* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-data-experiment/meat/faahKO.Rcheck'
* using R version 2.7.2 (2008年08月25日)
* using session charset: ISO8859-1
* checking for file 'faahKO/DESCRIPTION' ... OK
* this is package 'faahKO' version '1.2.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'faahKO' 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 faahKO-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'faahKO-Ex.R' failed.
The error most likely occurred in:
> ### * faahko
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: faahko
> ### Title: FAAH knockout LC/MS data xcmsSet
> ### Aliases: faahko faahKO
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## The directory with the NetCDF LC/MS files
> cdfpath <- file.path(.find.package("faahKO"), "cdf")
> cdfpath
[1] "/home/biocbuild/bbs-2.2-data-experiment/meat/faahKO.Rcheck/faahKO/cdf"
> list.files(cdfpath, recursive = TRUE)
 [1] "KO/ko15.CDF" "KO/ko16.CDF" "KO/ko18.CDF" "KO/ko19.CDF" "KO/ko21.CDF"
 [6] "KO/ko22.CDF" "WT/wt15.CDF" "WT/wt16.CDF" "WT/wt18.CDF" "WT/wt19.CDF"
[11] "WT/wt21.CDF" "WT/wt22.CDF"
> 
> if (require(xcms)) {
+ 
+ ## xcmsSet Summary
+ show(faahko)
+ 
+ ## Access raw data file
+ ko15 <- xcmsRaw(filepaths(faahko)[1], profmethod = "bin", profstep = 0.1)
+ ko15
+ 
+ }
Loading required package: xcms
An "xcmsSet" object with 12 samples
Time range: 2506.1-4147.7 seconds (41.8-69.1 minutes)
Mass range: 200.1-599.3338 m/z
Peaks: 4776 (about 398 per sample)
Peak Groups: 0 
Sample classes: KO, WT 
Profile settings: method = bin
 step = 0.1
Memory usage: 0.645 MB
Error in file.exists(filename) : could not find function "filepaths"
Calls: xcmsRaw -> file.exists
Execution halted

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