############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mitoClone2_1.13.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mitoClone2.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mitoClone2.buildbin-libdir mitoClone2_1.13.0.tar.gz' >>>>>>> * installing *source* package ‘mitoClone2’ ... ** 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 -std=gnu++17 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite mkdir -p "/Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/" cp scite "/Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/" rm scite 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/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c bam2R_10x.cpp -o bam2R_10x.o bam2R_10x.cpp:6:2: warning: '/*' within block comment [-Wcomment] /************************************************************************************** ^ bam2R_10x.cpp:8:1: warning: '/*' within block comment [-Wcomment] /********************************************************************** ^ bam2R_10x.cpp:21:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :3:9: note: previous definition is here #define R_NO_REMAP 1 ^ bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable] int bc_absent; ^ bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable] hts_itr_t *iter = NULL; ^ bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable] int c = 0; ^ 6 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o mitoClone2.so bam2R_10x.o /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (mitoClone2) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so >>>>>>> >>>>>>> Paths before fix: mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so: mitoClone2.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) /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5) /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) /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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.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" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.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" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so" >>>>>>> Paths after fix: mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so: mitoClone2.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) /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5) /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) /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)