BioC 2.12: CHECK report for MSnbase on pelham

Package: MSnbase

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.8.0.tar.gz

StartedAt: 2013-05-01 08:29:20 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 08:36:30 -0700 (Wed, 01 May 2013)

EllapsedTime: 429.5 seconds

RetCode: 0

Status: OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MSnbase.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MSnbase/DESCRIPTION' ... OK
* this is package 'MSnbase' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'MSnbase' can be installed ... [22s/24s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 installed files from 'inst/doc' ... OK
* checking examples ... [113s/135s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plotMzDelta-methods   23.393  2.549  31.191
writeMzTabData        10.195  0.159  20.602
readMgfData            9.299  0.197   9.828
nQuants                6.273  0.055   6.431
impute-methods         6.043  0.068   6.217
plotNA-methods         5.907  0.068   6.392
normalise-methods      5.661  0.040   5.768
exprsToRatios-methods  5.624  0.052   5.745
purityCorrect-methods  5.549  0.122   6.038
quantify-methods       5.323  0.090   5.665
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [49s/50s]
 [49s/50s] 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/MSnbase.Rcheck/00check.log'
for details.

* installing *source* package 'MSnbase' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'scale' from package 'base' in package 'MSnbase'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	0.511	0.032	0.608
MSnProcess-class	0.008	0.002	0.012
MSnSet-class	1.378	0.043	1.457
NAnnotatedDataFrame-class	0.048	0.003	0.057
ReporterIons-class	0.045	0.004	0.062
TMT6	0.031	0.002	0.038
clean-methods	2.102	0.040	2.211
combineFeatures	1.008	0.032	1.067
exprsToRatios-methods	5.624	0.052	5.745
extractPrecSpectra-methods	0.435	0.007	0.447
featureCV	0.682	0.013	0.700
fillUp	0.019	0.004	0.025
formatRt	0.010	0.003	0.013
getVariableName	0.013	0.004	0.018
iTRAQ4	0.040	0.006	0.047
impute-methods	6.043	0.068	6.217
itraqdata	0.091	0.011	0.104
nQuants	6.273	0.055	6.431
normalise-methods	5.661	0.040	5.768
pSet-class	0.021	0.008	0.052
plot-methods	2.109	0.033	2.610
plot2d-methods	1.760	0.028	3.319
plotDensity-methods	1.591	0.026	2.735
plotMzDelta-methods	23.393	2.549	31.191
plotNA-methods	5.907	0.068	6.392
precSelection	0.078	0.015	0.094
purityCorrect-methods	5.549	0.122	6.038
quantify-methods	5.323	0.090	5.665
readIspyData	0.002	0.004	0.008
readMSData	0.498	0.022	0.532
readMSnSet	0.004	0.006	0.015
readMgfData	9.299	0.197	9.828
readMzTabData	0.395	0.011	0.593
removePeaks-methods	2.579	0.076	2.963
removeReporters-methods	1.369	0.038	1.440
trimMz-methods	0.236	0.020	0.261
writeMgfData-methods	0.006	0.010	0.016
writeMzTabData	10.195	0.159	20.602

Summary

Command output