############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.56.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R oligo.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oligo.buildbin-libdir oligo_1.56.0.tar.gz' >>>>>>> * installing *source* package ‘oligo’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c DABG.c -o DABG.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ParserGzXYS.c -o ParserGzXYS.o ParserGzXYS.c:18:17: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types] while (!gzeof(file)){ ^~~~ * /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/zlib.h:1608:38: note: passing argument to parameter 'file' here ZEXTERN int ZEXPORT gzeof OF((gzFile file)); ^ ParserGzXYS.c:19:12: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types] gzgets(file, buffer, 1000); ^~~~ * /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/zlib.h:1505:42: note: passing argument to parameter 'file' here ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); ^ ParserGzXYS.c:46:6: warning: incompatible pointer types assigning to 'gzFile *' (aka 'struct gzFile_s **') from 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types] fp = gzopen(currentFile, "rb"); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ ParserGzXYS.c:50:10: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types] gzgets(fp, buffer, LINEMAX); ^~ * /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/zlib.h:1505:42: note: passing argument to parameter 'file' here ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); ^ ParserGzXYS.c:51:11: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types] gzclose(fp); ^~ * /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)); ^ ParserGzXYS.c:134:6: warning: incompatible pointer types assigning to 'gzFile *' (aka 'struct gzFile_s **') from 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types] fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb"); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParserGzXYS.c:138:11: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types] gzclose(fp); ^~ * /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)); ^ 7 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ParserXYS.c -o ParserXYS.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c baseProfile.c -o baseProfile.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c basecontent.c -o basecontent.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c chipbackground.c -o chipbackground.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mas5calls.c -o mas5calls.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rma2.c -o rma2.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rma_common.c -o rma_common.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c trimmed.c -o trimmed.o 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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.13-bioc/meat/oligo.buildbin-libdir/00LOCK-oligo/00new/oligo/libs ** R ** inst ** byte-compile and prepare package for lazy loading Note: in method for ‘pm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" Note: in method for ‘mm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" ** 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 (oligo) >>>>>>> >>>>>>> FIXING LINKS FOR oligo.buildbin-libdir/oligo/libs/oligo.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" "oligo.buildbin-libdir/oligo/libs/oligo.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so" install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so" install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so"