############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf BufferedMatrix.buildbin-libdir && mkdir BufferedMatrix.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BufferedMatrix_1.68.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BufferedMatrix.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BufferedMatrix.buildbin-libdir BufferedMatrix_1.68.0.tar.gz' >>>>>>> * installing *source* package ‘BufferedMatrix’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] if (!(Matrix->readonly) & setting){ ^ ~ doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first if (!(Matrix->readonly) & setting){ ^ ( ) doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning if (!(Matrix->readonly) & setting){ ^ ( ) doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function] static int sort_double(const double *a1,const double *a2){ ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.buildbin-libdir/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’ Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’ Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’ Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’ Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’ Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’ ** 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 (BufferedMatrix) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/BufferedMatrix.so >>>>>>> >>>>>>> Paths before fix: BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/BufferedMatrix.so: BufferedMatrix.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/BufferedMatrix.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/BufferedMatrix.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/BufferedMatrix.so" >>>>>>> Paths after fix: BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/BufferedMatrix.so: BufferedMatrix.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)