BioC 2.12: CHECK report for MSnbase on petty

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: 2013-03-25 03:43:13 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:49:13 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 359.9 seconds

RetCode: 0

Status: OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MSnbase.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [20s/21s] 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 ... [106s/114s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plotMzDelta-methods   16.313  3.669  20.108
writeMzTabData        10.471  0.182  18.297
readMgfData            9.435  0.252   9.724
quantify-methods       6.684  0.090   6.777
plotNA-methods         5.626  0.079   5.710
purityCorrect-methods  5.577  0.098   5.675
impute-methods         5.446  0.062   5.532
exprsToRatios-methods  5.314  0.067   5.382
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [47s/47s]
 [48s/48s] 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	0.544	0.037	0.583
MSnProcess-class	0.009	0.006	0.015
MSnSet-class	1.797	0.105	1.903
NAnnotatedDataFrame-class	0.056	0.014	0.070
ReporterIons-class	0.040	0.016	0.057
TMT6	0.035	0.011	0.047
clean-methods	2.886	0.047	2.937
combineFeatures	1.006	0.048	1.058
exprsToRatios-methods	5.314	0.067	5.382
extractPrecSpectra-methods	0.278	0.023	0.305
featureCV	0.605	0.044	0.649
fillUp	0.017	0.009	0.026
formatRt	0.005	0.004	0.009
getVariableName	0.007	0.007	0.013
iTRAQ4	0.023	0.009	0.033
impute-methods	5.446	0.062	5.532
itraqdata	0.260	0.033	0.292
nQuants	4.520	0.063	4.616
normalise-methods	4.058	0.059	4.121
pSet-class	0.013	0.017	0.035
plot-methods	1.832	0.180	2.023
plot2d-methods	1.478	0.127	1.608
plotDensity-methods	1.706	0.131	1.842
plotMzDelta-methods	16.313	3.669	20.108
plotNA-methods	5.626	0.079	5.710
precSelection	0.057	0.022	0.079
purityCorrect-methods	5.577	0.098	5.675
quantify-methods	6.684	0.090	6.777
readIspyData	0.003	0.005	0.008
readMSData	0.389	0.031	0.421
readMSnSet	0.004	0.007	0.010
readMgfData	9.435	0.252	9.724
readMzTabData	0.473	0.014	0.548
removePeaks-methods	3.270	0.120	3.392
removeReporters-methods	1.232	0.090	1.323
trimMz-methods	0.189	0.027	0.216
writeMgfData-methods	0.005	0.010	0.015
writeMzTabData	10.471	0.182	18.297

Summary

Command output