BioC 2.12: CHECK report for ROntoTools on george2

Package: ROntoTools

Version: 1.0.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ROntoTools_1.0.0.tar.gz

StartedAt: 2013-10-09 04:42:39 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:50:48 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 488.8 seconds

RetCode: 0

Status:  OK

CheckDir: ROntoTools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ROntoTools.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.0.0’
* 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 ... [20s/21s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 examples ... [235s/238s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
Summary-methods        42.275  0.208  43.032
plot.peRes-methods     38.503  0.016  38.695
peEdgeRenderInfo       35.334  0.084  36.063
pe                     34.150  0.032  34.692
peNodeRenderInfo       32.866  0.080  33.163
plot.pePathway-methods 32.290  0.044  32.448
setEdgeWeights          8.060  0.012   8.073
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [64s/65s]
 [65s/65s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* 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	42.275	0.208	43.032
alpha1MR	0.040	0.008	0.045
alphaMLG	0.036	0.008	0.046
compute.fischer	0.020	0.000	0.022
compute.normalInv	0.02	0.00	0.02
keggPathwayGraphs	0.612	0.000	0.612
keggPathwayNames	0.416	0.000	0.416
nodeWeights	0.048	0.000	0.048
pe	34.150	0.032	34.692
peEdgeRenderInfo	35.334	0.084	36.063
peNodeRenderInfo	32.866	0.080	33.163
plot.pePathway-methods	32.290	0.044	32.448
plot.peRes-methods	38.503	0.016	38.695
setEdgeWeights	8.060	0.012	8.073
setNodeWeights	0.664	0.008	0.672