BioC 2.13: CHECK report for geNetClassifier on zin1

Package: geNetClassifier

Version: 1.2.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.2.0.tar.gz

StartedAt: 2014-04-05 01:24:00 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:25:25 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 85.5 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.2.0’
* 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 ... [4s/4s] 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘EBarrays’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 7.753  0.104   7.995
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [2s/2s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	1.160	0.036	1.200
GeneralizationError-class	0.508	0.024	0.556
GenesNetwork-class	1.196	0.080	1.296
GenesRanking-class	0.844	0.024	0.874
calculateGenesRanking	0.532	0.016	0.552
externalValidation.probMatrix	1.064	0.016	1.085
externalValidation.stats	0.784	0.012	0.799
gClasses-methods	0.292	0.004	0.296
geNetClassifier	0.252	0.004	0.259
genesDetails-methods	0.396	0.008	0.406
getEdges-methods	0.276	0.004	0.279
getNodes-methods	0.272	0.004	0.275
getNumEdges-methods	0.276	0.004	0.281
getNumNodes-methods	0.280	0.000	0.277
getRanking-methods	0.308	0.008	0.318
getSubNetwork-methods	0.296	0.000	0.295
getTopRanking-methods	0.284	0.008	0.291
leukemiasClassifier	0.396	0.004	0.408
network2txt	0.412	0.004	0.424
numGenes-methods	0.284	0.004	0.307
numSignificantGenes-methods	0.280	0.004	0.285
overview-methods	0.332	0.004	0.338
plot.GeNetClassifierReturn	7.753	0.104	7.995
plot.GenesRanking	0.316	0.008	0.324
plotAssignments	0.964	0.016	0.983
plotDiscriminantPower	0.808	0.004	0.813
plotExpressionProfiles	1.868	0.020	1.913
plotNetwork	4.100	0.088	4.202
queryGeNetClassifier	1.124	0.028	1.193
querySummary	0.784	0.020	0.806