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Package 199/658HostnameOS / ArchBUILDCHECKBUILD BIN
edgeR 3.1.9
Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR
Last Changed Rev: 74597 / Revision: 74774
Last Changed Date: 2013-03-19 21:41:13 -0700 (Tue, 19 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: edgeR
Version: 3.1.9
Command: rm -rf edgeR.buildbin-libdir && mkdir edgeR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh edgeR_3.1.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R edgeR.buildbin-libdir
StartedAt: 2013-03-25 05:23:37 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 05:24:04 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 27.3 seconds
RetCode: 0
Status:  OK 
PackageFile: edgeR_3.1.9.tgz
PackageFileSize: 1.349 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=edgeR.buildbin-libdir edgeR_3.1.9.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./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_levenberg.cpp -o R_levenberg.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_one_group.cpp -o R_one_group.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/adj_coxreid.cpp -o core/adj_coxreid.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/glm_levenberg.cpp -o core/glm_levenberg.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/glm_one_group.cpp -o core/glm_one_group.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/interpolator.cpp -o core/interpolator.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c core/fmm_spline.c -o core/fmm_spline.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 R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.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-2.12-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/3.0/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/3.0/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/3.0/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/3.0/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_3.1.9.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./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_loess_by_col.cpp -o R_loess_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./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_levenberg.cpp -o R_levenberg.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_maximize_interpolant.cpp -o R_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./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_one_group.cpp -o R_one_group.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/adj_coxreid.cpp -o core/adj_coxreid.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/glm_levenberg.cpp -o core/glm_levenberg.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/glm_one_group.cpp -o core/glm_one_group.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c core/interpolator.cpp -o core/interpolator.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c core/fmm_spline.c -o core/fmm_spline.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 R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.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-2.12-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/3.0/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/3.0/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/3.0/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/3.0/Resources/lib/libreadline.dylib" "edgeR.buildbin-libdir/edgeR/libs/x86_64/edgeR.so"