BioC 2.12: CHECK report for MSnbase on lamb2

Package: MSnbase

Version: 1.7.16

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.7.16.tar.gz

StartedAt: 2013-01-16 04:39:40 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 04:44:51 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 311.1 seconds

RetCode: 0

Status: OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/MSnbase.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.7.16’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotMzDelta-methods 23.742  0.628  24.489
writeMzTabData       8.184  0.012  20.336
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’
 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
  ‘/loc/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	0.504	0.008	0.515
MSnProcess-class	0.012	0.000	0.013
MSnSet-class	1.256	0.020	1.284
NAnnotatedDataFrame-class	0.040	0.000	0.046
ReporterIons-class	0.036	0.000	0.036
TMT6	0.028	0.000	0.030
clean-methods	1.808	0.004	1.825
combineFeatures	0.668	0.016	0.693
exprsToRatios-methods	4.444	0.016	4.489
extractPrecSpectra-methods	0.401	0.000	0.463
featureCV	0.528	0.008	0.539
fillUp	0.016	0.000	0.016
formatRt	0.004	0.000	0.006
getVariableName	0.008	0.000	0.012
iTRAQ4	0.032	0.000	0.030
itraqdata	0.300	0.004	0.303
nQuants	4.588	0.012	4.615
normalise-methods	4.404	0.016	4.448
pSet-class	0.296	0.000	0.296
plot-methods	1.772	0.000	1.855
plot2d-methods	1.368	0.000	1.382
plotDensity-methods	1.136	0.004	1.141
plotMzDelta-methods	23.742	0.628	24.489
plotNA-methods	4.924	0.008	4.935
precSelection	0.068	0.000	0.067
purityCorrect-methods	4.192	0.000	4.198
quantify-methods	4.357	0.000	4.353
readIspyData	0.004	0.000	0.003
readMSData	0.424	0.016	0.442
readMSnSet	0.004	0.000	0.005
readMgfData	0.000	0.008	0.010
readMzTabData	0.252	0.008	0.430
removePeaks-methods	1.884	0.040	1.927
removeReporters-methods	0.868	0.008	0.877
trimMz-methods	0.176	0.000	0.175
writeMgfData-methods	0.008	0.000	0.007
writeMzTabData	8.184	0.012	20.336

Summary

Command output