BioC 3.0: CHECK report for BioNet on zin1

Package: BioNet

Version: 1.26.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.26.1.tar.gz

StartedAt: 2015-04-09 22:00:15 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:02:55 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 159.5 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.26.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/BioNet.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [10s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [66s/67s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runFastHeinz     10.009  0.016  10.102
largestScoreComp  6.341  0.008   6.358
permutateNodes    6.268  0.004   6.286
* 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
  ‘/home/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	0.572	0.024	0.598
bumOptim	0.584	0.000	0.587
compareNetworks	1.244	0.016	1.310
consensusScores	0.260	0.000	0.261
fbum	0	0	0
fbumLL	0.540	0.008	0.552
fdrThreshold	0.664	0.000	0.667
fitBumModel	1.344	0.012	1.358
getCompScores	1.576	0.012	1.594
getEdgeList	0.736	0.004	0.741
hist.bum	0.696	0.000	0.700
largestComp	1.692	0.004	1.702
largestScoreComp	6.341	0.008	6.358
loadNetwork.sif	0.000	0.000	0.001
makeNetwork	0.008	0.000	0.009
mapByVar	0.004	0.000	0.001
permutateNodes	6.268	0.004	6.286
piUpper	0.684	0.000	0.689
plot.bum	1.524	0.000	1.533
plot3dModule	2.376	0.008	2.437
plotLLSurface	0.577	0.004	0.586
plotModule	2.312	0.008	2.331
print.bum	0.704	0.000	0.705
pvaluesExample	0.008	0.000	0.006
readHeinzGraph	0.240	0.008	0.255
readHeinzTree	0.296	0.000	0.298
resamplingPvalues	4.436	0.040	4.513
rmSelfLoops	0.008	0.000	0.005
runFastHeinz	10.009	0.016	10.102
save3dModule	1.216	0.000	1.220
saveNetwork	0.784	0.004	0.792
scanFDR	0.556	0.000	0.557
scoreFunction	0.616	0.028	0.643
scoreNodes	2.216	0.008	2.228
scoreOffset	0.528	0.000	0.531
sortedEdgeList	3.576	0.000	3.582
subNetwork	0.032	0.000	0.029
summary.bum	0.532	0.000	0.533
writeHeinz	1.392	0.000	1.391
writeHeinzEdges	2.733	0.000	2.773
writeHeinzNodes	1.604	0.004	1.607