BioC 3.0: CHECK report for ROntoTools on perceval

Package: ROntoTools

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ROntoTools_1.6.1.tar.gz

StartedAt: 2015-04-10 05:55:51 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:01:15 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 323.2 seconds

RetCode: 0

Status:  OK

CheckDir: ROntoTools.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 ROntoTools_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ROntoTools.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ROntoTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ROntoTools’ version ‘1.6.1’
* 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 ‘ROntoTools’ can be installed ... [17s/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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘methods’ ‘Rgraphviz’
  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
peEdgeRenderInfo: no visible global function definition for
  ‘removedEdges’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [115s/116s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
Summary-methods        19.846  0.444  20.351
plot.peRes-methods     18.702  0.430  19.171
pe                     15.575  0.386  16.001
peNodeRenderInfo       15.088  0.409  15.782
peEdgeRenderInfo       14.289  0.409  14.770
plot.pePathway-methods 13.304  0.397  13.763
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [35s/36s]
 [35s/37s] OK
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ROntoTools.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Summary-methods	19.846	0.444	20.351
alpha1MR	0.019	0.001	0.021
alphaMLG	0.019	0.002	0.021
compute.fisher	0.000	0.000	0.001
compute.normalInv	0.001	0.000	0.002
keggPathwayGraphs	0.612	0.012	0.626
keggPathwayNames	0.766	0.010	0.777
nodeWeights	0.005	0.000	0.004
pe	15.575	0.386	16.001
peEdgeRenderInfo	14.289	0.409	14.770
peNodeRenderInfo	15.088	0.409	15.782
plot.pePathway-methods	13.304	0.397	13.763
plot.peRes-methods	18.702	0.430	19.171
setEdgeWeights	4.807	0.102	4.920
setNodeWeights	0.776	0.006	0.783