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Package 184/609HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 3.0.8
Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
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/edgeR
Last Changed Rev: 72255 / Revision: 74773
Last Changed Date: 2013-01-02 20:13:26 -0800 (Wed, 02 Jan 2013)
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: edgeR
Version: 3.0.8
Command: rm -rf edgeR.buildbin-libdir && mkdir edgeR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh edgeR_3.0.8.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R edgeR.buildbin-libdir
StartedAt: 2013-03-25 01:51:31 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:51:48 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 17.5 seconds
RetCode: 0
Status:  OK 
PackageFile: edgeR_3.0.8.tgz
PackageFileSize: 1.317 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=edgeR.buildbin-libdir edgeR_3.0.8.tar.gz'
>>>>>>> 

* installing *source* package 'edgeR' ...
** 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    -fPIC  -g -O2 -Wall -fasm-blocks  -c cr_adjustment.cpp -o cr_adjustment.o
cr_adjustment.cpp: In function 'SEXPREC* cr_adjustment(SEXPREC*, SEXPREC*, SEXPREC*)':
cr_adjustment.cpp:22: warning: comparison between signed and unsigned integer expressions
cr_adjustment.cpp:23: warning: comparison between signed and unsigned integer expressions
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fmm_spline.c -o fmm_spline.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c lowess_by_col.cpp -o lowess_by_col.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c maximize_interpolant.cpp -o maximize_interpolant.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c mglm_levenberg.cpp -o mglm_levenberg.o
mglm_levenberg.cpp: In function 'double deviance_nb(const std::deque<double, std::allocator<double> >&, const std::deque<double, std::allocator<double> >&, const double&)':
mglm_levenberg.cpp:16: 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    -fPIC  -g -O2 -Wall -fasm-blocks  -c simple_good_turing.cpp -o simple_good_turing.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o edgeR.so cr_adjustment.o fmm_spline.o lowess_by_col.o maximize_interpolant.o mglm_levenberg.o simple_good_turing.o -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'edgeR.Rnw' 
** testing if installed package can be loaded

* DONE (edgeR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR edgeR.buildbin-libdir/edgeR/libs/i386/edgeR.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" "edgeR.buildbin-libdir/edgeR/libs/i386/edgeR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "edgeR.buildbin-libdir/edgeR/libs/i386/edgeR.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" "edgeR.buildbin-libdir/edgeR/libs/i386/edgeR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "edgeR.buildbin-libdir/edgeR/libs/i386/edgeR.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=edgeR.buildbin-libdir --libs-only edgeR_3.0.8.tar.gz'
>>>>>>> 

* installing *source* package 'edgeR' ...
** 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    -fPIC  -g -O2 -Wall -fasm-blocks  -c cr_adjustment.cpp -o cr_adjustment.o
cr_adjustment.cpp: In function 'SEXPREC* cr_adjustment(SEXPREC*, SEXPREC*, SEXPREC*)':
cr_adjustment.cpp:22: warning: comparison between signed and unsigned integer expressions
cr_adjustment.cpp:23: warning: comparison between signed and unsigned integer expressions
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fmm_spline.c -o fmm_spline.o
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    -fPIC  -g -O2 -Wall -fasm-blocks  -c lowess_by_col.cpp -o lowess_by_col.o
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    -fPIC  -g -O2 -Wall -fasm-blocks  -c maximize_interpolant.cpp -o maximize_interpolant.o
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    -fPIC  -g -O2 -Wall -fasm-blocks  -c mglm_levenberg.cpp -o mglm_levenberg.o
mglm_levenberg.cpp: In function 'double deviance_nb(const std::deque<double, std::allocator<double> >&, const std::deque<double, std::allocator<double> >&, const double&)':
mglm_levenberg.cpp:16: 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    -fPIC  -g -O2 -Wall -fasm-blocks  -c simple_good_turing.cpp -o simple_good_turing.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o edgeR.so cr_adjustment.o fmm_spline.o lowess_by_col.o maximize_interpolant.o mglm_levenberg.o simple_good_turing.o -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRblas -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/x86_64

* DONE (edgeR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR edgeR.buildbin-libdir/edgeR/libs/x86_64/edgeR.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" "edgeR.buildbin-libdir/edgeR/libs/x86_64/edgeR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "edgeR.buildbin-libdir/edgeR/libs/x86_64/edgeR.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" "edgeR.buildbin-libdir/edgeR/libs/x86_64/edgeR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "edgeR.buildbin-libdir/edgeR/libs/x86_64/edgeR.so"