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BioC 3.0: BUILD BIN report for ncdfFlow on perceval

This page was generated on 2015-04-10 09:56:30 -0700 (Fri, 10 Apr 2015).

Package 596/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.12.0
Mike Jiang
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/ncdfFlow
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  OK  OK 

Summary

Package: ncdfFlow
Version: 2.12.0
Command: rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_2.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ncdfFlow.buildbin-libdir
StartedAt: 2015-04-10 08:28:26 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 08:29:23 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 57.5 seconds
RetCode: 0
Status:  OK 
PackageFile: ncdfFlow_2.12.0.tgz
PackageFileSize: 1.387 MiB

Command output

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###
### Running command:
###
###   rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_2.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ncdfFlow.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ncdfFlow.buildbin-libdir ncdfFlow_2.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘ncdfFlow’ ...
configure: search for hdf5 library in: /usr/lib
configure: found hdf5 library in: /usr/lib
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bitOps.cpp -o bitOps.o
bitOps.cpp: In function ‘Rcpp::LogicalVector toLogical(Rcpp::RawVector)’:
bitOps.cpp:23: warning: unused variable ‘nByte’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c hdfFlow.c -o hdfFlow.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c readFrame.cpp -o readFrame.o
readFrame.cpp: In function ‘Rcpp::NumericVector readSlice_cpp(std::string, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int&)’:
readFrame.cpp:140: warning: comparison between signed and unsigned integer expressions
readFrame.cpp:237: warning: comparison between signed and unsigned integer expressions
readFrame.cpp: In function ‘Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)’:
readFrame.cpp:373: 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 -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c wrappers.c -o wrappers.o
wrappers.c: In function ‘readSlice’:
wrappers.c:535: warning: unused variable ‘data_out’
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 ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o wrappers.o -L/usr/lib -lhdf5 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘ncdfFlow’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ncdfFlow)


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