Package: msdata

Version: 0.1.3

Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check msdata_0.1.3.tar.gz

StartedAt: 2008-10-16 13:34:52 -0700 (Thu, 16 Oct 2008)

EndedAt: 2008-10-16 13:35:02 -0700 (Thu, 16 Oct 2008)

EllapsedTime: 10.5 seconds

RetCode: 1

Status: ERROR

CheckDir: msdata.Rcheck

Warnings: NA

* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-data-experiment/meat/msdata.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'msdata/DESCRIPTION' ... OK
* this is package 'msdata' version '0.1.3'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'msdata' 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 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 data for non-ASCII characters ... OK
* creating msdata-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'msdata-Ex.R' failed.
The error most likely occurred in:

> ### * msdata
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: msdata
> ### Title: Sample FTICR, LC/MS and MS$^n$ data
> ### Aliases: msdata xs x
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## The directory with the mzData LC/MS files
> mzdatapath <- file.path(.find.package("msdata"), "iontrap")
> mzdatapath
[1] "/home/biocbuild/bbs-2.2-data-experiment/meat/msdata.Rcheck/msdata/iontrap"
> files <- list.files(mzdatapath, recursive = TRUE, full.names = TRUE)
> 
> if (require(xcms)) {
+ 
+ ## xcmsSet Summary
+ show(xs)
+ 
+ ## Access raw data file
+ x <- xcmsRaw(files[1])
+ x
+ 
+ }
Loading required package: xcms
Error in cat("An \"xcmsSet\" object with", length(object@sampnames), "samples\n\n") : 
  no slot of name "sampnames" for this object of class "xcmsSet"
Calls: show -> show -> cat
Execution halted

* Installing *source* package 'msdata' ...
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'msdata'
     Formats: text html latex example 
  msdata                            text    html    latex   example
** building package indices ...
* DONE (msdata)