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BioC 3.0: CHECK report for BioNet on perceval

This page was generated on 2015-04-10 09:55:12 -0700 (Fri, 10 Apr 2015).

Package 99/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNet 1.26.1
Marcus Dittrich
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BioNet
Last Changed Rev: 100741 / Revision: 102249
Last Changed Date: 2015-03-16 16:36:15 -0700 (Mon, 16 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

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 23:10:46 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:15:06 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 260.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BioNet.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /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-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 ‘1.26.1’
* 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 ... [14s/18s] 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:
  ‘genefilter’ ‘rgl’ ‘XML’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘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 ‘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’
.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’
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 ... [102s/103s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runFastHeinz      12.993  0.338  13.364
largestScoreComp  11.161  1.337  12.515
permutateNodes    10.812  1.324  12.142
resamplingPvalues  7.022  0.199   7.221
sortedEdgeList     5.224  0.041   5.265
* 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.

BioNet.Rcheck/00install.out:

* 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)

BioNet.Rcheck/BioNet-Ex.timings:

nameusersystemelapsed
aggrPvals0.8410.0730.937
bumOptim0.550.010.56
compareNetworks2.5190.0412.650
consensusScores0.3340.0150.349
fbum0.0000.0000.001
fbumLL0.5830.0120.595
fdrThreshold0.8560.0030.859
fitBumModel1.5910.0381.640
getCompScores2.4970.0252.525
getEdgeList1.1450.0171.163
hist.bum0.9360.0150.967
largestComp3.0080.0283.038
largestScoreComp11.161 1.33712.515
loadNetwork.sif0.0010.0010.001
makeNetwork0.0130.0000.012
mapByVar0.0010.0000.001
permutateNodes10.812 1.32412.142
piUpper0.6820.0030.685
plot.bum1.8540.0091.862
plot3dModule3.6110.0253.636
plotLLSurface0.6020.0070.811
plotModule3.3720.0163.388
print.bum0.6140.0010.615
pvaluesExample0.0090.0010.010
readHeinzGraph0.3420.0040.347
readHeinzTree0.3710.0050.375
resamplingPvalues7.0220.1997.221
rmSelfLoops0.0060.0010.007
runFastHeinz12.993 0.33813.364
save3dModule1.9130.0972.012
saveNetwork1.6640.0631.731
scanFDR0.5560.0040.561
scoreFunction0.6590.0581.088
scoreNodes3.1750.0713.257
scoreOffset0.5420.0030.551
sortedEdgeList5.2240.0415.265
subNetwork0.0640.0030.067
summary.bum0.5260.0090.536
writeHeinz1.7010.0471.750
writeHeinzEdges4.6760.1014.781
writeHeinzNodes2.4720.0222.496