BioC 3.2: CHECK report for geNetClassifier on linux1.bioconductor.org

Package: geNetClassifier

Version: 1.10.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.10.0.tar.gz

StartedAt: 2015-10-27 03:53:14 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:54:25 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 70.6 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.10.0’
* 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’
* 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 ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 5.328  0.145   5.418
* 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-3.2-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	1.118	0.016	1.138
GeneralizationError-class	0.638	0.020	0.663
GenesNetwork-class	1.432	0.076	1.515
GenesRanking-class	0.905	0.013	0.920
calculateGenesRanking	0.697	0.020	0.718
externalValidation.probMatrix	1.021	0.012	1.030
externalValidation.stats	0.961	0.017	0.976
gClasses-methods	0.388	0.008	0.397
geNetClassifier	0.286	0.004	0.290
geneSymbols	0.110	0.000	0.111
genesDetails-methods	0.575	0.000	0.573
getEdges-methods	0.352	0.000	0.352
getNodes-methods	0.367	0.004	0.370
getNumEdges-methods	0.341	0.000	0.340
getNumNodes-methods	0.351	0.004	0.354
getRanking-methods	0.410	0.008	0.418
getSubNetwork-methods	0.475	0.000	0.476
getTopRanking-methods	0.337	0.012	0.350
leukemiasClassifier	0.425	0.000	0.425
network2txt	0.469	0.004	0.473
numGenes-methods	0.327	0.008	0.337
numSignificantGenes-methods	0.404	0.000	0.406
overview-methods	0.449	0.000	0.449
plot.GeNetClassifierReturn	5.328	0.145	5.418
plot.GenesRanking	0.400	0.004	0.403
plotAssignments	0.992	0.003	0.993
plotDiscriminantPower	0.915	0.021	0.931
plotExpressionProfiles	1.502	0.045	1.535
plotNetwork	3.087	0.081	3.103
queryGeNetClassifier	1.306	0.000	1.309
querySummary	0.594	0.005	0.598