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: 2015-11-10 09:05:20 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 09:08:56 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 215.7 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 ... [93s/93s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.peRes-methods     16.327  0.308  16.637
Summary-methods        13.998  0.296  14.295
peNodeRenderInfo       13.293  0.312  13.643
pe                     12.321  0.288  12.610
plot.pePathway-methods 12.070  0.307  12.385
peEdgeRenderInfo       12.061  0.302  12.364
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [24s/24s]
 [24s/24s] 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	13.998	0.296	14.295
alpha1MR	0.018	0.001	0.018
alphaMLG	0.016	0.001	0.017
compute.fisher	0	0	0
compute.normalInv	0.001	0.000	0.001
keggPathwayGraphs	0.558	0.005	0.563
keggPathwayNames	0.395	0.005	0.400
nodeWeights	0.004	0.000	0.004
pe	12.321	0.288	12.610
peEdgeRenderInfo	12.061	0.302	12.364
peNodeRenderInfo	13.293	0.312	13.643
plot.pePathway-methods	12.070	0.307	12.385
plot.peRes-methods	16.327	0.308	16.637
setEdgeWeights	4.022	0.096	4.117
setNodeWeights	0.625	0.004	0.629