xcms 1.27.2
Ralf Tautenhahn
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms | | Last Changed Rev: 55296 / Revision: 55359 | | Last Changed Date: 2011-05-06 00:45:41 -0700 (Fri, 06 May 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=xcms.buildbin-libdir xcms_1.27.2.tar.gz'
>>>>>>>
* installing *source* package ‘xcms’ ...
** libs
*** arch - i386
rm -f obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c fastMatch.c -o fastMatch.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzROI.c -o mzROI.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c netCDF.c -o netCDF.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp.cpp -o ramp.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c rampR.cpp -o rampR.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c util.c -o util.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c xcms.c -o xcms.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386
*** arch - ppc
rm -f obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c fastMatch.c -o fastMatch.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzROI.c -o mzROI.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c netCDF.c -o netCDF.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp.cpp -o ramp.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c rampR.cpp -o rampR.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c util.c -o util.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c xcms.c -o xcms.o
g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/xcms.buildbin-libdir/xcms/libs/ppc
*** arch - x86_64
rm -f obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c fastMatch.c -o fastMatch.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzROI.c -o mzROI.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c netCDF.c -o netCDF.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp.cpp -o ramp.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c rampR.cpp -o rampR.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c util.c -o util.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c xcms.c -o xcms.o
g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/xcms.buildbin-libdir/xcms/libs/x86_64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘xcmsDirect.Rnw’
‘xcmsInstall.Rnw’
‘xcmsMSn.Rnw’
‘xcmsPreprocess.Rnw’
** testing if installed package can be loaded
* DONE (xcms)
>>>>>>>
>>>>>>> FIXING LINKS FOR xcms.buildbin-libdir/xcms/libs/i386/xcms.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" "xcms.buildbin-libdir/xcms/libs/i386/xcms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "xcms.buildbin-libdir/xcms/libs/i386/xcms.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" "xcms.buildbin-libdir/xcms/libs/i386/xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "xcms.buildbin-libdir/xcms/libs/i386/xcms.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR xcms.buildbin-libdir/xcms/libs/ppc/xcms.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" "xcms.buildbin-libdir/xcms/libs/ppc/xcms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "xcms.buildbin-libdir/xcms/libs/ppc/xcms.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" "xcms.buildbin-libdir/xcms/libs/ppc/xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "xcms.buildbin-libdir/xcms/libs/ppc/xcms.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR xcms.buildbin-libdir/xcms/libs/x86_64/xcms.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" "xcms.buildbin-libdir/xcms/libs/x86_64/xcms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "xcms.buildbin-libdir/xcms/libs/x86_64/xcms.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" "xcms.buildbin-libdir/xcms/libs/x86_64/xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "xcms.buildbin-libdir/xcms/libs/x86_64/xcms.so"