BioC 3.2: CHECK report for MSstats on perceval

Package: MSstats

Version: 2.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSstats_2.7.0.tar.gz

StartedAt: 2015-08-24 03:08:49 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:48:50 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 2401.1 seconds

RetCode: None

Status:  TIMEOUT

CheckDir: MSstats.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSstats_2.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MSstats.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘2.7.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘MSstats’ can be installed ... [21s/21s] 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 loading without being on the library search path ... OK
* checking 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 ... NOTE
.fit.model: no visible binding for global variable ‘LABEL’
.fit.model.single: no visible binding for global variable ‘i’
.fit.model.single: no visible binding for global variable ‘LABEL’
.iter.wls.fit.model: no visible binding for global variable ‘weight’
dataProcess: no visible binding for global variable ‘LABEL’
dataProcessPlots: no visible binding for global variable ‘LABEL’
groupComparisonPlots: no visible binding for global variable ‘logFC’
groupComparisonPlots: no visible binding for global variable ‘ciw’
transformMSnSetToMSstats: no visible global function definition for
  ‘pData’
transformMSnSetToMSstats: no visible global function definition for
  ‘exprs’
transformMSstatsToMSnSet: no visible global function definition for
  ‘sampleNames<-’
* 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 ...

* installing *source* package ‘MSstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSstats)

name	user	system	elapsed
QuantData	0.084	0.016	0.101
RawData	0.006	0.002	0.008
dataProcess	0.240	0.041	0.281
dataProcessPlots	8.931	0.087	9.220
designSampleSize	0.516	0.017	0.536
designSampleSizePlots	0.544	0.013	0.563
groupComparison	3.184	0.061	3.282
groupComparisonPlots	4.014	0.098	6.547
modelBasedQCPlots	1.688	0.035	3.197
quantification	1.255	0.022	2.402
testResultMultiComparisons	0.838	0.022	1.423
testResultOneComparison	0.733	0.018	1.470