cn.farms 1.1.1
Andreas Mitterecker
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.farms | | Last Changed Rev: 55081 / Revision: 55359 | | Last Changed Date: 2011-04-26 01:41:25 -0700 (Tue, 26 Apr 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=cn.farms.buildbin-libdir cn.farms_1.1.1.tar.gz'
>>>>>>>
* installing *source* package ‘cn.farms’ ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.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 -fPIC -g -O2 -c laplace.cpp -o laplace.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 -fPIC -g -O2 -c sparse_farms.c -o sparse_farms.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 cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.buildbin-libdir/cn.farms/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 R_init_cnfarms.c -o R_init_cnfarms.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 -fPIC -g -O2 -c laplace.cpp -o laplace.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 -fPIC -g -O2 -c sparse_farms.c -o sparse_farms.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 cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.buildbin-libdir/cn.farms/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 R_init_cnfarms.c -o R_init_cnfarms.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 -fPIC -g -O2 -c laplace.cpp -o laplace.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 -fPIC -g -O2 -c sparse_farms.c -o sparse_farms.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 cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x86_64
** R
** demo
** 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: tools
Loading required package: bit
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
Attaching package: ‘bit’
The following object(s) are masked from ‘package:base’:
xor
Loading package ff2.2-2
- getOption("fftempdir")=="/tmp/RtmpzkEhyi"
- 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
Attaching package ff
Attaching package: ‘ff’
The following object(s) are masked from ‘package:utils’:
write.csv, write.csv2
The following object(s) are masked from ‘package:base’:
is.factor, is.ordered
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: /private/tmp/RtmpzkEhyi/R.INSTALL6622ae8a/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Loading required package: snow
Attaching package: ‘snow’
The following object(s) are masked from ‘package:base’:
enquote
Parallel computing support for 'oligo/crlmm': Disabled
- Use options(cluster=makeCluster(...))
================================================================================
**************************************************************************
The plan to change the data format for CNA object has been postponed
in order to ensure backward compatibility with older versions of DNAcopy
**************************************************************************
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘cn.farms.Rnw’
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: /private/tmp/RtmpzkEhyi/R.INSTALL6622ae8a/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Use options(cluster=makeCluster(...))
================================================================================
* DONE (cn.farms)
>>>>>>>
>>>>>>> FIXING LINKS FOR cn.farms.buildbin-libdir/cn.farms/libs/i386/cn.farms.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" "cn.farms.buildbin-libdir/cn.farms/libs/i386/cn.farms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/i386/cn.farms.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" "cn.farms.buildbin-libdir/cn.farms/libs/i386/cn.farms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/i386/cn.farms.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR cn.farms.buildbin-libdir/cn.farms/libs/ppc/cn.farms.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" "cn.farms.buildbin-libdir/cn.farms/libs/ppc/cn.farms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/ppc/cn.farms.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" "cn.farms.buildbin-libdir/cn.farms/libs/ppc/cn.farms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/ppc/cn.farms.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR cn.farms.buildbin-libdir/cn.farms/libs/x86_64/cn.farms.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" "cn.farms.buildbin-libdir/cn.farms/libs/x86_64/cn.farms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/x86_64/cn.farms.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" "cn.farms.buildbin-libdir/cn.farms/libs/x86_64/cn.farms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/x86_64/cn.farms.so"