############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qrqc_1.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R qrqc.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=qrqc.buildbin-libdir qrqc_1.48.0.tar.gz' >>>>>>> * installing *source* package ‘qrqc’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_io.c -o R_init_io.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c io.c -o io.o io.c:348:14: warning: incompatible pointer types initializing 'gzFile *' (aka 'struct gzFile_s **') with an expression of type 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types] FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r"); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:351:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types] block = kseq_init(fp); ^~ * io.c:35:1: note: passing argument to parameter 'fd' here KSEQ_INIT(gzFile, gzread) ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:170:33: note: expanded from macro '__KSEQ_BASIC' SCOPE kseq_t *kseq_init(type_t fd) \ ^ io.c:453:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types] block = kseq_init(fp); ^~ * io.c:35:1: note: passing argument to parameter 'fd' here KSEQ_INIT(gzFile, gzread) ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:170:33: note: expanded from macro '__KSEQ_BASIC' SCOPE kseq_t *kseq_init(type_t fd) \ ^ io.c:454:14: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types] FILE_CLOSE(fp); ^~ * io.c:34:32: note: expanded from macro 'FILE_CLOSE' #define FILE_CLOSE(x) (gzclose(x)) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/zlib.h:1644:43: note: passing argument to parameter 'file' here ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^ io.c:35:1: warning: unused function 'kseq_destroy' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:176:13: note: expanded from macro '__KSEQ_BASIC' SCOPE void kseq_destroy(kseq_t *ks) \ ^ 5 warnings generated. clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.14-bioc/meat/qrqc.buildbin-libdir/00LOCK-qrqc/00new/qrqc/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 (qrqc) >>>>>>> >>>>>>> FIXING LINKS FOR qrqc.buildbin-libdir/qrqc/libs/qrqc.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "qrqc.buildbin-libdir/qrqc/libs/qrqc.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "qrqc.buildbin-libdir/qrqc/libs/qrqc.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "qrqc.buildbin-libdir/qrqc/libs/qrqc.so"