cn.farms 1.1.2
Andreas Mitterecker
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.farms | | Last Changed Rev: 55652 / Revision: 56603 | | Last Changed Date: 2011-05-17 16:01:16 -0700 (Tue, 17 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 |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | [ OK ] |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
install for i386
* installing *source* package 'cn.farms' ...
** libs
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:244:6: warning: unused variable 'method'
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sparse_farms.c -o sparse_farms.o
sparse_farms.c: In function 'normData':
sparse_farms.c:191:10: warning: unused variable 'k'
sparse_farms.c:191:6: warning: unused variable 'i'
sparse_farms.c: In function 'sparseFarmsC':
sparse_farms.c:262:41: warning: unused variable 'invpPsi'
sparse_farms.c:259:9: warning: unused variable 'sumhelp'
g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386
** 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")=="D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpiYcTiu"
- 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")==37570478.08 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==1878523904 -- 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 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpiYcTiu/R.INSTALL52e014af/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Loading required package: snow
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 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpiYcTiu/R.INSTALL52e014af/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(...))
================================================================================
add DLL for x64
* installing *source* package 'cn.farms' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_cnfarms.c -o R_init_cnfarms.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:244:6: warning: unused variable 'method'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sparse_farms.c -o sparse_farms.o
sparse_farms.c: In function 'normData':
sparse_farms.c:191:10: warning: unused variable 'k'
sparse_farms.c:191:6: warning: unused variable 'i'
sparse_farms.c: In function 'sparseFarmsC':
sparse_farms.c:262:41: warning: unused variable 'invpPsi'
sparse_farms.c:259:9: warning: unused variable 'sumhelp'
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x64
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpiQSLJ6/R.INSTALL384c21a4/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(...))
================================================================================
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.1.2.zip
* DONE (cn.farms)