Package: pdInfoBuilder

Version: 1.17.0

Command: /Users/biocbuild/BBS/utils/build-universal.sh pdInfoBuilder_1.17.0.tar.gz /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R pdInfoBuilder.buildbin-libdir

StartedAt: 2011-05-09 18:03:24 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 18:03:45 -0700 (Mon, 09 May 2011)

EllapsedTime: 21.1 seconds

RetCode: 0

Status:  OK

PackageFile: pdInfoBuilder_1.17.0.tgz

PackageFileSize: 351.9 KiB

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=pdInfoBuilder.buildbin-libdir pdInfoBuilder_1.17.0.tar.gz'
>>>>>>> 

* installing *source* package ‘pdInfoBuilder’ ...
** libs
*** arch - i386
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    -fPIC  -g -O2 -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/i386
*** arch - ppc
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    -fPIC  -g -O2 -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/ppc
*** arch - x86_64
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    -fPIC  -g -O2 -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/x86_64
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: DBI
Loading required package: oligoClasses
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Loading required package: preprocessCore
Loading package bit1.1-7

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit

Loading package ff2.2-2
- getOption("fftempdir")=="/tmp/RtmpZmjUiS"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system

================================================================================
Welcome to oligo version 1.17.1
================================================================================
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘BuildingPDInfoPkgs.Rnw’ 
   ‘howto-AffymetrixMapping.Rnw’ 
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
================================================================================
Welcome to oligo version 1.17.1
================================================================================

* DONE (pdInfoBuilder)


>>>>>>> 
>>>>>>> FIXING LINKS FOR pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/i386/pdInfoBuilder.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" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/i386/pdInfoBuilder.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/i386/pdInfoBuilder.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" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/i386/pdInfoBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/i386/pdInfoBuilder.so"


>>>>>>> 
>>>>>>> FIXING LINKS FOR pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/ppc/pdInfoBuilder.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" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/ppc/pdInfoBuilder.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/ppc/pdInfoBuilder.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" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/ppc/pdInfoBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/ppc/pdInfoBuilder.so"


>>>>>>> 
>>>>>>> FIXING LINKS FOR pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/x86_64/pdInfoBuilder.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" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/x86_64/pdInfoBuilder.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/x86_64/pdInfoBuilder.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" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/x86_64/pdInfoBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/x86_64/pdInfoBuilder.so"