############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh FLAMES_1.6.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R FLAMES.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=FLAMES.buildbin-libdir FLAMES_1.6.0.tar.gz' >>>>>>> * installing *source* package ‘FLAMES’ ... ** 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 C++17 using SDK: ‘MacOSX11.3.sdk’ 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/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/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++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/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppFunctions.cpp -o RcppFunctions.o In file included from RcppFunctions.cpp:7: In file included from ./main-functions/match_cell_barcode.h:13: ./main-functions/../utility/fastq_utils.h:12:1: warning: unused function 'kseq_init' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:165:16: note: expanded from macro '__KSEQ_BASIC' SCOPE kseq_t *kseq_init(type_t fd) \ ^ In file included from RcppFunctions.cpp:7: In file included from ./main-functions/match_cell_barcode.h:13: ./main-functions/../utility/fastq_utils.h:12:1: warning: unused function 'kseq_destroy' [-Wunused-function] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:171:13: note: expanded from macro '__KSEQ_BASIC' SCOPE void kseq_destroy(kseq_t *ks) \ ^ In file included from RcppFunctions.cpp:7: In file included from ./main-functions/match_cell_barcode.h:13: ./main-functions/../utility/fastq_utils.h:12:1: warning: unused function 'kseq_read' [-Wunused-function] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:238:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_READ(SCOPE) ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include/htslib/kseq.h:185:12: note: expanded from macro '__KSEQ_READ' SCOPE int kseq_read(kseq_t *seq) \ ^ 3 warnings generated. 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/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.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/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utility/edit_dist.cpp -o utility/edit_dist.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/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utility/fastq_utils.cpp -o utility/fastq_utils.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/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o 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/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam.c -o bam.o 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/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utility/ssw/ssw.c -o utility/ssw/ssw.o 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 FLAMES.so RcppExports.o RcppFunctions.o main-functions/match_cell_barcode.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.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/FLAMES.buildbin-libdir/00LOCK-FLAMES/00new/FLAMES/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 (FLAMES) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.so >>>>>>> >>>>>>> Paths before fix: FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.so: FLAMES.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" "FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.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" "FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.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" "FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.so" >>>>>>> Paths after fix: FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.so: FLAMES.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)