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BioC 3.1: BUILD BIN report for kebabs on petty

This page was generated on 2015-10-09 09:37:03 -0700 (Fri, 09 Oct 2015).

Package 516/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.2.3
Ulrich Bodenhofer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/kebabs
Last Changed Rev: 104034 / Revision: 109384
Last Changed Date: 2015-05-21 05:04:50 -0700 (Thu, 21 May 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: kebabs
Version: 1.2.3
Command: rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh kebabs_1.2.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R kebabs.buildbin-libdir
StartedAt: 2015-10-09 03:13:27 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:14:50 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 83.5 seconds
RetCode: 0
Status:  OK 
PackageFile: kebabs_1.2.3.tgz
PackageFileSize: 2.809 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh kebabs_1.2.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R kebabs.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=kebabs.buildbin-libdir kebabs_1.2.3.tar.gz'
>>>>>>> 

* installing *source* package ‘kebabs’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ByteStringVector.c -o ByteStringVector.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ExplicitRepC.cpp -o ExplicitRepC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GappyPairC.cpp -o GappyPairC.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c KernelUtils.cpp -o KernelUtils.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MismatchC.cpp -o MismatchC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MotifC.cpp -o MotifC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PredictionC.cpp -o PredictionC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PredictionProfileC.cpp -o PredictionProfileC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_kebabs.cpp -o R_init_kebabs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Rsvm.c -o Rsvm.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SparseMatrixHash.cpp -o SparseMatrixHash.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SpectrumC.cpp -o SpectrumC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SymmetricPairC.cpp -o SymmetricPairC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Utils.cpp -o Utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c svm.cpp -o svm.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 kebabs.so Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/kebabs.buildbin-libdir/kebabs/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘heatmap’ in package ‘kebabs’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (kebabs)


>>>>>>> 
>>>>>>> FIXING LINKS FOR kebabs.buildbin-libdir/kebabs/libs//kebabs.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" "kebabs.buildbin-libdir/kebabs/libs//kebabs.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "kebabs.buildbin-libdir/kebabs/libs//kebabs.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" "kebabs.buildbin-libdir/kebabs/libs//kebabs.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "kebabs.buildbin-libdir/kebabs/libs//kebabs.so"