############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R h5vc.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=h5vc.buildbin-libdir h5vc_2.34.0.tar.gz' >>>>>>> * installing *source* package ‘h5vc’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ 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 -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tallyBAM.cpp -o tallyBAM.o tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^ tallyBAM.cpp:60:18: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] }else if(p->indel > 0){ ^~~~~~~~~~~~ tallyBAM.cpp:64:16: note: uninitialized use occurs here str += c; ^ tallyBAM.cpp:60:15: note: remove the 'if' if its condition is always true }else if(p->indel > 0){ ^~~~~~~~~~~~~~~~ tallyBAM.cpp:55:15: note: initialize the variable 'c' to silence this warning char c; ^ = '\0' tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable] int len = nttable->end - nttable->beg; ^ tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ tallyBAM.cpp:43:12: warning: unused function 'pileup_func_old' [-Wunused-function] static int pileup_func_old(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data) ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o h5vc.so bam_plbuf.o tallyBAM.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc/meat/h5vc.buildbin-libdir/00LOCK-h5vc/00new/h5vc/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’ ** testing if installed package keeps a record of temporary installation path * DONE (h5vc) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR h5vc.buildbin-libdir/h5vc/libs/h5vc.so >>>>>>> >>>>>>> Paths before fix: h5vc.buildbin-libdir/h5vc/libs/h5vc.so: h5vc.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "h5vc.buildbin-libdir/h5vc/libs/h5vc.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "h5vc.buildbin-libdir/h5vc/libs/h5vc.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "h5vc.buildbin-libdir/h5vc/libs/h5vc.so" >>>>>>> Paths after fix: h5vc.buildbin-libdir/h5vc/libs/h5vc.so: h5vc.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)