BioC 2.9: CHECK report for MSnbase on wilson2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/MSnbase.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘1.1.7’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘MSnbase’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’
 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 ‘MSnbase’ ...
** R
** data
**  moving datasets to lazyload DB
** 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: reshape
Loading required package: plyr

Attaching package: ‘reshape’

The following object(s) are masked from ‘package:plyr’:

    rename, round_any

Loading required package: grid
Loading required package: proto
Creating a new generic function for "plot" in "MSnbase"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘MSnbase-demo.Rnw’ 
   ‘MSnbase-development.Rnw’ 
** testing if installed package can be loaded

* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	2.056	0.036	2.105
MSnProcess-class	0.004	0.000	0.001
MSnSet-class	5.784	0.016	5.885
NAnnotatedDataFrame-class	0.028	0.000	0.027
ReporterIons-class	0.016	0.000	0.016
TMT6	0.020	0.000	0.022
clean-methods	8.369	0.008	8.392
combineFeatures	5.512	0.008	5.542
extractPrecSpectra-methods	1.432	0.000	1.430
extractSpectra-methods	1.424	0.004	1.427
formatRt	0	0	0
iTRAQ4	0.016	0.004	0.017
pSet-class	0.000	0.000	0.001
plot-methods	10.481	0.032	10.581
plot2d-methods	3.196	0.012	3.545
purityCorrect-methods	5.085	0.012	5.107
quantify-methods	5.292	0.004	5.297
readIspyData	0	0	0
readMzXMLData	1.424	0.004	1.432
removePeaks-methods	7.756	0.012	7.788
trimMz-methods	1.569	0.004	1.577

Summary

Command output