############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf metaseqR2.buildbin-libdir && mkdir metaseqR2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh metaseqR2_1.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R metaseqR2.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=metaseqR2.buildbin-libdir metaseqR2_1.16.0.tar.gz' >>>>>>> * installing *source* package ‘metaseqR2’ ... ** 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 pval.c -o pval.o pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable] double esttotalperlength = total/2; ^ pval.c:29:13: warning: variable 'steps' set but not used [-Wunused-but-set-variable] long int steps = 0; ^ 2 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 metaseqR2.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/metaseqR2.buildbin-libdir/00LOCK-metaseqR2/00new/metaseqR2/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 (metaseqR2) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR metaseqR2.buildbin-libdir/metaseqR2/libs/metaseqR2.so >>>>>>> >>>>>>> Paths before fix: metaseqR2.buildbin-libdir/metaseqR2/libs/metaseqR2.so: metaseqR2.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" "metaseqR2.buildbin-libdir/metaseqR2/libs/metaseqR2.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "metaseqR2.buildbin-libdir/metaseqR2/libs/metaseqR2.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "metaseqR2.buildbin-libdir/metaseqR2/libs/metaseqR2.so" >>>>>>> Paths after fix: metaseqR2.buildbin-libdir/metaseqR2/libs/metaseqR2.so: metaseqR2.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)