BioC 2.14: CHECK report for MSnbase on petty

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: 2014-10-07 23:05:57 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:18:04 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 726.2 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-darwin10.8.0 (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 ... [31s/119s] 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 ... [116s/192s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
readMgfData           12.309  0.079  12.557
writeMzTabData        11.927  0.074  59.568
quantify-methods       9.105  0.030  12.578
nQuants                8.181  0.027  13.278
plotNA-methods         7.966  0.027  10.993
purityCorrect-methods  7.293  0.023  12.681
normalise-methods      7.217  0.024  13.997
impute-methods         7.206  0.013   7.252
exprsToRatios-methods  7.151  0.015   7.201
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat.R’ [72s/89s]
 [73s/89s] 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	0.628	0.017	0.744
MSnProcess-class	0.004	0.000	0.004
MSnSet-class	1.979	0.024	2.006
NAnnotatedDataFrame-class	0.050	0.001	0.050
ReporterIons-class	0.027	0.000	0.028
TMT6	0.027	0.001	0.052
addIdentificationData-methods	0.972	0.015	1.003
chromatogram-methods	0.096	0.029	0.562
clean-methods	2.946	0.025	2.975
combineFeatures	1.732	0.014	1.751
exprsToRatios-methods	7.151	0.015	7.201
extractPrecSpectra-methods	0.518	0.004	0.526
featureCV	0.841	0.003	0.848
fillUp	0.015	0.001	0.015
formatRt	0.002	0.000	0.002
getVariableName	0.005	0.000	0.005
iTRAQ4	0.032	0.000	0.033
impute-methods	7.206	0.013	7.252
itraqdata	0.067	0.001	0.067
nQuants	8.181	0.027	13.278
normalise-methods	7.217	0.024	13.997
pSet-class	0.004	0.001	0.005
plot-methods	2.255	0.041	4.133
plot2d-methods	1.501	0.010	2.821
plotDensity-methods	1.520	0.008	1.649
plotMzDelta-methods	3.426	0.055	3.494
plotNA-methods	7.966	0.027	10.993
precSelection	0.075	0.002	0.144
purityCorrect-methods	7.293	0.023	12.681
quantify-methods	9.105	0.030	12.578
readIspyData	0.001	0.000	0.001
readMSData	0.503	0.004	0.508
readMSnSet	0.001	0.001	0.002
readMgfData	12.309	0.079	12.557
readMzTabData	0.460	0.003	0.659
removeNoId-methods	1.144	0.009	1.163
removePeaks-methods	3.383	0.023	3.423
removeReporters-methods	1.254	0.007	1.262
trimMz-methods	0.228	0.007	0.235
writeMgfData-methods	0.003	0.000	0.003
writeMzTabData	11.927	0.074	59.568
xic-methods	0.001	0.000	0.001