BioC 3.2: CHECK report for ROntoTools on perceval

Package: ROntoTools

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ROntoTools_1.10.0.tar.gz

StartedAt: 2015-10-27 11:54:47 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:58:23 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 215.5 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 ROntoTools_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ROntoTools.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 ‘ROntoTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ROntoTools’ version ‘1.10.0’
* 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 ‘ROntoTools’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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 ... [92s/92s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.peRes-methods     16.047  0.296  16.442
Summary-methods        14.077  0.286  14.364
peNodeRenderInfo       12.928  0.281  13.211
pe                     12.865  0.269  13.133
peEdgeRenderInfo       12.160  0.298  12.460
plot.pePathway-methods 11.746  0.246  12.005
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [24s/24s]
 [24s/25s] 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

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	14.077	0.286	14.364
alpha1MR	0.017	0.001	0.018
alphaMLG	0.017	0.001	0.018
compute.fisher	0.001	0.000	0.001
compute.normalInv	0.001	0.000	0.001
keggPathwayGraphs	0.584	0.004	0.588
keggPathwayNames	0.404	0.005	0.409
nodeWeights	0.004	0.000	0.004
pe	12.865	0.269	13.133
peEdgeRenderInfo	12.160	0.298	12.460
peNodeRenderInfo	12.928	0.281	13.211
plot.pePathway-methods	11.746	0.246	12.005
plot.peRes-methods	16.047	0.296	16.442
setEdgeWeights	4.167	0.066	4.232
setNodeWeights	0.625	0.004	0.629