################################################################################################################################################################## Running command:###### rm -rf SPOTlight.buildbin-libdir && mkdir SPOTlight.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SPOTlight_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SPOTlight.buildbin-libdir###############################################################################################################################################################>>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SPOTlight.buildbin-libdir SPOTlight_1.14.0.tar.gz'>>>>>>> * installing *source* package ‘SPOTlight’ ...** this is package ‘SPOTlight’ version ‘1.14.0’** using staged installation** libsusing C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’using C++11using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.oclang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c nmf.cpp -o nmf.onmf.cpp:61:13: warning: private field 'col_' is not used [-Wunused-private-field] int col_, index, max_index; ^1 warning generated.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 SPOTlight.so RcppExports.o nmf.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Users/biocbuild/bbs-3.22-bioc/meat/SPOTlight.buildbin-libdir/00LOCK-SPOTlight/00new/SPOTlight/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 (SPOTlight)>>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SPOTlight.buildbin-libdir/SPOTlight/libs/SPOTlight.so>>>>>>> >>>>>>> Paths before fix:SPOTlight.buildbin-libdir/SPOTlight/libs/SPOTlight.so:SPOTlight.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.2)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)/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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "SPOTlight.buildbin-libdir/SPOTlight/libs/SPOTlight.so"install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "SPOTlight.buildbin-libdir/SPOTlight/libs/SPOTlight.so"install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "SPOTlight.buildbin-libdir/SPOTlight/libs/SPOTlight.so"install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "SPOTlight.buildbin-libdir/SPOTlight/libs/SPOTlight.so"install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "SPOTlight.buildbin-libdir/SPOTlight/libs/SPOTlight.so">>>>>>> Paths after fix:SPOTlight.buildbin-libdir/SPOTlight/libs/SPOTlight.so:SPOTlight.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.2)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
