############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf cancerclass.buildbin-libdir && mkdir cancerclass.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cancerclass_1.49.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cancerclass.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cancerclass.buildbin-libdir cancerclass_1.49.0.tar.gz' >>>>>>> * installing *source* package ‘cancerclass’ ... ** 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 -fPIC -falign-functions=64 -Wall -g -O2 -c copa.c -o copa.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cor.c -o cor.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fc.c -o fc.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c help.c -o help.o help.c:263:12: warning: variable 'mean1' set but not used [-Wunused-but-set-variable] double mean1, mean2, var1, var2 = 0.0; ^ help.c:263:19: warning: variable 'mean2' set but not used [-Wunused-but-set-variable] double mean1, mean2, var1, var2 = 0.0; ^ help.c:335:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign] var=var; ///(to-from-1); R=var(N-1) => /(count-1) ~~~^~~~ help.c:325:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count=0; ^ help.c:344:13: warning: variable 'anzahl' set but not used [-Wunused-but-set-variable] int i,k,anzahl=0; ^ help.c:368:13: warning: variable 'anzahl' set but not used [-Wunused-but-set-variable] int i,k,anzahl=0; ^ 6 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ort.c -o ort.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c os.c -o os.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c shift.c -o shift.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c statistics.c -o statistics.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c student.c -o student.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c throw.c -o throw.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c welch.c -o welch.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c wilcox.c -o wilcox.o wilcox.c:37:8: warning: variable 'overall' set but not used [-Wunused-but-set-variable] int overall = 0; ^ wilcox.c:75:8: warning: variable 'overall' set but not used [-Wunused-but-set-variable] int overall = 0; ^ 2 warnings generated. 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 cancerclass.so copa.o cor.o fc.o help.o ort.o os.o shift.o statistics.o student.o throw.o welch.o wilcox.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/cancerclass.buildbin-libdir/00LOCK-cancerclass/00new/cancerclass/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 (cancerclass) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.so >>>>>>> >>>>>>> Paths before fix: cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.so: cancerclass.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/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" "cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.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" "cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.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" "cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.so" >>>>>>> Paths after fix: cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.so: cancerclass.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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)