BioC 2.13: CHECK report for MSnbase on zin1

Package: MSnbase

Version: 1.10.4

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.10.4.tar.gz

StartedAt: 2014-04-05 02:38:50 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:42:37 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 227.0 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/MSnbase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.10.4’
* 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 ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Unexported object imported by a ‘:::’ call: ‘Biobase:::.showAnnotatedDataFrame’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘MSnbase-demo.Rnw’, ‘MSnbase-development.Rnw’, ‘MSnbase-io.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [56s/72s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
writeMzTabData 6.332  0.020  18.485
readMgfData    6.084  0.000   6.114
impute-methods 3.505  0.008   5.337
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [29s/29s]
 [29s/29s] OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘multicore’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.456	0.012	0.486
MSnProcess-class	0.004	0.000	0.005
MSnSet-class	1.028	0.000	1.031
NAnnotatedDataFrame-class	0.168	0.000	0.168
ReporterIons-class	0.016	0.004	0.023
TMT6	0.012	0.004	0.017
chromatogram-methods	0.060	0.008	0.125
clean-methods	1.492	0.016	1.511
combineFeatures	0.860	0.012	0.873
exprsToRatios-methods	3.608	0.000	4.609
extractPrecSpectra-methods	0.256	0.004	0.519
featureCV	0.420	0.000	0.837
fillUp	0.012	0.000	0.021
formatRt	0.000	0.000	0.003
getVariableName	0.004	0.000	0.005
iTRAQ4	0.02	0.00	0.04
impute-methods	3.505	0.008	5.337
itraqdata	0.036	0.004	0.039
nQuants	3.764	0.004	3.792
normalise-methods	3.384	0.000	3.391
pSet-class	0.004	0.000	0.006
plot-methods	1.248	0.000	1.252
plot2d-methods	0.952	0.004	0.956
plotDensity-methods	0.868	0.004	0.875
plotMzDelta-methods	2.832	0.024	2.859
plotNA-methods	3.613	0.000	3.615
precSelection	0.044	0.000	0.044
purityCorrect-methods	3.596	0.000	3.604
quantify-methods	3.304	0.000	3.306
readIspyData	0.000	0.000	0.001
readMSData	0.260	0.004	0.264
readMSnSet	0.000	0.000	0.001
readMgfData	6.084	0.000	6.114
readMzTabData	0.236	0.000	0.346
removePeaks-methods	1.705	0.000	1.708
removeReporters-methods	0.772	0.000	0.775
trimMz-methods	0.172	0.000	0.170
writeMgfData-methods	0.020	0.000	0.019
writeMzTabData	6.332	0.020	18.485
xic-methods	0.004	0.000	0.006