flowWorkspace 0.99.9
Greg Finak
| Snapshot Date: 2011-06-02 07:21:07 -0700 (Thu, 02 Jun 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace | | Last Changed Rev: 55821 / Revision: 55954 | | Last Changed Date: 2011-05-25 04:16:37 -0700 (Wed, 25 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=flowWorkspace.buildbin-libdir flowWorkspace_0.99.9.tar.gz'
>>>>>>>
* installing *source* package ‘flowWorkspace’ ...
checking searching for non-standard locations of system libraries... /opt/local
done
checking for gcc... gcc-4.2 -arch i386 -std=gnu99
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -arch i386 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for nc_def_compound in -lnetcdf... no
configure: WARNING: --with-netcdf was given, but test for netcdf failed
configure: WARNING: Package should still build but you won't have netcdf functionality
checking for an ANSI C-conforming const... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating R/AllMethods.R
config.status: creating R/ncdfFlowSet-functions.R
config.status: creating src/Makevars
config.status: creating src/netCDF.c
** 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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c bitOps.c -o bitOps.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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c init.c -o init.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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c netCDF.c -o netCDF.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 flowWorkspace.so bitOps.o init.o netCDF.o -L/opt/local/lib -L/usr/local/lib -L/usr/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: graph
Attaching package: ‘XML’
The following object(s) are masked from ‘package:graph’:
addNode
Loading required package: Biobase
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: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
Attaching package: ‘flowCore’
The following object(s) are masked from ‘package:stats’:
alias, filter
Loading required package: lattice
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: grid
Creating a new generic function for "lapply" in "flowWorkspace"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘flowWorkspace.Rnw’
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
* DONE (flowWorkspace)
>>>>>>>
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/flowWorkspace.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" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/flowWorkspace.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" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/flowWorkspace.so"
>>>>>>>
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=flowWorkspace.buildbin-libdir --libs-only flowWorkspace_0.99.9.tar.gz'
>>>>>>>
* installing *source* package ‘flowWorkspace’ ...
checking searching for non-standard locations of system libraries... /opt/local
done
checking for gcc... gcc-4.2 -arch ppc -std=gnu99
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -arch ppc -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch ppc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -arch ppc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for nc_def_compound in -lnetcdf... no
configure: WARNING: --with-netcdf was given, but test for netcdf failed
configure: WARNING: Package should still build but you won't have netcdf functionality
checking for an ANSI C-conforming const... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating R/AllMethods.R
config.status: creating R/ncdfFlowSet-functions.R
config.status: creating src/Makevars
config.status: creating src/netCDF.c
** libs
*** 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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c bitOps.c -o bitOps.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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c init.c -o init.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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c netCDF.c -o netCDF.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 flowWorkspace.so bitOps.o init.o netCDF.o -L/opt/local/lib -L/usr/local/lib -L/usr/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/ppc
* DONE (flowWorkspace)
>>>>>>>
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs/ppc/flowWorkspace.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" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/ppc/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/ppc/flowWorkspace.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" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/ppc/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/ppc/flowWorkspace.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=flowWorkspace.buildbin-libdir --libs-only flowWorkspace_0.99.9.tar.gz'
>>>>>>>
* installing *source* package ‘flowWorkspace’ ...
checking searching for non-standard locations of system libraries... /opt/local
done
checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -arch x86_64 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for nc_def_compound in -lnetcdf... no
configure: WARNING: --with-netcdf was given, but test for netcdf failed
configure: WARNING: Package should still build but you won't have netcdf functionality
checking for an ANSI C-conforming const... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating R/AllMethods.R
config.status: creating R/ncdfFlowSet-functions.R
config.status: creating src/Makevars
config.status: creating src/netCDF.c
** libs
*** 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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c bitOps.c -o bitOps.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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c init.c -o init.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 -DPACKAGE_NAME=\"flowWorkspace\" -DPACKAGE_TARNAME=\"flowworkspace\" -DPACKAGE_VERSION=\"0.99.1\" -DPACKAGE_STRING=\"flowWorkspace\ 0.99.1\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I/usr/local/include -g -O2 -I/opt/local/include -I/usr/local/include -I/usr/include -fPIC -g -O2 -c netCDF.c -o netCDF.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 flowWorkspace.so bitOps.o init.o netCDF.o -L/opt/local/lib -L/usr/local/lib -L/usr/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x86_64
* DONE (flowWorkspace)
>>>>>>>
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs/x86_64/flowWorkspace.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" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/x86_64/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/x86_64/flowWorkspace.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" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/x86_64/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/x86_64/flowWorkspace.so"