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Package 235/609HostnameOS / ArchBUILDCHECKBUILD BIN
GeneNetworkBuilder 1.0.1
Jianhong Ou
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/GeneNetworkBuilder
Last Changed Rev: 71815 / Revision: 74773
Last Changed Date: 2012-12-11 10:11:24 -0800 (Tue, 11 Dec 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: GeneNetworkBuilder
Version: 1.0.1
Command: rm -rf GeneNetworkBuilder.buildbin-libdir && mkdir GeneNetworkBuilder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneNetworkBuilder_1.0.1.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R GeneNetworkBuilder.buildbin-libdir
StartedAt: 2013-03-25 01:53:19 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:53:41 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 22.3 seconds
RetCode: 0
Status:  OK 
PackageFile: GeneNetworkBuilder_1.0.1.tgz
PackageFileSize: 3.211 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneNetworkBuilder.buildbin-libdir GeneNetworkBuilder_1.0.1.tar.gz'
>>>>>>> 

* installing *source* package 'GeneNetworkBuilder' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c geneTree.cpp -o geneTree.o
geneTree.cpp: In member function 'void GTree::ChangeTolerance(node*)':
geneTree.cpp:112: warning: comparison between signed and unsigned integer expressions
geneTree.cpp: In member function 'std::vector<node*, std::allocator<node*> > GTree::Travel()':
geneTree.cpp:207: warning: comparison between signed and unsigned integer expressions
geneTree.cpp: In member function 'void GTree::verifyFilter(int)':
geneTree.cpp:275: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c nodefilter.cpp -o nodefilter.o
nodefilter.cpp: In function 'SEXPREC* filterNodes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
nodefilter.cpp:76: warning: comparison between signed and unsigned integer expressions
nodefilter.cpp:86: warning: comparison between signed and unsigned integer expressions
nodefilter.cpp:94: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneNetworkBuilder.so geneTree.o nodefilter.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/lib/i386/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GeneNetworkBuilder.Rnw' 
** testing if installed package can be loaded

* DONE (GeneNetworkBuilder)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386/GeneNetworkBuilder.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386/GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386/GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386/GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/i386/GeneNetworkBuilder.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=GeneNetworkBuilder.buildbin-libdir --libs-only GeneNetworkBuilder_1.0.1.tar.gz'
>>>>>>> 

* installing *source* package 'GeneNetworkBuilder' ...
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c geneTree.cpp -o geneTree.o
geneTree.cpp: In member function 'void GTree::ChangeTolerance(node*)':
geneTree.cpp:112: warning: comparison between signed and unsigned integer expressions
geneTree.cpp: In member function 'std::vector<node*, std::allocator<node*> > GTree::Travel()':
geneTree.cpp:207: warning: comparison between signed and unsigned integer expressions
geneTree.cpp: In member function 'void GTree::verifyFilter(int)':
geneTree.cpp:275: warning: comparison between signed and unsigned integer expressions
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c nodefilter.cpp -o nodefilter.o
nodefilter.cpp: In function 'SEXPREC* filterNodes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
nodefilter.cpp:76: warning: comparison between signed and unsigned integer expressions
nodefilter.cpp:86: warning: comparison between signed and unsigned integer expressions
nodefilter.cpp:94: warning: comparison between signed and unsigned integer expressions
Error in tools:::file_path_as_absolute(base:::system.file(..., package = "Rcpp")) : 
  file '' does not exist
Calls: <Anonymous> ... RcppLdFlags -> RcppLdPath -> Rcpp.system.file -> <Anonymous>
Execution halted
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneNetworkBuilder.so geneTree.o nodefilter.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in tools:::file_path_as_absolute(base:::system.file(..., package = "Rcpp")) : 
  file '' does not exist
Calls: <Anonymous> ... RcppLdFlags -> RcppLdPath -> Rcpp.system.file -> <Anonymous>
Execution halted
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x86_64

* DONE (GeneNetworkBuilder)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x86_64/GeneNetworkBuilder.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x86_64/GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x86_64/GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x86_64/GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/x86_64/GeneNetworkBuilder.so"