BioC 2.12: CHECK report for MSnbase on george2

Package: MSnbase

Version: 1.8.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.8.0.tar.gz

StartedAt: 2013-10-09 03:33:59 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:41:46 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 467.6 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 3.0.1 (2013-05-16)
* 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 ‘1.8.0’
* 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 ... [28s/35s] 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 ... [131s/144s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plotMzDelta-methods   34.058  0.644  35.036
writeMzTabData        12.225  0.084  24.163
readMgfData            9.701  0.024   9.855
plotNA-methods         6.916  0.028   6.943
purityCorrect-methods  6.473  0.004   6.498
normalise-methods      6.324  0.004   6.328
exprsToRatios-methods  6.197  0.012   6.226
nQuants                6.157  0.016   6.185
quantify-methods       5.612  0.000   5.697
impute-methods         5.588  0.008   5.608
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [58s/59s]
 [59s/59s] 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
** testing if installed package can be loaded
* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	0.732	0.020	0.784
MSnProcess-class	0.020	0.000	0.019
MSnSet-class	2.104	0.040	2.157
NAnnotatedDataFrame-class	0.056	0.000	0.055
ReporterIons-class	0.048	0.000	0.050
TMT6	0.048	0.000	0.045
clean-methods	2.356	0.004	2.363
combineFeatures	0.928	0.036	0.982
exprsToRatios-methods	6.197	0.012	6.226
extractPrecSpectra-methods	0.652	0.000	0.654
featureCV	0.764	0.004	0.770
fillUp	0.028	0.000	0.028
formatRt	0.012	0.000	0.012
getVariableName	0.440	0.000	0.441
iTRAQ4	0.036	0.000	0.036
impute-methods	5.588	0.008	5.608
itraqdata	0.468	0.004	0.473
nQuants	6.157	0.016	6.185
normalise-methods	6.324	0.004	6.328
pSet-class	0.032	0.008	0.040
plot-methods	2.504	0.012	2.518
plot2d-methods	1.872	0.008	1.881
plotDensity-methods	1.537	0.024	1.558
plotMzDelta-methods	34.058	0.644	35.036
plotNA-methods	6.916	0.028	6.943
precSelection	0.128	0.000	0.129
purityCorrect-methods	6.473	0.004	6.498
quantify-methods	5.612	0.000	5.697
readIspyData	0.004	0.000	0.011
readMSData	0.620	0.000	0.626
readMSnSet	0.004	0.000	0.005
readMgfData	9.701	0.024	9.855
readMzTabData	0.568	0.000	0.713
removePeaks-methods	2.676	0.008	2.752
removeReporters-methods	1.500	0.008	1.512
trimMz-methods	0.260	0.000	0.259
writeMgfData-methods	0.012	0.000	0.013
writeMzTabData	12.225	0.084	24.163