BioC 2.12: CHECK report for MSnbase on pelham

Package: MSnbase

Version: 1.7.25

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.7.25.tar.gz

StartedAt: 2013-03-24 08:01:18 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 08:08:01 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 402.7 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 beta (2013-03-21 r62346)
* 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 '1.7.25'
* 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/23s] 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 ... [116s/131s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plotMzDelta-methods   23.986  2.436  26.709
writeMzTabData        11.726  0.123  22.589
readMgfData            9.381  0.158   9.761
plotNA-methods         6.163  0.057   6.249
nQuants                5.865  0.042   6.028
quantify-methods       5.764  0.118   5.918
exprsToRatios-methods  5.786  0.056   6.511
normalise-methods      5.645  0.048   6.028
purityCorrect-methods  5.485  0.052   5.574
impute-methods         5.347  0.043   5.798
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [50s/51s]
 [51s/51s] 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
   'MSnbase-demo.Rnw' 
   'MSnbase-development.Rnw' 
   'MSnbase-io.Rnw' 
** testing if installed package can be loaded
* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	0.582	0.024	0.682
MSnProcess-class	0.010	0.002	0.015
MSnSet-class	1.763	0.052	2.023
NAnnotatedDataFrame-class	0.055	0.002	0.064
ReporterIons-class	0.045	0.006	0.065
TMT6	0.048	0.004	0.052
clean-methods	2.196	0.027	2.553
combineFeatures	0.858	0.028	1.018
exprsToRatios-methods	5.786	0.056	6.511
extractPrecSpectra-methods	0.458	0.007	0.559
featureCV	0.687	0.015	0.762
fillUp	0.025	0.004	0.031
formatRt	0.010	0.001	0.012
getVariableName	0.320	0.002	0.367
iTRAQ4	0.029	0.006	0.040
impute-methods	5.347	0.043	5.798
itraqdata	0.341	0.012	0.355
nQuants	5.865	0.042	6.028
normalise-methods	5.645	0.048	6.028
pSet-class	0.019	0.009	0.028
plot-methods	2.157	0.029	2.255
plot2d-methods	1.628	0.018	1.665
plotDensity-methods	1.654	0.033	1.712
plotMzDelta-methods	23.986	2.436	26.709
plotNA-methods	6.163	0.057	6.249
precSelection	0.077	0.011	0.087
purityCorrect-methods	5.485	0.052	5.574
quantify-methods	5.764	0.118	5.918
readIspyData	0.003	0.005	0.007
readMSData	0.478	0.017	0.498
readMSnSet	0.003	0.006	0.009
readMgfData	9.381	0.158	9.761
readMzTabData	0.510	0.015	0.649
removePeaks-methods	2.716	0.067	2.798
removeReporters-methods	1.431	0.052	1.489
trimMz-methods	0.249	0.023	0.272
writeMgfData-methods	0.006	0.011	0.018
writeMzTabData	11.726	0.123	22.589

Summary

Command output