############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf qckitfastq.buildbin-libdir && mkdir qckitfastq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qckitfastq_1.19.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R qckitfastq.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=qckitfastq.buildbin-libdir qckitfastq_1.19.0.tar.gz' >>>>>>> * installing *source* package ‘qckitfastq’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++14 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RSeqAn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RSeqAn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calc_adapter_content.cpp -o calc_adapter_content.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RSeqAn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gzstream.cpp -o gzstream.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RSeqAn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_fastq.cpp -o read_fastq.o read_fastq.cpp:30:32: warning: unused variable 'it' [-Wunused-variable] std::vector::iterator it; ^ read_fastq.cpp:158:36: warning: unused variable 'qual_by_col_it' [-Wunused-variable] std::vector::iterator qual_by_col_it; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/qckitfastq.buildbin-libdir/00LOCK-qckitfastq/00new/qckitfastq/libs ** R ** 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 (qckitfastq) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR qckitfastq.buildbin-libdir/qckitfastq/libs/qckitfastq.so >>>>>>> >>>>>>> Paths before fix: qckitfastq.buildbin-libdir/qckitfastq/libs/qckitfastq.so: qckitfastq.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/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/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "qckitfastq.buildbin-libdir/qckitfastq/libs/qckitfastq.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "qckitfastq.buildbin-libdir/qckitfastq/libs/qckitfastq.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "qckitfastq.buildbin-libdir/qckitfastq/libs/qckitfastq.so" >>>>>>> Paths after fix: qckitfastq.buildbin-libdir/qckitfastq/libs/qckitfastq.so: qckitfastq.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/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)