BioC 2.12: CHECK report for geNetClassifier on petty

Package: geNetClassifier

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.0.2.tar.gz

StartedAt: 2013-10-08 22:31:42 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:36:17 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 275.0 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 3.0.1 (2013-05-16)
* 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 '1.0.2'
* 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 ... [8s/9s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [146s/160s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plot.GeNetClassifierReturn 32.643 33.455  75.075
plotNetwork                21.709 22.083  47.281
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [4s/4s]
 [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	2.123	0.112	2.275
GeneralizationError-class	0.927	0.057	0.985
GenesNetwork-class	2.143	0.223	2.442
GenesRanking-class	1.336	0.088	1.423
calculateGenesRanking	1.033	0.070	1.105
externalValidation.probMatrix	1.788	0.092	1.891
externalValidation.stats	1.309	0.108	1.426
gClasses-methods	0.488	0.030	0.521
geNetClassifier	0.472	0.064	0.537
genesDetails-methods	0.776	0.046	0.822
getEdges-methods	0.514	0.030	0.551
getNodes-methods	0.505	0.032	0.544
getNumEdges-methods	0.468	0.030	0.500
getNumNodes-methods	0.510	0.027	0.540
getRanking-methods	0.598	0.038	0.647
getSubNetwork-methods	0.549	0.035	0.586
getTopRanking-methods	0.513	0.029	0.563
leukemiasClassifier	0.624	0.048	0.942
network2txt	0.639	0.053	0.971
numGenes-methods	0.505	0.029	0.552
numSignificantGenes-methods	0.531	0.037	0.591
overview-methods	0.611	0.043	0.661
plot.GeNetClassifierReturn	32.643	33.455	75.075
plot.GenesRanking	0.577	0.039	0.623
plotAssignments	1.915	0.097	2.033
plotDiscriminantPower	1.515	0.136	1.713
plotExpressionProfiles	3.829	0.256	4.111
plotNetwork	21.709	22.083	47.281
queryGeNetClassifier	2.182	0.146	2.410
querySummary	1.348	0.105	1.477