BioC 3.2: CHECK report for geNetClassifier on oaxaca

Package: geNetClassifier

Version: 1.9.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geNetClassifier_1.9.3.tar.gz

StartedAt: 2015-08-24 00:11:44 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:13:21 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 97.3 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geNetClassifier_1.9.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.3’
* 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
'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’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [30s/41s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 5.920  0.440   6.869
GenesNetwork-class         1.374  0.144  11.410
* 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	1.064	0.052	1.153
GeneralizationError-class	0.540	0.023	0.563
GenesNetwork-class	1.374	0.144	11.410
GenesRanking-class	0.810	0.046	0.871
calculateGenesRanking	0.594	0.024	0.626
externalValidation.probMatrix	1.007	0.036	1.100
externalValidation.stats	0.915	0.042	0.957
gClasses-methods	0.301	0.010	0.311
geNetClassifier	0.212	0.013	0.225
geneSymbols	0.094	0.001	0.095
genesDetails-methods	0.495	0.023	0.598
getEdges-methods	0.308	0.011	0.318
getNodes-methods	0.324	0.008	0.332
getNumEdges-methods	0.311	0.008	0.318
getNumNodes-methods	0.304	0.009	0.313
getRanking-methods	0.363	0.010	0.374
getSubNetwork-methods	0.336	0.011	0.346
getTopRanking-methods	0.357	0.010	0.366
leukemiasClassifier	0.420	0.021	0.449
network2txt	0.450	0.024	0.493
numGenes-methods	0.311	0.008	0.320
numSignificantGenes-methods	0.353	0.011	0.363
overview-methods	0.397	0.015	0.411
plot.GeNetClassifierReturn	5.920	0.440	6.869
plot.GenesRanking	0.365	0.016	0.382
plotAssignments	0.988	0.039	1.028
plotDiscriminantPower	0.801	0.046	0.849
plotExpressionProfiles	1.367	0.067	1.495
plotNetwork	3.917	0.286	4.218
queryGeNetClassifier	1.203	0.050	1.253
querySummary	0.884	0.038	0.922