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Package 199/251HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: Ringo
Version: 1.3.2
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check Ringo_1.3.2.tar.gz
StartedAt: 2007-12-11 04:54:31 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 04:55:17 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 46.5 seconds
RetCode: 1
Status: ERROR
CheckDir: Ringo.Rcheck
Warnings: NA

Command output

* 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

Ringo.Rcheck/00install.out:

* 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)