############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.79.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DNAcopy.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DNAcopy.buildbin-libdir DNAcopy_1.79.0.tar.gz' >>>>>>> * installing *source* package ‘DNAcopy’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ using SDK: ‘MacOSX11.3.sdk’ /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c cbsWtstats.f -o cbsWtstats.o cbsWtstats.f:283:72: 283 | iseg(2) = tmaxj | ^ Warning: ‘tmaxj’ may be used uninitialized [-Wmaybe-uninitialized] cbsWtstats.f:17:23: 17 | 2 tmaxi, tmaxj, nal0 | ^ note: ‘tmaxj’ was declared here cbsWtstats.f:282:72: 282 | iseg(1) = tmaxi | ^ Warning: ‘tmaxi’ may be used uninitialized [-Wmaybe-uninitialized] cbsWtstats.f:17:16: 17 | 2 tmaxi, tmaxj, nal0 | ^ note: ‘tmaxi’ was declared here /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c cbststats.f -o cbststats.o cbststats.f:11:63: 11 | 1 nb2, bi, bj, ilo, ihi, jlo, jhi, alenmax, i2j, sxmxi, | ^ Warning: ‘sxmxi’ may be used uninitialized [-Wmaybe-uninitialized] /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c changepoints-wtd.f -o changepoints-wtd.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c changepoints.f -o changepoints.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c esegment.f -o esegment.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 flchoose.c -o flchoose.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 fphyper.c -o fphyper.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 fpnorm.c -o fpnorm.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c getbdry.f -o getbdry.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 init.c -o init.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c prune.f -o prune.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 rshared.c -o rshared.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c segmentp.f -o segmentp.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c smoothCNA.f -o smoothCNA.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c tailprobs.f -o tailprobs.o 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 DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o init.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/DNAcopy.buildbin-libdir/00LOCK-DNAcopy/00new/DNAcopy/libs ** R ** data *** moving datasets to lazyload DB ** demo ** 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 (DNAcopy) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so >>>>>>> >>>>>>> Paths before fix: DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so: DNAcopy.so (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /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" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so" >>>>>>> Paths after fix: DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so: DNAcopy.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /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)