############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf atSNP.buildbin-libdir && mkdir atSNP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh atSNP_1.21.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R atSNP.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=atSNP.buildbin-libdir atSNP_1.21.0.tar.gz' >>>>>>> * installing *source* package ‘atSNP’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ImportanceSample.cpp -o ImportanceSample.o ImportanceSample.cpp:77:9: warning: variable 'mean_sample' set but not used [-Wunused-but-set-variable] double mean_sample = 0; ^ ImportanceSample.cpp:78:9: warning: variable 'mean_adj_score' set but not used [-Wunused-but-set-variable] double mean_adj_score = 0; ^ ImportanceSample.cpp:309:6: warning: variable 'snp_id' set but not used [-Wunused-but-set-variable] int snp_id = 0; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ImportanceSampleChange.cpp -o ImportanceSampleChange.o ImportanceSampleChange.cpp:49:9: warning: variable 'mean_score' set but not used [-Wunused-but-set-variable] double mean_score = 0; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ImportanceSampleDiff.cpp -o ImportanceSampleDiff.o ImportanceSampleDiff.cpp:85:9: warning: variable 'mean_diff' set but not used [-Wunused-but-set-variable] double mean_diff = 0; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MotifScore.cpp -o MotifScore.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o atSNP.so ImportanceSample.o ImportanceSampleChange.o ImportanceSampleDiff.o MotifScore.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/atSNP.buildbin-libdir/00LOCK-atSNP/00new/atSNP/libs ** R ** data ** 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 (atSNP) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR atSNP.buildbin-libdir/atSNP/libs/atSNP.so >>>>>>> >>>>>>> Paths before fix: atSNP.buildbin-libdir/atSNP/libs/atSNP.so: atSNP.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/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) /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-arm64/Resources/lib/libgcc_s.1.1.dylib" "atSNP.buildbin-libdir/atSNP/libs/atSNP.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "atSNP.buildbin-libdir/atSNP/libs/atSNP.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "atSNP.buildbin-libdir/atSNP/libs/atSNP.so" >>>>>>> Paths after fix: atSNP.buildbin-libdir/atSNP/libs/atSNP.so: atSNP.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/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) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)