BioC 3.3: CHECK report for geNetClassifier on morelia

Package: geNetClassifier

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geNetClassifier_1.11.0.tar.gz

StartedAt: 2015-10-22 06:25:23 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 06:26:39 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 75.9 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_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/geNetClassifier.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.11.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/32s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
GenesNetwork-class 1.021  0.123   11.46
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [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-3.3-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	0.821	0.040	0.947
GeneralizationError-class	0.446	0.025	0.472
GenesNetwork-class	1.021	0.123	11.460
GenesRanking-class	0.495	0.034	0.529
calculateGenesRanking	0.384	0.018	0.504
externalValidation.probMatrix	0.723	0.024	0.747
externalValidation.stats	0.653	0.026	0.680
gClasses-methods	0.215	0.009	0.223
geNetClassifier	0.162	0.011	0.172
geneSymbols	0.058	0.001	0.059
genesDetails-methods	0.327	0.020	0.347
getEdges-methods	0.256	0.010	0.265
getNodes-methods	0.240	0.007	0.246
getNumEdges-methods	0.314	0.007	0.322
getNumNodes-methods	0.248	0.006	0.255
getRanking-methods	0.364	0.011	0.376
getSubNetwork-methods	0.247	0.008	0.256
getTopRanking-methods	0.240	0.004	0.245
leukemiasClassifier	0.274	0.010	0.284
network2txt	0.288	0.016	0.305
numGenes-methods	0.220	0.006	0.226
numSignificantGenes-methods	0.224	0.007	0.231
overview-methods	0.262	0.009	0.271
plot.GeNetClassifierReturn	3.777	0.327	4.395
plot.GenesRanking	0.234	0.008	0.243
plotAssignments	0.685	0.026	0.710
plotDiscriminantPower	0.591	0.064	0.722
plotExpressionProfiles	0.916	0.076	1.106
plotNetwork	2.898	0.239	3.128
queryGeNetClassifier	0.988	0.033	1.019
querySummary	0.774	0.028	0.818