BioC 3.3: CHECK report for ROntoTools on linux2.bioconductor.org

Package: ROntoTools

Version: 1.11.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ROntoTools_1.11.0.tar.gz

StartedAt: 2015-10-27 07:42:39 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:45:25 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 165.3 seconds

RetCode: 0

Status:  OK

CheckDir: ROntoTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ROntoTools_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ROntoTools.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.11.0’
* 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 ... [7s/7s] 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:
  ‘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’
Undefined global functions or variables:
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [78s/78s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot.peRes-methods     15.366  0.032  15.434
peEdgeRenderInfo       12.078  0.040  12.139
Summary-methods        11.516  0.092  11.639
peNodeRenderInfo       10.535  0.008  10.555
pe                     10.414  0.036  10.461
plot.pePathway-methods  8.516  0.024   8.558
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [19s/19s]
 [20s/20s] 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
  ‘/home/biocbuild/bbs-3.3-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	11.516	0.092	11.639
alpha1MR	0.012	0.000	0.012
alphaMLG	0.013	0.000	0.013
compute.fisher	0	0	0
compute.normalInv	0.001	0.000	0.000
keggPathwayGraphs	0.525	0.004	0.529
keggPathwayNames	0.559	0.008	0.567
nodeWeights	0.003	0.000	0.003
pe	10.414	0.036	10.461
peEdgeRenderInfo	12.078	0.040	12.139
peNodeRenderInfo	10.535	0.008	10.555
plot.pePathway-methods	8.516	0.024	8.558
plot.peRes-methods	15.366	0.032	15.434
setEdgeWeights	3.520	0.004	3.529
setNodeWeights	0.710	0.000	0.709