BioC 3.0: CHECK report for BioNet on oaxaca

Package: BioNet

Version: 1.26.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.26.1.tar.gz

StartedAt: 2015-04-09 21:45:40 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:49:12 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 211.8 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 --no-multiarch BioNet_1.26.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/BioNet.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 ‘BioNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNet’ version ‘1.26.1’
* 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 ... [12s/13s] 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:
  ‘XML’ ‘genefilter’ ‘rgl’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘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
.XGMML.destription: no visible global function definition for ‘xmlNode’
.XGMML.destription: no visible global function definition for
  ‘append.xmlNode’
.XGMML.edges: no visible binding for global variable ‘xmlNode’
.XGMML.edges: no visible global function definition for ‘addAttributes’
.XGMML.edges: no visible global function definition for
  ‘append.xmlNode’
.XGMML.nodes: no visible binding for global variable ‘xmlNode’
.XGMML.nodes: no visible global function definition for ‘addAttributes’
.XGMML.nodes: no visible global function definition for
  ‘append.xmlNode’
.affyID2ppiID: no visible global function definition for ‘annotation’
.affyID2ppiID: no visible global function definition for ‘featureNames’
.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’
getCompScores: no visible global function definition for ‘listLen’
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 ‘listLen’
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’
mapByVar: no visible global function definition for ‘exprs’
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’
saveNetwork: no visible global function definition for ‘append.xmlNode’
saveNetwork: no visible global function definition for ‘saveXML’
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 ... [84s/85s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runFastHeinz      13.102  0.318  13.467
largestScoreComp   8.871  0.711   9.736
permutateNodes     8.842  0.731   9.615
resamplingPvalues  5.248  0.141   5.471
* 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/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	0.646	0.051	0.700
bumOptim	0.335	0.009	0.343
compareNetworks	1.511	0.033	1.623
consensusScores	0.375	0.005	0.381
fbum	0.001	0.001	0.001
fbumLL	0.510	0.011	0.522
fdrThreshold	0.326	0.014	0.340
fitBumModel	1.263	0.027	1.310
getCompScores	2.262	0.020	2.320
getEdgeList	0.916	0.011	0.931
hist.bum	0.535	0.022	0.559
largestComp	2.461	0.038	2.515
largestScoreComp	8.871	0.711	9.736
loadNetwork.sif	0.001	0.001	0.000
makeNetwork	0.013	0.000	0.014
mapByVar	0.001	0.000	0.001
permutateNodes	8.842	0.731	9.615
piUpper	0.416	0.010	0.438
plot.bum	1.437	0.013	1.469
plot3dModule	2.804	0.120	2.968
plotLLSurface	0.355	0.007	0.363
plotModule	2.879	0.057	2.945
print.bum	0.359	0.009	0.367
pvaluesExample	0.009	0.002	0.010
readHeinzGraph	0.375	0.003	0.404
readHeinzTree	0.376	0.004	0.380
resamplingPvalues	5.248	0.141	5.471
rmSelfLoops	0.007	0.001	0.007
runFastHeinz	13.102	0.318	13.467
save3dModule	1.561	0.104	1.666
saveNetwork	1.131	0.044	1.179
scanFDR	0.389	0.011	0.401
scoreFunction	0.466	0.052	0.520
scoreNodes	2.645	0.187	2.855
scoreOffset	0.365	0.016	0.390
sortedEdgeList	4.077	0.035	4.127
subNetwork	0.037	0.002	0.038
summary.bum	0.334	0.010	0.346
writeHeinz	1.851	0.177	2.035
writeHeinzEdges	3.631	0.226	3.883
writeHeinzNodes	2.209	0.146	2.363