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###
### Running command:
###
### rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.66.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R oligo.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oligo.buildbin-libdir oligo_1.66.0.tar.gz'
>>>>>>>
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DABG.c -o DABG.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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/MacOSX11.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/MacOSX11.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/MacOSX11.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/MacOSX11.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/MacOSX11.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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ParserXYS.c -o ParserXYS.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c baseProfile.c -o baseProfile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c basecontent.c -o basecontent.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chipbackground.c -o chipbackground.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mas5calls.c -o mas5calls.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rma2.c -o rma2.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rma_common.c -o rma_common.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c trimmed.c -o trimmed.o
trimmed.c:48:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
trimmed.c:48:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
trimmed.c:48:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
3 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -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-3.18-bioc-mac-arm64/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 PATHS TO DYNAMIC LIBRARIES FOR oligo.buildbin-libdir/oligo/libs/oligo.so
>>>>>>>
>>>>>>> Paths before fix:
oligo.buildbin-libdir/oligo/libs/oligo.so:
oligo.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)
/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.3)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/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-arm64/Resources/lib/libgcc_s.1.1.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so"
>>>>>>> Paths after fix:
oligo.buildbin-libdir/oligo/libs/oligo.so:
oligo.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/4.3-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.3)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
