BioC 3.2: CHECK report for GeneExpressionSignature on perceval

Package: GeneExpressionSignature

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneExpressionSignature_1.16.0.tar.gz

StartedAt: 2015-10-27 08:04:57 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:07:07 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 130.1 seconds

RetCode: 0

Status:  OK

CheckDir: GeneExpressionSignature.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 GeneExpressionSignature_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GeneExpressionSignature.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneExpressionSignature/DESCRIPTION’ ... OK
* this is package ‘GeneExpressionSignature’ version ‘1.16.0’
* 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 ‘GeneExpressionSignature’ can be installed ... [9s/9s] 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘PGSEA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
integratePRL: no visible global function definition for ‘phenoData’
integratePRL: no visible global function definition for ‘exprs’
RankMerging: no visible global function definition for ‘exprs’
RankMerging: no visible global function definition for ‘phenoData’
ScoreGSEA : PRL.Distance: no visible global function definition for
  ‘exprs’
ScoreGSEA: no visible global function definition for ‘exprs’
ScorePGSEA: no visible global function definition for ‘exprs’
ScorePGSEA: no visible global function definition for ‘PGSEA’
* 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 ... [44s/44s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
SignatureDistance 10.730  1.066  11.797
ScoreGSEA         10.528  1.078  11.606
ScorePGSEA         7.897  0.939   8.837
RankMerging        5.643  0.274   5.917
* 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/GeneExpressionSignature.Rcheck/00check.log’
for details.

* installing *source* package ‘GeneExpressionSignature’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneExpressionSignature)

name	user	system	elapsed
RankMerging	5.643	0.274	5.917
ScoreGSEA	10.528	1.078	11.606
ScorePGSEA	7.897	0.939	8.837
SignatureDistance	10.730	1.066	11.797
exampleSet	0.335	0.014	0.348
getRLs	0.889	0.041	0.930