BioC 2.13: CHECK report for geNetClassifier on perceval

Package: geNetClassifier

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.2.0.tar.gz

StartedAt: 2014-04-05 01:32:26 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:35:56 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 209.7 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [7s/7s] 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘geNetClassifier-manual.pdf’ from 287Kb to 179Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [113s/117s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 23.30 26.910  51.881
plotNetwork                15.61 16.724  32.899
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/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	2.050	0.123	2.281
GeneralizationError-class	0.708	0.075	0.797
GenesNetwork-class	1.801	0.257	2.157
GenesRanking-class	1.216	0.098	1.384
calculateGenesRanking	0.796	0.094	0.921
externalValidation.probMatrix	1.740	0.108	1.929
externalValidation.stats	1.751	0.118	1.881
gClasses-methods	0.313	0.027	0.343
geNetClassifier	0.389	0.059	0.460
genesDetails-methods	0.551	0.057	0.654
getEdges-methods	0.316	0.033	0.389
getNodes-methods	0.311	0.035	0.377
getNumEdges-methods	0.322	0.031	0.355
getNumNodes-methods	0.317	0.025	0.349
getRanking-methods	0.386	0.047	0.492
getSubNetwork-methods	0.356	0.039	0.408
getTopRanking-methods	0.343	0.030	0.390
leukemiasClassifier	0.442	0.056	0.504
network2txt	0.507	0.050	0.578
numGenes-methods	0.332	0.035	0.370
numSignificantGenes-methods	0.524	0.040	0.566
overview-methods	0.405	0.042	0.452
plot.GeNetClassifierReturn	23.300	26.910	51.881
plot.GenesRanking	0.391	0.042	0.474
plotAssignments	1.606	0.109	1.726
plotDiscriminantPower	1.055	0.123	1.205
plotExpressionProfiles	2.530	0.253	2.857
plotNetwork	15.610	16.724	32.899
queryGeNetClassifier	2.463	0.169	2.806
querySummary	1.392	0.124	1.659