BioC 2.12: CHECK report for MSnbase on george2

Package: MSnbase

Version: 1.7.25

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.7.25.tar.gz

StartedAt: 2013-03-25 03:19:44 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:27:42 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 478.6 seconds

RetCode: 0

Status: OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/MSnbase.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.7.25’
* 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 ... [29s/30s] 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 ... [139s/152s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plotMzDelta-methods   36.834  0.772  38.180
writeMzTabData        13.301  0.064  23.712
readMgfData           10.329  0.024  10.568
nQuants                6.617  0.024   6.768
plotNA-methods         6.612  0.008   6.624
quantify-methods       6.396  0.028   6.482
normalise-methods      6.296  0.012   6.349
impute-methods         6.204  0.012   6.215
purityCorrect-methods  6.157  0.008   6.554
exprsToRatios-methods  6.056  0.020   6.095
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [58s/63s]
 [58s/63s] 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
  ‘/home/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	0.840	0.048	0.903
MSnProcess-class	0.016	0.000	0.014
MSnSet-class	1.876	0.024	1.919
NAnnotatedDataFrame-class	0.060	0.000	0.062
ReporterIons-class	0.460	0.020	0.539
TMT6	0.032	0.004	0.039
clean-methods	2.076	0.012	2.180
combineFeatures	1.353	0.024	1.465
exprsToRatios-methods	6.056	0.020	6.095
extractPrecSpectra-methods	0.696	0.004	0.699
featureCV	0.836	0.008	0.848
fillUp	0.040	0.000	0.038
formatRt	0.008	0.004	0.011
getVariableName	0.024	0.000	0.024
iTRAQ4	0.064	0.004	0.067
impute-methods	6.204	0.012	6.215
itraqdata	0.504	0.004	0.505
nQuants	6.617	0.024	6.768
normalise-methods	6.296	0.012	6.349
pSet-class	0.440	0.004	0.446
plot-methods	2.140	0.032	2.189
plot2d-methods	1.965	0.032	1.999
plotDensity-methods	2.040	0.000	2.041
plotMzDelta-methods	36.834	0.772	38.180
plotNA-methods	6.612	0.008	6.624
precSelection	0.092	0.008	0.101
purityCorrect-methods	6.157	0.008	6.554
quantify-methods	6.396	0.028	6.482
readIspyData	0.004	0.000	0.005
readMSData	0.688	0.000	0.691
readMSnSet	0.004	0.000	0.006
readMgfData	10.329	0.024	10.568
readMzTabData	0.428	0.004	0.614
removePeaks-methods	3.148	0.000	3.184
removeReporters-methods	1.668	0.012	1.713
trimMz-methods	0.312	0.008	0.321
writeMgfData-methods	0.008	0.000	0.011
writeMzTabData	13.301	0.064	23.712

Summary

Command output