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BioC 3.5: BUILD BIN report for CNPBayes on veracruz2

This page was generated on 2017-08-16 13:33:47 -0400 (Wed, 16 Aug 2017).

Package 249/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.6.1
Jacob Carey
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CNPBayes
Last Changed Rev: 129423 / Revision: 131943
Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: CNPBayes
Version: 1.6.1
Command: rm -rf CNPBayes.buildbin-libdir && mkdir CNPBayes.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNPBayes_1.6.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CNPBayes.buildbin-libdir
StartedAt: 2017-08-16 09:55:50 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 09:57:07 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 76.5 seconds
RetCode: 0
Status:  OK 
PackageFile: CNPBayes_1.6.1.tgz
PackageFileSize: 2.139 MiB

Command output

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##############################################################################
###
### Running command:
###
###   rm -rf CNPBayes.buildbin-libdir && mkdir CNPBayes.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNPBayes_1.6.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CNPBayes.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNPBayes.buildbin-libdir CNPBayes_1.6.1.tar.gz'
>>>>>>> 

* installing *source* package ‘CNPBayes’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c miscfunctions.cpp -o miscfunctions.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c reduced_pooledvariance.cpp -o reduced_pooledvariance.o
reduced_pooledvariance.cpp:46:10: warning: unused variable 'prod' [-Wunused-variable]
  double prod ;
         ^
reduced_pooledvariance.cpp:86:7: warning: unused variable 'K' [-Wunused-variable]
  int K = thetastar.size() ;
      ^
reduced_pooledvariance.cpp:330:7: warning: unused variable 'K' [-Wunused-variable]
  int K = thetastar.size() ;
      ^
reduced_pooledvariance.cpp:617:7: warning: unused variable 'N' [-Wunused-variable]
  int N = x.size() ;
      ^
reduced_pooledvariance.cpp:682:7: warning: unused variable 'K' [-Wunused-variable]
  int K = thetastar.size() ;
      ^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c singlebatch_pooledvar.cpp -o singlebatch_pooledvar.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c update.cpp -o update.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updates_batch.cpp -o updates_batch.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updates_marginal.cpp -o updates_marginal.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updates_reduced_batch.cpp -o updates_reduced_batch.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updates_reduced_marginal.cpp -o updates_reduced_marginal.o
clang++ -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 -o CNPBayes.so RcppExports.o miscfunctions.o reduced_pooledvariance.o singlebatch_pooledvar.o update.o updates_batch.o updates_marginal.o updates_reduced_batch.o updates_reduced_marginal.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNPBayes)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "CNPBayes.buildbin-libdir/CNPBayes/libs//CNPBayes.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "CNPBayes.buildbin-libdir/CNPBayes/libs//CNPBayes.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "CNPBayes.buildbin-libdir/CNPBayes/libs//CNPBayes.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "CNPBayes.buildbin-libdir/CNPBayes/libs//CNPBayes.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "CNPBayes.buildbin-libdir/CNPBayes/libs//CNPBayes.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "CNPBayes.buildbin-libdir/CNPBayes/libs//CNPBayes.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "CNPBayes.buildbin-libdir/CNPBayes/libs//CNPBayes.so"