############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Harman.buildbin-libdir && mkdir Harman.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Harman_1.33.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Harman.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Harman.buildbin-libdir Harman_1.33.0.tar.gz' >>>>>>> * installing *source* package ‘Harman’ ... ** using staged installation ** libs 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 -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I. -fPIC -falign-functions=64 -Wall -g -O2 -c Harman.cpp -o Harman.o In file included from Harman.cpp:182: ./CSelectRandom.h:283:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable] size_t seed ; ^ ./CSelectRandom.h:372:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable] size_t seed ; ^ ./CSelectRandom.h:392:11: warning: unused variable 'currindex' [-Wunused-variable] size_t currindex ; ^ ./CSelectRandom.h:394:35: warning: unused variable 'it1' [-Wunused-variable] std::vector::iterator it1, it2 ; ^ ./CSelectRandom.h:394:40: warning: unused variable 'it2' [-Wunused-variable] std::vector::iterator it1, it2 ; ^ ./CSelectRandom.h:639:11: warning: unused variable 'time1' [-Wunused-variable] double time1, time2 ; ^ ./CSelectRandom.h:638:25: warning: unused variable 'ts2' [-Wunused-variable] struct timespec ts1, ts2 ; ^ ./CSelectRandom.h:638:20: warning: unused variable 'ts1' [-Wunused-variable] struct timespec ts1, ts2 ; ^ ./CSelectRandom.h:639:18: warning: unused variable 'time2' [-Wunused-variable] double time1, time2 ; ^ ./CSelectRandom.h:1019:23: warning: unused variable 'randData2' [-Wunused-variable] size_t randData1, randData2 ; ^ 10 warnings generated. 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 Harman.so Harman.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/Harman.buildbin-libdir/00LOCK-Harman/00new/Harman/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 (Harman) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Harman.buildbin-libdir/Harman/libs/Harman.so >>>>>>> >>>>>>> Paths before fix: Harman.buildbin-libdir/Harman/libs/Harman.so: Harman.so (compatibility version 0.0.0, current version 0.0.0) /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" "Harman.buildbin-libdir/Harman/libs/Harman.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" "Harman.buildbin-libdir/Harman/libs/Harman.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" "Harman.buildbin-libdir/Harman/libs/Harman.so" >>>>>>> Paths after fix: Harman.buildbin-libdir/Harman/libs/Harman.so: Harman.so (compatibility version 0.0.0, current version 0.0.0) /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)