############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf multtest.buildbin-libdir && mkdir multtest.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh multtest_2.59.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R multtest.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=multtest.buildbin-libdir multtest_2.59.0.tar.gz' >>>>>>> * installing *source* package ‘multtest’ ... ** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c Rpack.c -o Rpack.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c VScount.c -o VScount.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c block_sampling_fixed.c -o block_sampling_fixed.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c bootloop.c -o bootloop.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c mt.c -o mt.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c pairt_sampling.c -o pairt_sampling.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c random.c -o random.o random.c:48:6: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] z1=abs(seed); /*setting the seed to z1 and initialize it*/ ^ random.c:48:6: note: use function 'labs' instead z1=abs(seed); /*setting the seed to z1 and initialize it*/ ^~~ labs 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c sampling.c -o sampling.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c sampling_fixed.c -o sampling_fixed.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c stat_func.c -o stat_func.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSEDOUBLE -fPIC -falign-functions=64 -Wall -g -O2 -c stat_order.c -o stat_order.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/multtest.buildbin-libdir/00LOCK-multtest/00new/multtest/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 (multtest) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR multtest.buildbin-libdir/multtest/libs/multtest.so >>>>>>> >>>>>>> Paths before fix: multtest.buildbin-libdir/multtest/libs/multtest.so: multtest.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /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) >>>>>>> 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" "multtest.buildbin-libdir/multtest/libs/multtest.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" "multtest.buildbin-libdir/multtest/libs/multtest.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" "multtest.buildbin-libdir/multtest/libs/multtest.so" >>>>>>> Paths after fix: multtest.buildbin-libdir/multtest/libs/multtest.so: multtest.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /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)