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Package 237/514HostnameOS / ArchBUILDCHECKBUILD BIN
GSVA 1.2.4
Justin Guinney
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GSVA
Last Changed Rev: 61398 / Revision: 64395
Last Changed Date: 2011-12-16 01:46:22 -0800 (Fri, 16 Dec 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: GSVA
Version: 1.2.4
Command: rm -rf GSVA.buildbin-libdir && mkdir GSVA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GSVA_1.2.4.tar.gz /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R GSVA.buildbin-libdir
StartedAt: 2012-03-24 05:21:01 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 05:21:30 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 28.8 seconds
RetCode: 0
Status:  OK 
PackageFile: GSVA_1.2.4.tgz
PackageFileSize: 2.046 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GSVA.buildbin-libdir GSVA_1.2.4.tar.gz'
>>>>>>> 

* installing *source* package 'GSVA' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
Found the Gnu Scientific Library
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c assess_density_test.c -o assess_density_test.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22: warning: unused variable 'mx_value'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c register_cmethods.c -o register_cmethods.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GSVA.so assess_density_test.o ks_test.o register_cmethods.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/GSVA.buildbin-libdir/GSVA/libs/i386
** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GSVA.Rnw' 
** testing if installed package can be loaded

* DONE (GSVA)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "GSVA.buildbin-libdir/GSVA/libs/i386/GSVA.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "GSVA.buildbin-libdir/GSVA/libs/i386/GSVA.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "GSVA.buildbin-libdir/GSVA/libs/i386/GSVA.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "GSVA.buildbin-libdir/GSVA/libs/i386/GSVA.so"


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --no-multiarch --no-test-load --library=GSVA.buildbin-libdir --libs-only GSVA_1.2.4.tar.gz'
>>>>>>> 

* installing *source* package 'GSVA' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
Found the Gnu Scientific Library
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c assess_density_test.c -o assess_density_test.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22: warning: unused variable 'mx_value'
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c register_cmethods.c -o register_cmethods.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GSVA.so assess_density_test.o ks_test.o register_cmethods.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/GSVA.buildbin-libdir/GSVA/libs/ppc

* DONE (GSVA)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GSVA.buildbin-libdir/GSVA/libs/ppc/GSVA.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "GSVA.buildbin-libdir/GSVA/libs/ppc/GSVA.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "GSVA.buildbin-libdir/GSVA/libs/ppc/GSVA.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "GSVA.buildbin-libdir/GSVA/libs/ppc/GSVA.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "GSVA.buildbin-libdir/GSVA/libs/ppc/GSVA.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=GSVA.buildbin-libdir --libs-only GSVA_1.2.4.tar.gz'
>>>>>>> 

* installing *source* package 'GSVA' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
Found the Gnu Scientific Library
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c assess_density_test.c -o assess_density_test.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22: warning: unused variable 'mx_value'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c register_cmethods.c -o register_cmethods.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GSVA.so assess_density_test.o ks_test.o register_cmethods.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/GSVA.buildbin-libdir/GSVA/libs/x86_64

* DONE (GSVA)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "GSVA.buildbin-libdir/GSVA/libs/x86_64/GSVA.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "GSVA.buildbin-libdir/GSVA/libs/x86_64/GSVA.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "GSVA.buildbin-libdir/GSVA/libs/x86_64/GSVA.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "GSVA.buildbin-libdir/GSVA/libs/x86_64/GSVA.so"