf netReg.buildbin-libdir && mkdir netReg.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netReg_1.8.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R netReg.buildbin-libdir
StartedAt: 2019-10-16 09:02:30 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:05:00 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 149.5 seconds
RetCode: 0
Status:  OK 
PackageFile: netReg_1.8.0.tgz
PackageFileSize: 2.733 MiB

Command output

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###
### Running command:
###
###   rm -rf netReg.buildbin-libdir && mkdir netReg.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netReg_1.8.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R netReg.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=netReg.buildbin-libdir netReg_1.8.0.tar.gz'
>>>>>>> 

* installing *source* package ‘netReg’ ...
** using staged installation
configure: R home found in /Library/Frameworks/R.framework/Resources
configure: setting CXX to clang++ -std=gnu++11
checking whether configure should try to set CXXFLAGS... no
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++ -std=gnu++11 accepts -g... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for ranlib... ranlib
checking for library containing cblas_dgemm... no
configure: using rblas
checking whether clang++ -std=gnu++11 supports C++11 features by default... yes
checking for clang++ -std=gnu++11 option to support OpenMP... unsupported
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged

	Have fun with: netReg

	CXX:        clang++ -std=gnu++11
	CXXFLAGS:   -Wall -g -O2
	CPPFLAGS:   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include

** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c cv_set.cpp -o cv_set.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c data_factory.cpp -o data_factory.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c edgenet.cpp -o edgenet.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c edgenet_model_selection.cpp -o edgenet_model_selection.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c edgenet_wrapper.cpp -o edgenet_wrapper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c graph_functions.cpp -o graph_functions.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c graph_model_cv_data.cpp -o graph_model_cv_data.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c netReg_wrapper.cpp -o netReg_wrapper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c stat_functions.cpp -o stat_functions.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2  -fPIC  -Wall -g -O2  -c vector_functions.cpp -o vector_functions.o
clang++ -std=gnu++11 -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 netReg.so cv_set.o data_factory.o edgenet.o edgenet_model_selection.o edgenet_wrapper.o graph_functions.o graph_model_cv_data.o netReg_wrapper.o stat_functions.o vector_functions.o -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/netReg.buildbin-libdir/00LOCK-netReg/00new/netReg/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (netReg)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "netReg.buildbin-libdir/netReg/libs//netReg.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "netReg.buildbin-libdir/netReg/libs//netReg.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "netReg.buildbin-libdir/netReg/libs//netReg.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "netReg.buildbin-libdir/netReg/libs//netReg.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "netReg.buildbin-libdir/netReg/libs//netReg.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "netReg.buildbin-libdir/netReg/libs//netReg.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "netReg.buildbin-libdir/netReg/libs//netReg.so"