cn.farms 1.1.2
Andreas Mitterecker
| Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.farms | | Last Changed Rev: 55652 / Revision: 56351 | | 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 |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.1.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘cn.farms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* 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 -Wall -pedantic -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 -Wall -fasm-blocks -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: warning: unused variable ‘method’
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 -Wall -pedantic -c sparse_farms.c -o sparse_farms.o
sparse_farms.c: In function ‘normData’:
sparse_farms.c:191: warning: unused variable ‘k’
sparse_farms.c:191: warning: unused variable ‘i’
sparse_farms.c: In function ‘sparseFarmsC’:
sparse_farms.c:262: warning: unused variable ‘invpPsi’
sparse_farms.c:259: warning: unused variable ‘sumhelp’
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.Rcheck/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")=="/tmp/RtmprRAmcc"
- 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 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: /Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck/00_pkg_src/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.....: /Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck/00_pkg_src/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)