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BioC 3.0: BUILD BIN report for QuasR on perceval

This page was generated on 2015-04-10 09:57:41 -0700 (Fri, 10 Apr 2015).

Package 706/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.6.2
Michael Stadler
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/QuasR
Last Changed Rev: 96362 / Revision: 102249
Last Changed Date: 2014-11-03 01:29:24 -0800 (Mon, 03 Nov 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS [ OK ]
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: QuasR
Version: 1.6.2
Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QuasR_1.6.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R QuasR.buildbin-libdir
StartedAt: 2015-04-10 08:35:34 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 08:36:29 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 54.8 seconds
RetCode: 0
Status:  OK 
PackageFile: QuasR_1.6.2.tgz
PackageFileSize: 1.541 MiB

Command output

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###
### Running command:
###
###   rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QuasR_1.6.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R QuasR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.6.2.tar.gz'
>>>>>>> 

* installing *source* package ‘QuasR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_QuasR.cpp -o R_init_QuasR.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c cat_bam.c -o cat_bam.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c count_alignments.c -o count_alignments.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c count_alignments_subregions.c -o count_alignments_subregions.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c count_junctions.cpp -o count_junctions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c export_wig.c -o export_wig.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c idxstats_bam.c -o idxstats_bam.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c profile_alignments.c -o profile_alignments.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c quantify_methylation.cpp -o quantify_methylation.o
quantify_methylation.cpp: In function ‘SEXPREC* quantify_methylation_singleAlignments(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
quantify_methylation.cpp:1070: warning: comparison between signed and unsigned integer expressions
quantify_methylation.cpp:1070: warning: comparison between signed and unsigned integer expressions
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c split_sam_chr.c -o split_sam_chr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c utilities.c -o utilities.o
llvm-g++-4.2 -arch x86_64 -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 QuasR.so R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o -lz /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/QuasR.buildbin-libdir/QuasR/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 (QuasR)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"