BioC 3.0: CHECK report for geNetClassifier on oaxaca

Package: geNetClassifier

Version: 1.6.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.6.3.tar.gz

StartedAt: 2015-04-09 23:50:35 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:53:05 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 149.8 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 --no-multiarch geNetClassifier_1.6.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.3’
* 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 ... [5s/5s] 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 loading without being on the library search path ... 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 ... [75s/82s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plot.GeNetClassifierReturn 16.675 14.900  32.423
plotNetwork                11.258  9.698  21.032
GenesNetwork-class          1.361  0.127   7.184
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	1.242	0.059	1.414
GeneralizationError-class	0.581	0.021	0.671
GenesNetwork-class	1.361	0.127	7.184
GenesRanking-class	0.813	0.031	0.856
calculateGenesRanking	0.623	0.023	0.660
externalValidation.probMatrix	1.243	0.036	1.298
externalValidation.stats	1.103	0.036	1.144
gClasses-methods	0.342	0.007	0.351
geNetClassifier	0.242	0.011	0.261
geneSymbols	0.097	0.001	0.099
genesDetails-methods	0.546	0.020	0.568
getEdges-methods	0.359	0.014	0.374
getNodes-methods	0.350	0.011	0.361
getNumEdges-methods	0.348	0.011	0.362
getNumNodes-methods	0.353	0.010	0.365
getRanking-methods	0.422	0.013	0.438
getSubNetwork-methods	0.376	0.018	0.395
getTopRanking-methods	0.355	0.014	0.371
leukemiasClassifier	0.451	0.014	0.466
network2txt	0.485	0.022	0.656
numGenes-methods	0.349	0.009	0.358
numSignificantGenes-methods	0.359	0.011	0.370
overview-methods	0.433	0.014	0.448
plot.GeNetClassifierReturn	16.675	14.900	32.423
plot.GenesRanking	0.375	0.014	0.389
plotAssignments	1.039	0.028	1.069
plotDiscriminantPower	0.921	0.063	0.990
plotExpressionProfiles	1.777	0.088	1.902
plotNetwork	11.258	9.698	21.032
queryGeNetClassifier	1.596	0.051	1.687
querySummary	1.019	0.037	1.063