############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.67.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GLAD.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GLAD.buildbin-libdir GLAD_2.67.0.tar.gz' >>>>>>> * installing *source* package ‘GLAD’ ... ** using staged installation checking for pkg-config... /opt/R/x86_64/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes GSL has been found on the operating system operating system: Darwin configure: creating ./config.status config.status: creating src/Makevars src/Makevars file PKG_LIBS = -L/opt/R/x86_64/lib -lgsl -lgslcblas -lm PKG_CPPFLAGS = -DIS_MAC_OS ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BkpInfo.cpp -o BkpInfo.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HaarSeg.cpp -o HaarSeg.o HaarSeg.cpp:50:12: warning: variable 'lowSquareSum' set but not used [-Wunused-but-set-variable] double lowSquareSum = 0; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MoveBkp.cpp -o MoveBkp.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OutliersGNL.cpp -o OutliersGNL.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chrBreakpoints.cpp -o chrBreakpoints.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cutree.cpp -o cutree.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c daglad.cpp -o daglad.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distance.cpp -o distance.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c filterBkp.cpp -o filterBkp.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findCluster.cpp -o findCluster.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glad-utils.cpp -o glad-utils.o glad-utils.cpp:862:27: warning: unused variable 'it_new_end_NormalCluster' [-Wunused-variable] vector::iterator it_new_end_NormalCluster; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hclust.cpp -o hclust.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c laws.c -o laws.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c loopRemove.cpp -o loopRemove.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/opt/R/x86_64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/GLAD.buildbin-libdir/00LOCK-GLAD/00new/GLAD/libs ** R ** data ** demo ** 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 (GLAD) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GLAD.buildbin-libdir/GLAD/libs/GLAD.so >>>>>>> >>>>>>> Paths before fix: GLAD.buildbin-libdir/GLAD/libs/GLAD.so: GLAD.so (compatibility version 0.0.0, current version 0.0.0) /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 4.4.0) /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" "GLAD.buildbin-libdir/GLAD/libs/GLAD.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" "GLAD.buildbin-libdir/GLAD/libs/GLAD.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" "GLAD.buildbin-libdir/GLAD/libs/GLAD.so" >>>>>>> Paths after fix: GLAD.buildbin-libdir/GLAD/libs/GLAD.so: GLAD.so (compatibility version 0.0.0, current version 0.0.0) /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 4.4.0) /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)