############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GrafGen.buildbin-libdir && mkdir GrafGen.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GrafGen_1.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GrafGen.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GrafGen.buildbin-libdir GrafGen_1.2.0.tar.gz' >>>>>>> * installing *source* package ‘GrafGen’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AncestrySnps.cpp -o AncestrySnps.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BedFileSnpGeno.cpp -o BedFileSnpGeno.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BimFileAncestrySnps.cpp -o BimFileAncestrySnps.o BimFileAncestrySnps.cpp:144:9: warning: variable 'numSwaps' set but not used [-Wunused-but-set-variable] int numSwaps = 0; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FamFileSamples.cpp -o FamFileSamples.o FamFileSamples.cpp:65:9: warning: variable 'lineNo' set but not used [-Wunused-but-set-variable] int lineNo = 0; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GrafGenHp_init.c -o GrafGenHp_init.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GrafPop.cpp -o GrafPop.o In file included from GrafPop.cpp:1: ./GrafPop.h:1:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SampleGenoAncestry.cpp -o SampleGenoAncestry.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SampleGenoDist.cpp -o SampleGenoDist.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Util.cpp -o Util.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VcfSampleAncestrySnpGeno.cpp -o VcfSampleAncestrySnpGeno.o VcfSampleAncestrySnpGeno.cpp:93:9: warning: variable 'buffNo' set but not used [-Wunused-but-set-variable] int buffNo = 0; ^ VcfSampleAncestrySnpGeno.cpp:312:9: warning: variable 'ancSnpNo' set but not used [-Wunused-but-set-variable] int ancSnpNo = 0; // Final list of ancestry SNPs to be used for ancestry inference ^ 2 warnings generated. 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 GrafGen.so AncestrySnps.o BedFileSnpGeno.o BimFileAncestrySnps.o FamFileSamples.o GrafGenHp_init.o GrafPop.o SampleGenoAncestry.o SampleGenoDist.o Util.o VcfSampleAncestrySnpGeno.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/GrafGen.buildbin-libdir/00LOCK-GrafGen/00new/GrafGen/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 (GrafGen) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GrafGen.buildbin-libdir/GrafGen/libs/GrafGen.so >>>>>>> >>>>>>> Paths before fix: GrafGen.buildbin-libdir/GrafGen/libs/GrafGen.so: GrafGen.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 4.4.2) /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" "GrafGen.buildbin-libdir/GrafGen/libs/GrafGen.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "GrafGen.buildbin-libdir/GrafGen/libs/GrafGen.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "GrafGen.buildbin-libdir/GrafGen/libs/GrafGen.so" >>>>>>> Paths after fix: GrafGen.buildbin-libdir/GrafGen/libs/GrafGen.so: GrafGen.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 4.4.2) /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)