Package: HDF5Array

Version: 1.12.3

Command: rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HDF5Array_1.12.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R HDF5Array.buildbin-libdir

StartedAt: 2019-10-16 08:45:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 08:45:38 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 38.6 seconds

RetCode: 0

Status:  OK

PackageFile: HDF5Array_1.12.3.tgz

PackageFileSize: 9.409 MiB

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### Running command:
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###   rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HDF5Array_1.12.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R HDF5Array.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HDF5Array.buildbin-libdir HDF5Array_1.12.3.tar.gz'
>>>>>>> 

* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c DSet.c -o DSet.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c array_selection.c -o array_selection.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c h5mread.c -o h5mread.o
h5mread.c:1194:22: warning: unused function 'select_elements_from_chunk' [-Wunused-function]
static long long int select_elements_from_chunk(const DSet *dset,
                     ^
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 HDF5Array.so DSet.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/HDF5Array.buildbin-libdir/00LOCK-HDF5Array/00new/HDF5Array/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (HDF5Array)


>>>>>>> 
>>>>>>> FIXING LINKS FOR HDF5Array.buildbin-libdir/HDF5Array/libs//HDF5Array.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" "HDF5Array.buildbin-libdir/HDF5Array/libs//HDF5Array.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs//HDF5Array.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" "HDF5Array.buildbin-libdir/HDF5Array/libs//HDF5Array.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs//HDF5Array.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs//HDF5Array.so"