Package: PCAtools

Version: 1.3.0

Command: rm -rf PCAtools.buildbin-libdir && mkdir PCAtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PCAtools_1.3.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R PCAtools.buildbin-libdir

StartedAt: 2020-01-16 11:29:05 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 11:29:55 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 50.0 seconds

RetCode: 0

Status:  OK

PackageFile: PCAtools_1.3.0.tgz

PackageFileSize: 5.151 MiB

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### Running command:
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###   rm -rf PCAtools.buildbin-libdir && mkdir PCAtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PCAtools_1.3.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R PCAtools.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PCAtools.buildbin-libdir PCAtools_1.3.0.tar.gz'
>>>>>>> 

* installing *source* package ‘PCAtools’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c shuffle_matrix.cpp -o shuffle_matrix.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 PCAtools.so RcppExports.o shuffle_matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/PCAtools.buildbin-libdir/00LOCK-PCAtools/00new/PCAtools/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 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 (PCAtools)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "PCAtools.buildbin-libdir/PCAtools/libs//PCAtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "PCAtools.buildbin-libdir/PCAtools/libs//PCAtools.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "PCAtools.buildbin-libdir/PCAtools/libs//PCAtools.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "PCAtools.buildbin-libdir/PCAtools/libs//PCAtools.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "PCAtools.buildbin-libdir/PCAtools/libs//PCAtools.so"