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BioC 3.0: CHECK report for ROntoTools on perceval

This page was generated on 2015-04-10 09:57:58 -0700 (Fri, 10 Apr 2015).

Package 769/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ROntoTools 1.6.1
Calin Voichita
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ROntoTools
Last Changed Rev: 97967 / Revision: 102249
Last Changed Date: 2015-01-02 12:36:53 -0800 (Fri, 02 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ROntoTools
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ROntoTools_1.6.1.tar.gz
StartedAt: 2015-04-10 05:55:51 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 06:01:15 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 323.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ROntoTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ROntoTools_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ROntoTools.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.1’
* 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 ... [17s/18s] 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:
  ‘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 ... [115s/116s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
Summary-methods        19.846  0.444  20.351
plot.peRes-methods     18.702  0.430  19.171
pe                     15.575  0.386  16.001
peNodeRenderInfo       15.088  0.409  15.782
peEdgeRenderInfo       14.289  0.409  14.770
plot.pePathway-methods 13.304  0.397  13.763
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [35s/36s]
 [35s/37s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ROntoTools.Rcheck/00check.log’
for details.

ROntoTools.Rcheck/00install.out:

* 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)

ROntoTools.Rcheck/ROntoTools-Ex.timings:

nameusersystemelapsed
Summary-methods19.846 0.44420.351
alpha1MR0.0190.0010.021
alphaMLG0.0190.0020.021
compute.fisher0.0000.0000.001
compute.normalInv0.0010.0000.002
keggPathwayGraphs0.6120.0120.626
keggPathwayNames0.7660.0100.777
nodeWeights0.0050.0000.004
pe15.575 0.38616.001
peEdgeRenderInfo14.289 0.40914.770
peNodeRenderInfo15.088 0.40915.782
plot.pePathway-methods13.304 0.39713.763
plot.peRes-methods18.702 0.43019.171
setEdgeWeights4.8070.1024.920
setNodeWeights0.7760.0060.783