BioC 2.14: CHECK report for MSstats on morelia

Package: MSstats

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSstats_2.2.0.tar.gz

StartedAt: 2014-10-08 00:17:23 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:22:29 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 306.7 seconds

RetCode: 0

Status:  OK

CheckDir: MSstats.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 MSstats_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/MSstats.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 ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘2.2.0’
* 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 ... [20s/24s] 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’
* 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 ... [28s/65s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
dataProcessPlots     7.724  0.038  18.631
groupComparisonPlots 3.078  0.028  13.680
groupComparison      1.801  0.021   7.545
* checking for unstated dependencies in vignettes ... OK
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/MSstats.Rcheck/00check.log’
for details.

* 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	0.095	0.005	2.596
RawData	0.004	0.001	0.004
dataProcess	0.460	0.015	2.464
dataProcessPlots	7.724	0.038	18.631
designSampleSize	0.661	0.013	3.668
designSampleSizePlots	0.415	0.007	0.445
groupComparison	1.801	0.021	7.545
groupComparisonPlots	3.078	0.028	13.680
modelBasedQCPlots	1.156	0.010	2.450
quantification	1.132	0.006	1.700
testResultMultiComparisons	0.732	0.005	0.750
testResultOneComparison	0.485	0.005	0.491
transformMSnSetToMSstats	0.819	0.009	0.971
transformMSstatsToMSnSet	0.135	0.001	0.136