BioC 3.3: CHECK report for BioNet on morelia

Package: BioNet

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioNet_1.31.0.tar.gz

StartedAt: 2015-10-22 03:52:38 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 03:54:53 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 135.2 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_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/BioNet.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 ‘BioNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNet’ version ‘1.31.0’
* 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 ... [6s/6s] 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:
  ‘RBGL’ ‘graph’
  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’
Undefined global functions or variables:
  addEdge adj connComp connectedComp eWV edgeMatrix edgeNames
  isDirected nodeData nodes nodes<- numEdges numNodes par3d removeEdge
  rgl.bg rgl.open rgl.postscript rgl.texts rowttests subGraph
* 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 ... [69s/69s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
runFastHeinz   25.339  0.258  25.604
permutateNodes  4.924  0.399   5.323
* 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/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	0.477	0.052	0.530
bumOptim	0.203	0.003	0.206
compareNetworks	0.751	0.023	0.883
consensusScores	0.391	0.002	0.393
fbum	0.000	0.000	0.001
fbumLL	0.264	0.000	0.264
fdrThreshold	0.202	0.002	0.204
fitBumModel	1.208	0.012	1.222
getCompScores	1.484	0.023	1.532
getEdgeList	0.624	0.012	0.635
hist.bum	0.452	0.004	0.457
largestComp	1.015	0.021	1.037
largestScoreComp	4.308	0.385	4.694
loadNetwork.sif	0.000	0.000	0.001
makeNetwork	0.01	0.00	0.01
mapByVar	0.001	0.000	0.001
permutateNodes	4.924	0.399	5.323
piUpper	0.287	0.001	0.288
plot.bum	0.917	0.001	0.918
plot3dModule	1.805	0.094	1.899
plotLLSurface	0.365	0.012	0.377
plotModule	1.615	0.078	1.693
print.bum	0.234	0.006	0.240
pvaluesExample	0.005	0.000	0.005
readHeinzGraph	0.211	0.002	0.212
readHeinzTree	0.225	0.002	0.227
resamplingPvalues	3.272	0.115	3.387
rmSelfLoops	0.003	0.000	0.004
runFastHeinz	25.339	0.258	25.604
save3dModule	1.211	0.107	1.319
saveNetwork	1.015	0.029	1.044
scanFDR	0.294	0.006	0.301
scoreFunction	0.265	0.036	0.314
scoreNodes	1.826	0.094	1.921
scoreOffset	0.205	0.003	0.208
sortedEdgeList	2.600	0.025	2.625
subNetwork	0.026	0.001	0.027
summary.bum	0.291	0.008	0.300
writeHeinz	1.542	0.108	1.652
writeHeinzEdges	2.721	0.177	2.899
writeHeinzNodes	1.475	0.089	1.563