BioC 3.2: CHECK report for BioNet on perceval

Package: BioNet

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioNet_1.30.0.tar.gz

StartedAt: 2015-11-10 02:35:41 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:38:58 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 197.4 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.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 BioNet_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BioNet.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNet’ version ‘1.30.0’
* 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 ‘BioNet’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘graph’ ‘RBGL’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.affyID2ppiID: no visible global function definition for ‘nodeData’
.saveGraph.net: no visible global function definition for ‘nodes’
.saveGraph.net: no visible global function definition for ‘isDirected’
.saveGraph.net: no visible global function definition for ‘eWV’
.saveGraph.net: no visible global function definition for ‘edgeMatrix’
.saveGraph.tab: no visible global function definition for ‘edgeNames’
.saveGraph.tgf: no visible global function definition for ‘nodes’
.saveGraph.tgf: no visible global function definition for ‘eWV’
.saveGraph.tgf: no visible global function definition for ‘edgeMatrix’
.subNetwork0: no visible global function definition for ‘subGraph’
.subNetwork0: no visible global function definition for ‘nodes’
.subNetwork1: no visible global function definition for ‘adj’
.subNetwork1: no visible global function definition for ‘subGraph’
.subNetwork1: no visible global function definition for ‘nodes’
consensusScores : <anonymous>: no visible global function definition
  for ‘nodes’
consensusScores: no visible global function definition for ‘numNodes’
consensusScores: no visible global function definition for ‘nodes’
consensusScores: no visible global function definition for ‘numEdges’
getCompScores: no visible global function definition for ‘connComp’
getEdgeList: no visible global function definition for ‘edgeMatrix’
getEdgeList: no visible global function definition for ‘nodes’
largestComp: no visible global function definition for ‘connectedComp’
largestComp: no visible global function definition for ‘subGraph’
largestScoreComp: no visible global function definition for ‘nodes’
largestScoreComp: no visible global function definition for ‘subGraph’
loadNetwork.tab: no visible global function definition for ‘addEdge’
makeNetwork: no visible global function definition for ‘addEdge’
permutateNodes: no visible global function definition for ‘nodes<-’
permutateNodes: no visible global function definition for ‘nodes’
plot3dModule: no visible global function definition for ‘rgl.open’
plot3dModule: no visible global function definition for ‘par3d’
plot3dModule: no visible global function definition for ‘rgl.texts’
plot3dModule: no visible global function definition for ‘rgl.bg’
readHeinzTree: no visible global function definition for ‘edgeNames’
readHeinzTree: no visible global function definition for ‘removeEdge’
resamplingPvalues: no visible global function definition for
  ‘rowttests’
rmSelfLoops: no visible global function definition for ‘edgeNames’
rmSelfLoops: no visible global function definition for ‘numEdges’
rmSelfLoops: no visible global function definition for ‘removeEdge’
save3dModule: no visible global function definition for ‘rgl.bg’
save3dModule: no visible global function definition for
  ‘rgl.postscript’
scoreNodes: no visible global function definition for ‘nodes’
sortedEdgeList: no visible global function definition for ‘isDirected’
* 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 ... [105s/105s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runFastHeinz      35.401  0.443  35.846
permutateNodes     7.110  0.874   7.984
largestScoreComp   6.970  0.950   7.920
sortedEdgeList     5.493  0.047   5.540
resamplingPvalues  4.858  0.138   5.034
* 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/BioNet.Rcheck/00check.log’
for details.

* installing *source* package ‘BioNet’ ...
** 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 (BioNet)

name	user	system	elapsed
aggrPvals	0.595	0.059	0.711
bumOptim	0.558	0.005	0.562
compareNetworks	1.019	0.019	1.120
consensusScores	0.470	0.011	0.480
fbum	0.000	0.000	0.001
fbumLL	0.960	0.013	0.972
fdrThreshold	0.555	0.001	0.555
fitBumModel	1.601	0.003	1.604
getCompScores	2.210	0.019	2.238
getEdgeList	0.963	0.018	0.981
hist.bum	0.679	0.006	0.687
largestComp	2.268	0.017	2.286
largestScoreComp	6.97	0.95	7.92
loadNetwork.sif	0.001	0.001	0.001
makeNetwork	0.011	0.000	0.010
mapByVar	0.001	0.000	0.001
permutateNodes	7.110	0.874	7.984
piUpper	0.792	0.019	0.810
plot.bum	1.540	0.012	1.552
plot3dModule	2.578	0.029	2.607
plotLLSurface	0.673	0.004	0.677
plotModule	2.774	0.010	2.783
print.bum	0.591	0.001	0.592
pvaluesExample	0.009	0.001	0.009
readHeinzGraph	0.448	0.004	0.452
readHeinzTree	0.448	0.004	0.452
resamplingPvalues	4.858	0.138	5.034
rmSelfLoops	0.006	0.000	0.007
runFastHeinz	35.401	0.443	35.846
save3dModule	1.694	0.015	1.710
saveNetwork	1.566	0.041	1.608
scanFDR	0.614	0.006	0.620
scoreFunction	0.768	0.060	0.828
scoreNodes	2.941	0.033	2.985
scoreOffset	0.557	0.003	0.563
sortedEdgeList	5.493	0.047	5.540
subNetwork	0.060	0.001	0.062
summary.bum	0.524	0.006	0.530
writeHeinz	1.613	0.045	1.658
writeHeinzEdges	3.576	0.098	3.674
writeHeinzNodes	1.947	0.040	1.988