BioC 2.12: CHECK report for geNetClassifier on george2

Package: geNetClassifier

Version: 1.0.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.0.2.tar.gz

StartedAt: 2013-10-09 02:03:16 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:05:50 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 154.4 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/geNetClassifier.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 ‘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/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 ... [53s/54s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plot.GeNetClassifierReturn 11.581  0.400  12.427
plotNetwork                 6.996  0.232   7.329
* 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
  ‘/home/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	2.836	0.124	2.993
GeneralizationError-class	0.720	0.020	0.742
GenesNetwork-class	1.600	0.100	1.841
GenesRanking-class	1.068	0.040	1.110
calculateGenesRanking	0.924	0.016	0.964
externalValidation.probMatrix	2.904	0.052	3.064
externalValidation.stats	1.632	0.052	1.686
gClasses-methods	0.344	0.012	0.356
geNetClassifier	0.233	0.016	0.251
genesDetails-methods	0.904	0.036	0.939
getEdges-methods	0.312	0.016	0.327
getNodes-methods	0.316	0.016	0.331
getNumEdges-methods	0.304	0.028	0.334
getNumNodes-methods	0.316	0.016	0.333
getRanking-methods	0.440	0.032	0.471
getSubNetwork-methods	0.384	0.036	0.420
getTopRanking-methods	0.360	0.008	0.368
leukemiasClassifier	0.524	0.036	0.558
network2txt	0.488	0.020	0.509
numGenes-methods	0.336	0.012	0.349
numSignificantGenes-methods	0.408	0.008	0.417
overview-methods	0.500	0.016	0.574
plot.GeNetClassifierReturn	11.581	0.400	12.427
plot.GenesRanking	0.380	0.032	0.415
plotAssignments	2.340	0.056	2.397
plotDiscriminantPower	1.268	0.088	1.354
plotExpressionProfiles	3.012	0.100	3.116
plotNetwork	6.996	0.232	7.329
queryGeNetClassifier	2.221	0.052	2.273
querySummary	1.320	0.036	1.360