Package: clusterExperiment

Version: 2.7.0

Command: rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh clusterExperiment_2.7.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R clusterExperiment.buildbin-libdir

StartedAt: 2020-01-16 10:39:23 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 10:41:07 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 104.6 seconds

RetCode: 0

Status:  OK

PackageFile: clusterExperiment_2.7.0.tgz

PackageFileSize: 10.94 MiB

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### Running command:
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###   rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh clusterExperiment_2.7.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R clusterExperiment.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=clusterExperiment.buildbin-libdir clusterExperiment_2.7.0.tar.gz'
>>>>>>> 

* installing *source* package ‘clusterExperiment’ ...
** 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' -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c search_pairs.cpp -o search_pairs.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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c subsampleLoop.cpp -o subsampleLoop.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 clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -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-3.11-bioc/meat/clusterExperiment.buildbin-libdir/00LOCK-clusterExperiment/00new/clusterExperiment/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
From .checkSubclasses(): subclass "ReshapedHDF5Matrix" of class "HDF5Matrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x7fc93b45f498>, where2=<environment: namespace:clusterExperiment>]
From .checkSubclasses(): subclass "ReshapedHDF5Matrix" of class "HDF5Matrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x7fc93b45f498>, where2=<environment: namespace:clusterExperiment>]
From .checkSubclasses(): subclass "ReshapedHDF5Matrix" of class "HDF5Matrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x7fc93b45f498>, where2=<environment: namespace:clusterExperiment>]
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
** 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 (clusterExperiment)


>>>>>>> 
>>>>>>> FIXING LINKS FOR clusterExperiment.buildbin-libdir/clusterExperiment/libs//clusterExperiment.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" "clusterExperiment.buildbin-libdir/clusterExperiment/libs//clusterExperiment.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs//clusterExperiment.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" "clusterExperiment.buildbin-libdir/clusterExperiment/libs//clusterExperiment.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs//clusterExperiment.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs//clusterExperiment.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs//clusterExperiment.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs//clusterExperiment.so"