############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_2.52.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ncdfFlow.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ncdfFlow.buildbin-libdir ncdfFlow_2.52.0.tar.gz' >>>>>>> * installing *source* package ‘ncdfFlow’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cpp11.cpp -o cpp11.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hdfFlow.cpp -o hdfFlow.o hdfFlow.cpp:493:14: warning: variable 'status' set but not used [-Wunused-but-set-variable] herr_t status; ^ 1 warning generated. mkdir -p "/Users/biocbuild/bbs-3.20-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib" ar rs "/Users/biocbuild/bbs-3.20-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a" cpp11.o hdfFlow.o ar: creating archive /Users/biocbuild/bbs-3.20-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ncdfFlow.so cpp11.o hdfFlow.o /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/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 (ncdfFlow) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.so >>>>>>> >>>>>>> Paths before fix: ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.so: ncdfFlow.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) >>>>>>> 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" "ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.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" "ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.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" "ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.so" >>>>>>> Paths after fix: ncdfFlow.buildbin-libdir/ncdfFlow/libs/ncdfFlow.so: ncdfFlow.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)