BioC 2.14: CHECK report for ROntoTools on zin2

Package: ROntoTools

Version: 1.4.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ROntoTools_1.4.0.tar.gz

StartedAt: 2014-10-08 02:31:23 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:34:59 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 215.7 seconds

RetCode: 0

Status:  OK

CheckDir: ROntoTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ROntoTools_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ROntoTools.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-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 ‘1.4.0’
* 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 ... [8s/8s] 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [110s/110s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
peNodeRenderInfo       25.377  0.020  25.495
peEdgeRenderInfo       21.050  0.012  21.102
plot.peRes-methods     16.133  0.004  16.293
Summary-methods        14.001  0.032  14.055
pe                     12.252  0.020  12.319
plot.pePathway-methods 11.789  0.016  11.825
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [23s/23s]
 [23s/23s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-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	14.001	0.032	14.055
alpha1MR	0.012	0.000	0.015
alphaMLG	0.012	0.000	0.015
compute.fisher	0	0	0
compute.normalInv	0.000	0.000	0.001
keggPathwayGraphs	0.424	0.008	0.430
keggPathwayNames	0.452	0.000	0.454
nodeWeights	0.004	0.000	0.004
pe	12.252	0.020	12.319
peEdgeRenderInfo	21.050	0.012	21.102
peNodeRenderInfo	25.377	0.020	25.495
plot.pePathway-methods	11.789	0.016	11.825
plot.peRes-methods	16.133	0.004	16.293
setEdgeWeights	3.360	0.004	3.369
setNodeWeights	0.564	0.000	0.563