Package: MSnbase

Version: 1.1.17

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.1.17.tar.gz

StartedAt: 2011-07-07 01:32:45 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:36:53 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 247.8 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/MSnbase.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.1.17’
* 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
Creating a generic function for "plot" from package "graphics" in package “MSnbase”
** 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 generic function for "plot" from package "graphics" in package “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	0.776	0.016	0.797
MSnProcess-class	0.004	0.000	0.001
MSnSet-class	0.932	0.020	0.952
NAnnotatedDataFrame-class	0.028	0.000	0.028
ReporterIons-class	0.016	0.000	0.014
TMT6	0.012	0.000	0.014
clean-methods	0.636	0.004	0.640
combineFeatures	0.928	0.004	0.932
extractPrecSpectra-methods	0.552	0.000	0.552
extractSpectra-methods	0.540	0.000	0.542
formatRt	0	0	0
iTRAQ4	0.016	0.000	0.016
itraqdata	0.848	0.020	0.865
normalise-methods	4.673	0.104	5.457
pSet-class	0.004	0.000	0.002
plot-methods	4.620	0.100	5.663
plot2d-methods	3.180	0.068	4.099
plotDensity-methods	3.244	0.000	3.296
plotMzDelta-methods	32.662	0.616	33.506
precSelection	0.056	0.000	0.059
purityCorrect-methods	1.100	0.004	1.104
quantify-methods	1.112	0.000	1.115
readIspyData	0	0	0
readMzXMLData	0.632	0.000	0.634
removePeaks-methods	0.725	0.000	0.726
removeReporters-methods	3.196	0.004	3.207
trimMz-methods	0.644	0.000	0.648