############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GlobalAncova.buildbin-libdir && mkdir GlobalAncova.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GlobalAncova_4.23.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GlobalAncova.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GlobalAncova.buildbin-libdir GlobalAncova_4.23.0.tar.gz' >>>>>>> * installing *source* package ‘GlobalAncova’ ... ** 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 GlobalAncova.c -o GlobalAncova.o GlobalAncova.c:34:7: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*sD)*(*sD)*sizeof(double)); ^~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:39:7: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*sD)*(*sD)*sizeof(double) ); ^~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:44:7: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*zD)*(*sD)*sizeof(double) ); ^~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:49:7: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*zD)*(*zD)*sizeof(double) ); ^~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:89:7: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*zxx)*(*zD_full) * sizeof(double) ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:101:9: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*zxx)*(*zD_red) * sizeof(double) ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:149:6: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*zrr) * sizeof(double) ); ^~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:154:5: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*zrr) * sizeof(double)); ^~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:159:5: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*n_test_genes) * sizeof(double)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:164:5: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*sD_full)*(*sD_full) * sizeof(double)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:171:7: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*N_Subjects) * sizeof(int)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:251:6: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*zrr) * sizeof(double) ); ^~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:256:5: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*zrr) * sizeof(double)); ^~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:261:5: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*n_test_genes) * sizeof(double)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:266:5: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*sD_full)*(*sD_full) * sizeof(double)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalAncova.c:273:7: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (*N_Subjects) * sizeof(int)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 16 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 ludcmp.c -o ludcmp.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 matrix.c -o matrix.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 GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/GlobalAncova.buildbin-libdir/00LOCK-GlobalAncova/00new/GlobalAncova/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 (GlobalAncova) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GlobalAncova.buildbin-libdir/GlobalAncova/libs/GlobalAncova.so >>>>>>> >>>>>>> Paths before fix: GlobalAncova.buildbin-libdir/GlobalAncova/libs/GlobalAncova.so: GlobalAncova.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" "GlobalAncova.buildbin-libdir/GlobalAncova/libs/GlobalAncova.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" "GlobalAncova.buildbin-libdir/GlobalAncova/libs/GlobalAncova.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" "GlobalAncova.buildbin-libdir/GlobalAncova/libs/GlobalAncova.so" >>>>>>> Paths after fix: GlobalAncova.buildbin-libdir/GlobalAncova/libs/GlobalAncova.so: GlobalAncova.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)