############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ADaCGH2.buildbin-libdir && mkdir ADaCGH2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ADaCGH2_2.44.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ADaCGH2.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ADaCGH2.buildbin-libdir ADaCGH2_2.44.0.tar.gz' >>>>>>> * installing *source* package ‘ADaCGH2’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c r_haarseg.c -o r_haarseg.o r_haarseg.c:61:12: warning: variable 'lowSquareSum' set but not used [-Wunused-but-set-variable] double lowSquareSum; ^ r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable] double totalNorm; ^ r_haarseg.c:152:8: warning: '/*' within block comment [-Wcomment] }/* for j */ ^ r_haarseg.c:176:8: warning: '/*' within block comment [-Wcomment] }/* for j */ ^ r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable] int k,j; ^ 5 warnings generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ADaCGH2.so init.o r_haarseg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/ADaCGH2.buildbin-libdir/00LOCK-ADaCGH2/00new/ADaCGH2/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 (ADaCGH2) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ADaCGH2.buildbin-libdir/ADaCGH2/libs/ADaCGH2.so >>>>>>> >>>>>>> Paths before fix: ADaCGH2.buildbin-libdir/ADaCGH2/libs/ADaCGH2.so: ADaCGH2.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 4.4.0) /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-arm64/Resources/lib/libgcc_s.1.1.dylib" "ADaCGH2.buildbin-libdir/ADaCGH2/libs/ADaCGH2.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "ADaCGH2.buildbin-libdir/ADaCGH2/libs/ADaCGH2.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "ADaCGH2.buildbin-libdir/ADaCGH2/libs/ADaCGH2.so" >>>>>>> Paths after fix: ADaCGH2.buildbin-libdir/ADaCGH2/libs/ADaCGH2.so: ADaCGH2.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 4.4.0) /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)