netReg 0.99.4
Simon Dirmeier
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/netReg | | Last Changed Rev: 127735 / Revision: 129046 | | Last Changed Date: 2017-03-27 04:07:28 -0400 (Mon, 27 Mar 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | [ OK ] | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf netReg.buildbin-libdir && mkdir netReg.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netReg_0.99.4.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_0.99.4.tar.gz'
>>>>>>>
* installing *source* package ‘netReg’ ...
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 -mtune=core2 -g -O2
CPPFLAGS: -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -g -O2 -c edgenet_binomial.cpp -o edgenet_binomial.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -g -O2 -c edgenet_gaussian.cpp -o edgenet_gaussian.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -g -O2 -c edgenet_gaussian_model_selection.cpp -o edgenet_gaussian_model_selection.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -g -O2 -c graph_penalized_linear_model_cv_data.cpp -o graph_penalized_linear_model_cv_data.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -g -O2 -c math_functions.cpp -o math_functions.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSE_RCPPARMADILLO -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2 -g -O2 -I. -fPIC -Wall -mtune=core2 -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 edgenet_binomial.o edgenet_gaussian.o edgenet_gaussian_model_selection.o edgenet_wrapper.o graph_functions.o graph_penalized_linear_model_cv_data.o math_functions.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/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/netReg.buildbin-libdir/netReg/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/Resources/lib/libquadmath.0.dylib" "netReg.buildbin-libdir/netReg/libs//netReg.so"