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BioC 3.2: BUILD BIN report for Rsubread on perceval

This page was generated on 2015-11-10 14:46:57 -0800 (Tue, 10 Nov 2015).

Package 919/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 1.20.2
Wei Shi
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rsubread
Last Changed Rev: 110347 / Revision: 110496
Last Changed Date: 2015-11-04 21:07:15 -0800 (Wed, 04 Nov 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsubread
Version: 1.20.2
Command: rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsubread_1.20.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rsubread.buildbin-libdir
StartedAt: 2015-11-10 11:45:00 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 11:45:19 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 18.9 seconds
RetCode: 0
Status:  OK 
PackageFile: Rsubread_1.20.2.tgz
PackageFileSize: 6.702 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsubread_1.20.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rsubread.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsubread.buildbin-libdir Rsubread_1.20.2.tar.gz'
>>>>>>> 

* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Darwin.
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c HelperFunctions.c -o HelperFunctions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c R_wrapper.c -o R_wrapper.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c SNPCalling.c -o SNPCalling.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c aligner.c -o aligner.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c atgcContent.c -o atgcContent.o
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:73: warning: unused variable ‘data_ready’
atgcContent.c:71: warning: unused variable ‘offset’
atgcContent.c:70: warning: unused variable ‘readlen’
atgcContent.c:68: warning: unused variable ‘z’
atgcContent.c:67: warning: unused variable ‘len’
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:109: warning: unused variable ‘z’
atgcContent.c:108: warning: unused variable ‘len’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c build-sam-index.c -o build-sam-index.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c core-bigtable.c -o core-bigtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c core-indel.c -o core-indel.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c core-interface-aligner.c -o core-interface-aligner.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c core-interface-subjunc.c -o core-interface-subjunc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c core-junction.c -o core-junction.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c core.c -o core.o
core.c: In function ‘do_iteration_two’:
core.c:2491: warning: unused variable ‘current_result’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c detectionCall.c -o detectionCall.o
detectionCall.c: In function ‘build_ir_data_structure_map’:
detectionCall.c:176: warning: unused variable ‘read_entrezid’
detectionCall.c: In function ‘simplify_SAM_file’:
detectionCall.c:214: warning: unused variable ‘z’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function ‘build_ir_data_structure’:
detectionCallAnnotation.c:117: warning: unused variable ‘read_length’
detectionCallAnnotation.c: In function ‘breakIntegenicRegion’:
detectionCallAnnotation.c:152: warning: unused variable ‘read_length’
detectionCallAnnotation.c:152: warning: unused variable ‘read_entrezid’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c exon-algorithms.c -o exon-algorithms.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c exon-align-indel.c -o exon-align-indel.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c exon-align.c -o exon-align.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c fullscan.c -o fullscan.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c fusion-align.c -o fusion-align.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c gene-algorithms.c -o gene-algorithms.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c gene-value-index.c -o gene-value-index.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c hashtable.c -o hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c index-builder.c -o index-builder.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c input-files.c -o input-files.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c interval_merge.c -o interval_merge.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c long-hashtable.c -o long-hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c mergeVCF.c -o mergeVCF.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c processExons.c -o processExons.o
processExons.c: In function ‘find_chr’:
processExons.c:237: warning: unused variable ‘pt’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c propmapped.c -o propmapped.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c qualityScores.c -o qualityScores.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c readSummary.c -o readSummary.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c removeDupReads.c -o removeDupReads.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c sam2bed.c -o sam2bed.o
sam2bed.c: In function ‘sam2bed’:
sam2bed.c:43: warning: unused variable ‘i’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c sambam-file.c -o sambam-file.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c seek-zlib.c -o seek-zlib.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c sorted-hashtable.c -o sorted-hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC  -mtune=core2 -g -O2 -Wall  -c sublog.c -o sublog.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o Rsubread.so HelperFunctions.o R_wrapper.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o fullscan.o fusion-align.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o long-hashtable.o mergeVCF.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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/3.2/Resources/lib/libgcc_s.1.dylib" "Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.so"