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BioC 3.0: BUILD BIN report for seqbias on perceval

This page was generated on 2015-04-10 09:55:33 -0700 (Fri, 10 Apr 2015).

Package 809/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.14.0
Daniel Jones
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/seqbias
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK [ OK ]
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: seqbias
Version: 1.14.0
Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqbias_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R seqbias.buildbin-libdir
StartedAt: 2015-04-10 08:44:10 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 08:44:59 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 48.6 seconds
RetCode: 0
Status:  OK 
PackageFile: seqbias_1.14.0.tgz
PackageFileSize: 889.8 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqbias_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R seqbias.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=seqbias.buildbin-libdir seqbias_1.14.0.tar.gz'
>>>>>>> 

* installing *source* package ‘seqbias’ ...
** libs
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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c common.c -o common.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c miscmath.c -o miscmath.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c pos_table.c -o pos_table.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c samtools_extra.c -o samtools_extra.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c kmer_matrix.cpp -o kmer_matrix.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c logger.cpp -o logger.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c motif.cpp -o motif.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c seqbias.cpp -o seqbias.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c sequencing_bias.cpp -o sequencing_bias.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c twobitseq.cpp -o twobitseq.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/directives.cpp -o yaml-cpp/directives.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/exp.cpp -o yaml-cpp/exp.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/node.cpp -o yaml-cpp/node.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/null.cpp -o yaml-cpp/null.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/parser.cpp -o yaml-cpp/parser.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/regex.cpp -o yaml-cpp/regex.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:
yaml-cpp/collectionstack.h:28: warning: unused parameter ‘type’
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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/stream.cpp -o yaml-cpp/stream.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"  -Wall -Wextra -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c yaml-cpp/tag.cpp -o yaml-cpp/tag.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 seqbias.so common.o miscmath.o pos_table.o samtools_extra.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /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/seqbias.buildbin-libdir/seqbias/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 (seqbias)


>>>>>>> 
>>>>>>> FIXING LINKS FOR seqbias.buildbin-libdir/seqbias/libs//seqbias.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" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.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" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"