BioC 3.0: CHECK report for ROntoTools on oaxaca

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 03:02:10 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:06:04 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 234.1 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-darwin13.4.0 (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 ... [12s/12s] 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:
  ‘Rgraphviz’ ‘methods’
  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 ... [91s/93s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.peRes-methods     16.952  0.220  17.700
Summary-methods        13.443  0.219  13.669
peNodeRenderInfo       12.564  0.237  12.833
peEdgeRenderInfo       12.390  0.243  12.792
plot.pePathway-methods 11.866  0.221  12.714
pe                     11.262  0.240  11.521
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [26s/26s]
 [26s/26s] 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	13.443	0.219	13.669
alpha1MR	0.021	0.001	0.022
alphaMLG	0.018	0.001	0.020
compute.fisher	0.001	0.000	0.001
compute.normalInv	0.001	0.000	0.001
keggPathwayGraphs	0.665	0.004	0.669
keggPathwayNames	0.460	0.002	0.463
nodeWeights	0.004	0.000	0.005
pe	11.262	0.240	11.521
peEdgeRenderInfo	12.390	0.243	12.792
peNodeRenderInfo	12.564	0.237	12.833
plot.pePathway-methods	11.866	0.221	12.714
plot.peRes-methods	16.952	0.220	17.700
setEdgeWeights	4.088	0.054	4.155
setNodeWeights	0.991	0.007	0.998