############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Repitools_1.52.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Repitools.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Repitools.buildbin-libdir Repitools_1.52.0.tar.gz' >>>>>>> * installing *source* package ‘Repitools’ ... ** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D R_NO_REMAP -I. -fPIC -falign-functions=64 -Wall -g -O2 -c const.c -o const.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D R_NO_REMAP -I. -fPIC -falign-functions=64 -Wall -g -O2 -c hyp2f1.c -o hyp2f1.o hyp2f1.c:126:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] double hyp2f1( a, b, c, x ) ^ hyp2f1.c:294:9: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] double hyt2f1( a, b, c, x, loss ) ^ hyp2f1.c:438:9: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] double hys2f1( a, b, c, x, loss ) ^ 3 warnings 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 mmeansd.cpp -o mmeansd.o mmeansd.cpp:33:24: warning: variable 'is' set but not used [-Wunused-but-set-variable] int * x, nval, hs, is, i; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D R_NO_REMAP -I. -fPIC -falign-functions=64 -Wall -g -O2 -c mtherr.c -o mtherr.o mtherr.c:77:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] int mtherr( name, code ) ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -D R_NO_REMAP -I. -fPIC -falign-functions=64 -Wall -g -O2 -c ringo_stuff.c -o ringo_stuff.o ringo_stuff.c:13:24: warning: unused variable 'Ringo_calls' [-Wunused-variable] static R_CallMethodDef Ringo_calls[] = { ^ 1 warning 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 Repitools.so const.o hyp2f1.o mmeansd.o mtherr.o ringo_stuff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/Repitools.buildbin-libdir/00LOCK-Repitools/00new/Repitools/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 (Repitools) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Repitools.buildbin-libdir/Repitools/libs/Repitools.so >>>>>>> >>>>>>> Paths before fix: Repitools.buildbin-libdir/Repitools/libs/Repitools.so: Repitools.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" "Repitools.buildbin-libdir/Repitools/libs/Repitools.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "Repitools.buildbin-libdir/Repitools/libs/Repitools.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "Repitools.buildbin-libdir/Repitools/libs/Repitools.so" >>>>>>> Paths after fix: Repitools.buildbin-libdir/Repitools/libs/Repitools.so: Repitools.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)