############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqTools_1.41.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R seqTools.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=seqTools.buildbin-libdir seqTools_1.41.0.tar.gz' >>>>>>> * installing *source* package ‘seqTools’ ... ** 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'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c seqTools.c -o seqTools.o seqTools.c:851:65: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] error("[count_genome_Kmers] character mismatch at position %u!"); ~^ seqTools.c:3296:71: warning: format specifies type 'int' but the argument has type 'double' [-Wformat] error("[scale_kmer_matrix] scale[%i]=%i must be >1!", column_index, scale); ~~ ^~~~~ %f seqTools.c:3306:75: warning: format specifies type 'int' but the argument has type 'double' [-Wformat] error("[scale_kmer_matrix] scale[%i] = %i must be >1!", column_index, scale); ~~ ^~~~~ %f 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 seqTools.so seqTools.o -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/seqTools.buildbin-libdir/00LOCK-seqTools/00new/seqTools/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: In fun(libname, pkgname) : Package 'zlibbioc' is deprecated and will be removed from Bioconductor version 3.22 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'zlibbioc' is deprecated and will be removed from Bioconductor version 3.22 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'zlibbioc' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package keeps a record of temporary installation path * DONE (seqTools) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR seqTools.buildbin-libdir/seqTools/libs/seqTools.so >>>>>>> >>>>>>> Paths before fix: seqTools.buildbin-libdir/seqTools/libs/seqTools.so: seqTools.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "seqTools.buildbin-libdir/seqTools/libs/seqTools.so" >>>>>>> Paths after fix: seqTools.buildbin-libdir/seqTools/libs/seqTools.so: seqTools.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)