BioC 2.14: CHECK report for MSnbase on morelia

Package: MSnbase

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.12.1.tar.gz

StartedAt: 2014-10-08 00:17:03 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:22:28 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 324.7 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/MSnbase.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ... [15s/18s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [61s/98s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
writeMzTabData   8.274  0.038  31.826
readMgfData      6.580  0.033   7.876
quantify-methods 4.864  0.013   6.553
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat.R’ [29s/38s]
 [29s/39s] 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
  ‘/Users/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	0.504	0.008	0.558
MSnProcess-class	0.003	0.001	0.003
MSnSet-class	0.997	0.010	1.006
NAnnotatedDataFrame-class	0.024	0.000	0.024
ReporterIons-class	0.017	0.001	0.017
TMT6	0.018	0.000	0.018
addIdentificationData-methods	0.550	0.007	0.557
chromatogram-methods	0.063	0.014	0.158
clean-methods	1.483	0.012	1.500
combineFeatures	0.843	0.008	1.258
exprsToRatios-methods	3.659	0.012	4.719
extractPrecSpectra-methods	0.273	0.003	0.276
featureCV	0.452	0.003	0.454
fillUp	0.009	0.000	0.009
formatRt	0.001	0.001	0.001
getVariableName	0.003	0.000	0.003
iTRAQ4	0.020	0.001	0.021
impute-methods	2.903	0.006	3.252
itraqdata	0.038	0.001	0.040
nQuants	4.403	0.015	4.422
normalise-methods	3.497	0.007	4.021
pSet-class	0.003	0.001	0.004
plot-methods	1.156	0.009	1.686
plot2d-methods	0.778	0.003	0.988
plotDensity-methods	0.868	0.003	0.875
plotMzDelta-methods	2.031	0.022	2.800
plotNA-methods	3.717	0.004	3.722
precSelection	0.039	0.001	0.040
purityCorrect-methods	3.254	0.004	3.780
quantify-methods	4.864	0.013	6.553
readIspyData	0	0	0
readMSData	0.276	0.002	0.278
readMSnSet	0.000	0.000	0.001
readMgfData	6.580	0.033	7.876
readMzTabData	0.276	0.002	0.387
removeNoId-methods	0.448	0.003	0.452
removePeaks-methods	1.670	0.012	2.044
removeReporters-methods	0.797	0.002	0.803
trimMz-methods	0.143	0.003	0.145
writeMgfData-methods	0.001	0.000	0.002
writeMzTabData	8.274	0.038	31.826
xic-methods	0.001	0.000	0.001