BioC 3.1: CHECK report for ROntoTools on petty

Package: ROntoTools

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ROntoTools_1.8.1.tar.gz

StartedAt: 2015-10-09 01:43:45 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:48:42 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 296.6 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_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ROntoTools.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.8.1’
* 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 ... [14s/14s] 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 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 ... [121s/122s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.peRes-methods     21.639  0.452  22.242
peNodeRenderInfo       18.179  0.413  18.609
peEdgeRenderInfo       16.715  0.384  17.108
pe                     16.552  0.372  16.938
Summary-methods        16.170  0.322  16.495
plot.pePathway-methods 15.884  0.422  16.486
setEdgeWeights          5.213  0.099   5.315
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [35s/36s]
 [35s/36s] 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-3.1-bioc/meat/ROntoTools.Rcheck/00check.log’
for details.

* installing *source* package ‘ROntoTools’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (ROntoTools)

name	user	system	elapsed
Summary-methods	16.170	0.322	16.495
alpha1MR	0.018	0.001	0.019
alphaMLG	0.021	0.001	0.022
compute.fisher	0.000	0.000	0.001
compute.normalInv	0.001	0.001	0.002
keggPathwayGraphs	0.792	0.014	0.806
keggPathwayNames	0.714	0.012	0.726
nodeWeights	0.006	0.001	0.006
pe	16.552	0.372	16.938
peEdgeRenderInfo	16.715	0.384	17.108
peNodeRenderInfo	18.179	0.413	18.609
plot.pePathway-methods	15.884	0.422	16.486
plot.peRes-methods	21.639	0.452	22.242
setEdgeWeights	5.213	0.099	5.315
setNodeWeights	0.816	0.004	0.819