BioC 2.12: CHECK report for MSnbase on petty

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: 2013-10-08 23:09:30 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:19:57 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 627.2 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 3.0.1 (2013-05-16)
* 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 ... [25s/26s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [136s/170s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plotMzDelta-methods   23.803  2.163  29.561
writeMzTabData        13.305  0.103  26.951
readMgfData           10.977  0.106  13.354
plotNA-methods         8.509  0.112  16.270
nQuants                8.081  0.056   8.177
impute-methods         7.554  0.041   7.704
normalise-methods      7.492  0.041   7.579
exprsToRatios-methods  7.461  0.044   7.614
quantify-methods       7.457  0.034  12.190
purityCorrect-methods  6.966  0.042   7.049
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [62s/74s]
 [62s/75s] 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	0.653	0.031	0.791
MSnProcess-class	0.010	0.002	0.013
MSnSet-class	1.898	0.050	1.990
NAnnotatedDataFrame-class	0.070	0.004	0.080
ReporterIons-class	0.048	0.004	0.052
TMT6	0.041	0.004	0.049
clean-methods	2.866	0.028	2.917
combineFeatures	1.107	0.021	1.166
exprsToRatios-methods	7.461	0.044	7.614
extractPrecSpectra-methods	0.488	0.005	0.494
featureCV	0.891	0.021	0.923
fillUp	0.024	0.003	0.026
formatRt	0.009	0.002	0.014
getVariableName	0.013	0.003	0.016
iTRAQ4	0.050	0.008	0.059
impute-methods	7.554	0.041	7.704
itraqdata	0.113	0.013	0.125
nQuants	8.081	0.056	8.177
normalise-methods	7.492	0.041	7.579
pSet-class	0.020	0.008	0.027
plot-methods	2.572	0.033	2.613
plot2d-methods	1.948	0.022	2.005
plotDensity-methods	1.758	0.041	1.804
plotMzDelta-methods	23.803	2.163	29.561
plotNA-methods	8.509	0.112	16.270
precSelection	0.091	0.007	0.098
purityCorrect-methods	6.966	0.042	7.049
quantify-methods	7.457	0.034	12.190
readIspyData	0.002	0.003	0.006
readMSData	0.517	0.019	0.864
readMSnSet	0.003	0.004	0.007
readMgfData	10.977	0.106	13.354
readMzTabData	0.802	0.013	1.015
removePeaks-methods	2.792	0.061	2.930
removeReporters-methods	1.559	0.038	1.644
trimMz-methods	0.273	0.019	0.323
writeMgfData-methods	0.006	0.009	0.015
writeMzTabData	13.305	0.103	26.951