Ringo 1.3.2
J. Toedling
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Ringo | | Last Changed Rev: 28828 / Revision: 29143 | | Last Changed Date: 2007-11-19 07:37:06 -0800 (Mon, 19 Nov 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | [ ERROR ] | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | ERROR | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | ERROR | OK |
* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/Ringo.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-11-18 r43497)
* checking for file 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.3.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Ringo' can be installed ... 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating Ringo-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'Ringo-Ex.R' failed.
The error most likely occurred in:
> ### * preprocess
>
> flush(stderr()); flush(stdout())
>
> ### Name: preprocess
> ### Title: Preprocess Nimblegen Raw Intensities
> ### Aliases: preprocess
> ### Keywords: manip
>
> ### ** Examples
>
> exDir <- system.file("exData",package="Ringo")
> exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
Reading targets file...
Reading raw intensities...
Read header information
Read /home/biocbuild/bbs-2.2-bioc/meat/Ringo.Rcheck/Ringo/exData/MOD_20551_PMT1_pair.txt
Read /home/biocbuild/bbs-2.2-bioc/meat/Ringo.Rcheck/Ringo/exData/MOD_20742_PMT1_pair.txt
Determining probe categories...
Matching patterns for: GENE_EXPR_OPTION PROBE_ID
Found 991 Probe
Found 0 Probe
Found 0 Negative
Found 0 Empty
Found 0 H_Code
Found 0 V_Code
Found 0 Random
Setting attributes: values Color
> exampleX <- preprocess(exRG)
Normalizing...
Warning: The function 'vsn' is deprecated.
It will stay around for some time, for backward compatibility.
For new projects, please use 'vsn2'.
Error in ncol(y@exprs) :
no slot of name "exprs" for this object of class "ExpressionSet"
Calls: preprocess -> switch -> normalizeBetweenArrays -> ncol
Execution halted
* Installing *source* package 'Ringo' ...
** libs
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c mmedian.cpp -o mmedian.o
g++ -shared -L/usr/local/lib64 -o Ringo.so mmedian.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: limma
Loading required package: vsn
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: RColorBrewer
** help
>>> Building/Updating help pages for package 'Ringo'
Formats: text html latex example
Ringo-internal text html latex
arrayImage text html latex example
asExprSet text html latex example
autocorr text html latex example
chipAlongChrom text html latex example
computeRunningMedians text html latex example
compute_gc text html latex example
corrPlot text html latex example
findPeaksOnSmoothed text html latex example
ftr2xys text html latex example
newPeak text html latex example
nimblegenNorm text html latex
peakByThreshold text html latex example
peakClass text html latex example
plotAutocorr text html latex example
plot_peak text html latex example
preprocess text html latex example
readNimblegen text html latex example
relatePeaks text html latex example
sliding_quantile text html latex example
** building package indices ...
* DONE (Ringo)