BioC 2.14: CHECK report for MSnbase on zin2

Package: MSnbase

Version: 1.12.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.12.1.tar.gz

StartedAt: 2014-10-08 01:19:31 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:23:39 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 247.9 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.12.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/MSnbase.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.12.1’
* 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 ... [13s/14s] 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 files in ‘vignettes’ ... OK
* checking examples ... [56s/76s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
writeMzTabData 6.068  0.076  18.539
readMgfData    6.076  0.016   6.255
plotNA-methods 3.521  0.000   5.311
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat.R’ [35s/35s]
 [35s/36s] 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	0.484	0.004	0.493
MSnProcess-class	0.000	0.004	0.002
MSnSet-class	0.888	0.012	1.021
NAnnotatedDataFrame-class	0.024	0.000	0.032
ReporterIons-class	0.016	0.000	0.015
TMT6	0.012	0.004	0.018
addIdentificationData-methods	0.532	0.004	0.543
chromatogram-methods	0.048	0.016	0.102
clean-methods	1.312	0.004	1.321
combineFeatures	0.996	0.004	1.004
exprsToRatios-methods	3.672	0.004	3.740
extractPrecSpectra-methods	0.268	0.000	0.307
featureCV	0.396	0.008	0.460
fillUp	0.008	0.000	0.008
formatRt	0.000	0.000	0.001
getVariableName	0.000	0.000	0.002
iTRAQ4	0.016	0.000	0.017
impute-methods	3.445	0.012	3.599
itraqdata	0.036	0.000	0.036
nQuants	3.672	0.004	3.734
normalise-methods	3.272	0.000	3.303
pSet-class	0.000	0.000	0.002
plot-methods	1.336	0.004	2.318
plot2d-methods	0.672	0.008	1.363
plotDensity-methods	0.728	0.004	1.465
plotMzDelta-methods	1.716	0.008	3.225
plotNA-methods	3.521	0.000	5.311
precSelection	0.028	0.004	0.030
purityCorrect-methods	3.220	0.008	3.234
quantify-methods	4.556	0.004	4.668
readIspyData	0	0	0
readMSData	0.256	0.004	0.266
readMSnSet	0.004	0.000	0.000
readMgfData	6.076	0.016	6.255
readMzTabData	0.236	0.000	0.390
removeNoId-methods	0.636	0.000	0.663
removePeaks-methods	1.653	0.056	1.735
removeReporters-methods	0.728	0.032	0.760
trimMz-methods	0.132	0.008	0.142
writeMgfData-methods	0.000	0.000	0.002
writeMzTabData	6.068	0.076	18.539
xic-methods	0.000	0.004	0.001