############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf gpuMagic.buildbin-libdir && mkdir gpuMagic.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gpuMagic_1.19.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gpuMagic.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gpuMagic.buildbin-libdir gpuMagic_1.19.0.tar.gz' >>>>>>> * installing *source* package ‘gpuMagic’ ... ** 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/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c C_Interface.cpp -o C_Interface.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_functionRegistration.cpp -o R_functionRegistration.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Tools.cpp -o Tools.o Tools.cpp:41:8: warning: format string is not a string literal (potentially insecure) [-Wformat-security] error(errorInfo.c_str()); ^~~~~~~~~~~~~~~~~ Tools.cpp:41:8: note: treat the string as an argument to avoid this error(errorInfo.c_str()); ^ "%s", Tools.cpp:51:10: warning: format string is not a string literal (potentially insecure) [-Wformat-security] warning(warningInfo.c_str()); ^~~~~~~~~~~~~~~~~~~ Tools.cpp:51:10: note: treat the string as an argument to avoid this warning(warningInfo.c_str()); ^ "%s", Tools.cpp:60:10: warning: format string is not a string literal (potentially insecure) [-Wformat-security] Rprintf(msg.c_str()); ^~~~~~~~~~~ Tools.cpp:60:10: note: treat the string as an argument to avoid this Rprintf(msg.c_str()); ^ "%s", 3 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kernelManager.cpp -o kernelManager.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c openArray.cpp -o openArray.o 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 gpuMagic.so C_Interface.o R_functionRegistration.o Tools.o kernelManager.o openArray.o -framework OpenCL -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/gpuMagic.buildbin-libdir/00LOCK-gpuMagic/00new/gpuMagic/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 (gpuMagic) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so >>>>>>> >>>>>>> Paths before fix: gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so: gpuMagic.so (compatibility version 0.0.0, current version 0.0.0) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL (compatibility version 1.0.0, current version 1.0.0) /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/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/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.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" "gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.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" "gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so" >>>>>>> Paths after fix: gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so: gpuMagic.so (compatibility version 0.0.0, current version 0.0.0) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL (compatibility version 1.0.0, current version 1.0.0) /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/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)