Package: geNetClassifier

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.0.0.tar.gz

StartedAt: 2013-05-01 05:52:36 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:56:31 -0700 (Wed, 01 May 2013)

EllapsedTime: 234.9 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/geNetClassifier.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'geNetClassifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geNetClassifier' 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 'geNetClassifier' can be installed ... [7s/8s] 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 ... NOTE
calculateGenesRanking: no visible global function definition for
  'brewer.pal'
plotErrorNumGenes: no visible global function definition for
  'brewer.pal'
plotNetwork: no visible global function definition for
  'graph.data.frame'
plotNetwork: no visible global function definition for 'vcount'
plotNetwork: no visible global function definition for
  'layout.fruchterman.reingold'
plotNetwork: no visible global function definition for
  'get.vertex.attribute'
plotNetwork: no visible global function definition for
  'get.edge.attribute'
plotNetwork: no visible global function definition for 'ecount'
plotNetwork: no visible global function definition for 'tkplot'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [133s/141s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plot.GeNetClassifierReturn 28.821 31.754  62.897
plotNetwork                18.797 20.699  40.766
GenesNetwork-class          1.897  0.352   5.741
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [3s/3s]
 [4s/4s] 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/geNetClassifier.Rcheck/00check.log'
for details.

* installing *source* package 'geNetClassifier' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geNetClassifier)

name	user	system	elapsed
GeNetClassifierReturn-class	2.076	0.126	2.260
GeneralizationError-class	0.874	0.080	0.965
GenesNetwork-class	1.897	0.352	5.741
GenesRanking-class	1.243	0.129	1.399
calculateGenesRanking	0.958	0.091	1.121
externalValidation.probMatrix	1.490	0.116	1.675
externalValidation.stats	1.182	0.105	1.339
gClasses-methods	0.427	0.031	0.489
geNetClassifier	0.428	0.075	0.529
genesDetails-methods	0.679	0.063	0.780
getEdges-methods	0.425	0.034	0.466
getNodes-methods	0.426	0.026	0.453
getNumEdges-methods	0.425	0.033	0.476
getNumNodes-methods	0.434	0.027	0.465
getRanking-methods	0.619	0.045	0.698
getSubNetwork-methods	0.464	0.036	0.538
getTopRanking-methods	0.445	0.038	0.527
leukemiasClassifier	0.556	0.053	0.651
network2txt	0.564	0.056	0.668
numGenes-methods	0.432	0.028	0.553
numSignificantGenes-methods	0.444	0.035	0.501
overview-methods	0.512	0.044	0.583
plot.GeNetClassifierReturn	28.821	31.754	62.897
plot.GenesRanking	0.506	0.043	0.563
plotAssignments	2.048	0.116	2.238
plotDiscriminantPower	1.319	0.139	1.552
plotExpressionProfiles	2.869	0.281	3.330
plotNetwork	18.797	20.699	40.766
queryGeNetClassifier	1.794	0.173	2.127
querySummary	1.353	0.122	1.528