BioC 3.3: CHECK report for geNetClassifier on linux2.bioconductor.org

Package: geNetClassifier

Version: 1.11.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.11.0.tar.gz

StartedAt: 2015-10-27 04:09:55 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:10:56 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 61.6 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/geNetClassifier.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-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 ‘1.11.0’
* 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 ... [3s/3s] 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
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘igraph’ ‘infotheo’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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’
plotAssignments: no visible binding for global variable ‘coordinates’
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’
Undefined global functions or variables:
  brewer.pal coordinates ecount get.edge.attribute get.vertex.attribute
  graph.data.frame layout.fruchterman.reingold tkplot vcount
* 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 ... [25s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [1s/1s] 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
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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	1.163	0.020	1.185
GeneralizationError-class	0.644	0.008	0.651
GenesNetwork-class	1.389	0.068	1.459
GenesRanking-class	0.815	0.021	0.834
calculateGenesRanking	0.568	0.000	0.568
externalValidation.probMatrix	0.744	0.008	0.755
externalValidation.stats	0.591	0.000	0.589
gClasses-methods	0.219	0.004	0.222
geNetClassifier	0.268	0.008	0.276
geneSymbols	0.107	0.000	0.107
genesDetails-methods	0.391	0.008	0.398
getEdges-methods	0.233	0.000	0.234
getNodes-methods	0.221	0.003	0.226
getNumEdges-methods	0.221	0.009	0.230
getNumNodes-methods	0.244	0.000	0.244
getRanking-methods	0.337	0.000	0.337
getSubNetwork-methods	0.239	0.000	0.238
getTopRanking-methods	0.226	0.003	0.230
leukemiasClassifier	0.274	0.008	0.282
network2txt	0.293	0.012	0.304
numGenes-methods	0.226	0.000	0.227
numSignificantGenes-methods	0.235	0.000	0.235
overview-methods	0.268	0.004	0.271
plot.GeNetClassifierReturn	4.462	0.114	4.516
plot.GenesRanking	0.253	0.000	0.252
plotAssignments	0.729	0.025	0.751
plotDiscriminantPower	0.836	0.020	0.858
plotExpressionProfiles	1.475	0.024	1.495
plotNetwork	4.079	0.124	4.176
queryGeNetClassifier	0.876	0.012	0.898
querySummary	0.841	0.011	0.856