##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsubread_2.10.5.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rsubread.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsubread.buildbin-libdir Rsubread_2.10.5.tar.gz'
>>>>>>> 

* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Darwin.
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c LRMbase-index.c -o LRMbase-index.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c LRMchro-event.c -o LRMchro-event.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c LRMfile-io.c -o LRMfile-io.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c LRMhashtable.c -o LRMhashtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c LRMhelper.c -o LRMhelper.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c LRMseek-zlib.c -o LRMseek-zlib.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c R_wrapper.c -o R_wrapper.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c RsimReads.c -o RsimReads.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c SNPCalling.c -o SNPCalling.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c aligner.c -o aligner.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c atgcContent.c -o atgcContent.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c build-sam-index.c -o build-sam-index.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c cell-counts.c -o cell-counts.o
cell-counts.c:4213:10: warning: unused variable 'tv2' [-Wunused-variable]
        void ** tv2 = me->appendix3;
                ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c core-bigtable.c -o core-bigtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c core-indel.c -o core-indel.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c core-junction.c -o core-junction.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c core.c -o core.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c detection-calls.c -o detection-calls.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c detectionCall.c -o detectionCall.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c exon-align-indel.c -o exon-align-indel.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c exon-align.c -o exon-align.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c flattenAnnotations.c -o flattenAnnotations.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c fullscan.c -o fullscan.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c fusion-align.c -o fusion-align.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c gen_rand_reads.c -o gen_rand_reads.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c gene-algorithms.c -o gene-algorithms.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c gene-value-index.c -o gene-value-index.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c hashtable.c -o hashtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c index-builder.c -o index-builder.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c input-blc.c -o input-blc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c input-files.c -o input-files.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c interval_merge.c -o interval_merge.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c long-hashtable.c -o long-hashtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c longread-mapping.c -o longread-mapping.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c mergeVCF.c -o mergeVCF.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c processExons.c -o processExons.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c propmapped.c -o propmapped.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c qualityScores.c -o qualityScores.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c read-repair.c -o read-repair.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c readSummary.c -o readSummary.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c removeDupReads.c -o removeDupReads.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c sam2bed.c -o sam2bed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c sambam-file.c -o sambam-file.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c seek-zlib.c -o seek-zlib.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c sublog.c -o sublog.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -Wall -g -O2  -c tx-unique.c -o tx-unique.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 Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.15-bioc/meat/Rsubread.buildbin-libdir/00LOCK-Rsubread/00new/Rsubread/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 (Rsubread)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"