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BioC 3.2: BUILD BIN report for birte on perceval

This page was generated on 2015-10-27 17:37:01 -0400 (Tue, 27 Oct 2015).

Package 114/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.6.0
Holger Froehlich
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/birte
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: birte
Version: 1.6.0
Command: rm -rf birte.buildbin-libdir && mkdir birte.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birte_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birte.buildbin-libdir
StartedAt: 2015-10-27 10:56:49 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 10:57:38 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 49.6 seconds
RetCode: 0
Status:  OK 
PackageFile: birte_1.6.0.tgz
PackageFileSize: 566.5 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf birte.buildbin-libdir && mkdir birte.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birte_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birte.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=birte.buildbin-libdir birte_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package ‘birte’ ...
** libs
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/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:
BayesNetwork.h:203:3: warning: "/*" within comment
BayesNetwork.cpp: In constructor ‘BayesNetwork::BayesNetwork(int, int, int, int, int, int**, double***, double***, double***, double***, int, int, int, int, int, double*, double*, double*, double*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, double*, double*, double*, double**, int**, int**, int**, int**, double**, double**, double**)’:
BayesNetwork.cpp:96: warning: unused variable ‘j’
BayesNetwork.cpp:96: warning: unused variable ‘r’
BayesNetwork.cpp: In destructor ‘virtual BayesNetwork::˜BayesNetwork()’:
BayesNetwork.cpp:221: warning: unused variable ‘i’
BayesNetwork.cpp:221: warning: unused variable ‘j’
BayesNetwork.cpp: In member function ‘virtual int BayesNetwork::expandDesignMatrix(int, int, int, std::list<int, std::allocator<int> >*, double**, int)’:
BayesNetwork.cpp:357: warning: unused variable ‘found’
BayesNetwork.cpp:357: warning: unused variable ‘i’
BayesNetwork.cpp: In member function ‘virtual int BayesNetwork::shrinkDesignMatrix(int, int, int)’:
BayesNetwork.cpp:380: warning: unused variable ‘k’
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::updateEvidence2(int, int, int, arma::colvec&)’:
BayesNetwork.cpp:599: warning: comparison between signed and unsigned integer expressions
BayesNetwork.cpp: In member function ‘virtual double BayesNetwork::swap_states(int**, int, int, std::set<int, std::less<int>, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::set<int, std::less<int>, std::allocator<int> >**, double)’:
BayesNetwork.cpp:669: warning: comparison between signed and unsigned integer expressions
BayesNetwork.cpp:665: warning: unused variable ‘pos_swaps’
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::MCMC(long int, long int, int, double*)’:
BayesNetwork.cpp:842: warning: unused variable ‘mir’
BayesNetwork.cpp:842: warning: unused variable ‘tf’
BayesNetwork.cpp:847: warning: unused variable ‘eff_samples’
BayesNetwork.cpp:909: warning: unused variable ‘u’
BayesNetwork.cpp:909: warning: unused variable ‘delta_prior’
BayesNetwork.cpp:909: warning: unused variable ‘eps_new’
BayesNetwork.cpp:909: warning: unused variable ‘eps_old’
BayesNetwork.cpp:909: warning: unused variable ‘delta_eps’
BayesNetwork.cpp:910: warning: unused variable ‘make_move_eps’
BayesNetwork.cpp:910: warning: unused variable ‘cond’
BayesNetwork.cpp: In member function ‘virtual double BayesNetwork::likelihood()’:
BayesNetwork.cpp:1074: warning: unused variable ‘j’
BayesNetwork.cpp:1075: warning: unused variable ‘bn’
BayesNetwork.cpp:1078: warning: unused variable ‘z’
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/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:
BayesNetwork.h:203:3: warning: "/*" within comment
Loading required package: Rcpp
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 birte.so BayesNetwork.o getStates.o -llapack -lblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Loading required package: Rcpp
installing to /Users/biocbuild/bbs-3.2-bioc/meat/birte.buildbin-libdir/birte/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (birte)


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