############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VegaMC_3.44.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VegaMC.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VegaMC.buildbin-libdir VegaMC_3.44.0.tar.gz' >>>>>>> * installing *source* package ‘VegaMC’ ... ** 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 run_vegaMC.c -o run_vegaMC.o run_vegaMC.c:144:62: warning: data argument not used by format string [-Wformat-extra-args] Rprintf("\tAberration Matrices Successfully Computed\n", num_seg_regions); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ run_vegaMC.c:150:13: warning: data argument not used by format string [-Wformat-extra-args] num_seg_regions); ^ run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] elem = strtok('\0', sep); ^~~~ run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] elem = strtok('\0', sep); ^~~~ run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable] char *elem, *brkt; ^ 5 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 sort_data.c -o sort_data.o sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] elem = strtok('\0', sep); ^~~~ sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] elem = strtok('\0', sep); ^~~~ 2 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 vegaMC.c -o vegaMC.o vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable] node deleted; ^ vegaMC.c:458:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] lambda_gradient = abs(lambda); ^ vegaMC.c:458:23: note: use function 'fabsf' instead lambda_gradient = abs(lambda); ^~~ fabsf vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable] int i, j, index; ^ 3 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 VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/VegaMC.buildbin-libdir/00LOCK-VegaMC/00new/VegaMC/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 (VegaMC) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so >>>>>>> >>>>>>> Paths before fix: VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so: VegaMC.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 4.4.2) /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" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.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" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.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" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so" >>>>>>> Paths after fix: VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so: VegaMC.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 4.4.2) /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)