BioC 2.14: CHECK report for geNetClassifier on petty

Package: geNetClassifier

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.4.0.tar.gz

StartedAt: 2014-10-07 22:09:57 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:14:45 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 287.9 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.0’
* 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 ... [9s/9s] 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
Package in Depends field not imported from: ‘minet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 ... [147s/163s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plot.GeNetClassifierReturn 32.892 33.215  79.623
plotNetwork                21.587 21.807  44.647
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [5s/5s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	2.125	0.104	2.409
GeneralizationError-class	0.925	0.044	0.970
GenesNetwork-class	2.203	0.205	2.481
GenesRanking-class	1.442	0.090	1.553
calculateGenesRanking	1.047	0.057	1.177
externalValidation.probMatrix	2.209	0.088	2.370
externalValidation.stats	1.947	0.079	2.181
gClasses-methods	0.485	0.029	0.527
geNetClassifier	0.328	0.032	0.379
genesDetails-methods	0.843	0.057	0.908
getEdges-methods	0.500	0.025	0.526
getNodes-methods	0.489	0.016	0.515
getNumEdges-methods	0.485	0.016	0.538
getNumNodes-methods	0.484	0.016	0.537
getRanking-methods	0.592	0.022	0.634
getSubNetwork-methods	0.555	0.031	0.591
getTopRanking-methods	0.514	0.023	0.559
leukemiasClassifier	0.647	0.027	0.720
network2txt	0.814	0.043	0.883
numGenes-methods	0.496	0.018	0.532
numSignificantGenes-methods	0.521	0.019	0.559
overview-methods	0.610	0.026	0.697
plot.GeNetClassifierReturn	32.892	33.215	79.623
plot.GenesRanking	0.572	0.038	0.647
plotAssignments	1.785	0.085	1.937
plotDiscriminantPower	1.490	0.114	1.617
plotExpressionProfiles	3.357	0.213	3.691
plotNetwork	21.587	21.807	44.647
queryGeNetClassifier	2.756	0.107	2.894
querySummary	1.737	0.071	1.811