Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-06-17 02:39:04 -0400 (Thu, 17 Jun 2021).

CHECK results for BioNet on machv2

To the developers/maintainers of the BioNet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioNet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 186/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNet 1.52.0  (landing page)
Marcus Dittrich
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/BioNet
Branch: RELEASE_3_13
Last Commit: 5045304
Last Changed Date: 2021-05-19 11:46:01 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioNet
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioNet_1.52.0.tar.gz
StartedAt: 2021-06-15 16:40:28 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 16:44:02 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 213.3 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 --install=check:BioNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioNet_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/BioNet.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.52.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BioNet’ can be installed ... 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
.XGMML.edges: no visible global function definition for ‘is’
.XGMML.nodes: no visible global function definition for ‘is’
.add.edge.attrs: no visible global function definition for ‘read.table’
.add.node.attrs: no visible global function definition for ‘read.table’
.affyID2ppiID: no visible global function definition for ‘is’
.affyID2ppiID: no visible global function definition for ‘nodeData’
.graph.eda: no visible global function definition for ‘is’
.graph.eda: no visible global function definition for ‘write.table’
.graph.noa: no visible global function definition for ‘is’
.graph.noa: no visible global function definition for ‘write.table’
.graph.sif: no visible global function definition for ‘write.table’
.graph.table: no visible global function definition for ‘write.table’
.node.color: no visible global function definition for
  ‘colorRampPalette’
.saveGraph.net: no visible global function definition for ‘nodes’
.saveGraph.net: no visible global function definition for ‘write.table’
.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 ‘write.table’
.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 ‘is’
.subNetwork0: no visible global function definition for ‘na.omit’
.subNetwork0: no visible global function definition for ‘subGraph’
.subNetwork0: no visible global function definition for ‘nodes’
.subNetwork1: no visible global function definition for ‘is’
.subNetwork1: no visible global function definition for ‘na.omit’
.subNetwork1: no visible global function definition for ‘adj’
.subNetwork1: no visible global function definition for ‘subGraph’
.subNetwork1: no visible global function definition for ‘nodes’
aggrPvals: no visible global function definition for ‘pbeta’
aggrPvals: no visible global function definition for ‘hist’
aggrPvals: no visible global function definition for ‘par’
bumOptim: no visible global function definition for ‘runif’
bumOptim: no visible global function definition for ‘optim’
compareNetworks: no visible global function definition for ‘is’
compareNetworks: no visible global function definition for ‘hist’
compareNetworks: no visible global function definition for ‘points’
compareNetworks: no visible global function definition for ‘legend’
consensusScores: no visible global function definition for ‘is’
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’
fitBumModel: no visible global function definition for ‘par’
fitBumModel: no visible global function definition for ‘hist’
getCompScores: no visible global function definition for ‘is’
getCompScores: no visible global function definition for ‘connComp’
getEdgeList: no visible global function definition for ‘is’
getEdgeList: no visible global function definition for ‘edgeMatrix’
getEdgeList: no visible global function definition for ‘nodes’
hist.bum: no visible global function definition for ‘hist’
hist.bum: no visible global function definition for ‘lines’
hist.bum: no visible global function definition for ‘abline’
hist.bum: no visible global function definition for ‘axis’
largestComp: no visible global function definition for ‘is’
largestComp: no visible global function definition for ‘connectedComp’
largestComp: no visible global function definition for ‘subGraph’
largestScoreComp: no visible global function definition for ‘is’
largestScoreComp: no visible global function definition for ‘na.omit’
largestScoreComp: no visible global function definition for ‘nodes’
largestScoreComp: no visible global function definition for ‘subGraph’
loadNetwork.sif: no visible global function definition for ‘read.table’
loadNetwork.tab: no visible global function definition for ‘new’
loadNetwork.tab: no visible global function definition for ‘addEdge’
makeNetwork: no visible global function definition for ‘new’
makeNetwork: no visible global function definition for ‘addEdge’
permutateNodes: no visible global function definition for ‘is’
permutateNodes: no visible global function definition for ‘nodes<-’
permutateNodes: no visible global function definition for ‘nodes’
plot.bum: no visible binding for global variable ‘uniroot’
plot.bum: no visible global function definition for ‘lines’
plot3dModule: no visible global function definition for ‘is’
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’
plotLLSurface: no visible binding for global variable ‘heat.colors’
plotLLSurface: no visible global function definition for
  ‘filled.contour’
plotLLSurface: no visible global function definition for ‘axis’
plotLLSurface: no visible global function definition for ‘abline’
plotLLSurface: no visible global function definition for ‘strheight’
plotLLSurface: no visible global function definition for ‘points’
plotLLSurface: no visible global function definition for ‘text’
plotModule: no visible global function definition for ‘is’
readHeinzGraph: no visible global function definition for ‘is’
readHeinzGraph: no visible global function definition for ‘read.table’
readHeinzTree: no visible global function definition for ‘read.table’
readHeinzTree: no visible global function definition for ‘is’
readHeinzTree: no visible global function definition for ‘edgeNames’
readHeinzTree: no visible global function definition for ‘removeEdge’
resamplingPvalues: no visible global function definition for
  ‘rowttests’
resamplingPvalues: no visible binding for global variable ‘var’
resamplingPvalues: no visible global function definition for ‘pt’
rmSelfLoops: no visible global function definition for ‘is’
rmSelfLoops: no visible global function definition for ‘edgeNames’
rmSelfLoops: no visible global function definition for ‘numEdges’
rmSelfLoops: no visible global function definition for ‘removeEdge’
runFastHeinz: no visible global function definition for ‘is’
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 ‘is’
scoreNodes: no visible global function definition for ‘is’
scoreNodes: no visible global function definition for ‘nodes’
sortedEdgeList: no visible global function definition for ‘is’
sortedEdgeList: no visible global function definition for ‘isDirected’
writeHeinz: no visible global function definition for ‘is’
writeHeinzEdges: no visible global function definition for ‘is’
writeHeinzEdges: no visible global function definition for
  ‘write.table’
writeHeinzNodes: no visible global function definition for ‘is’
writeHeinzNodes: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline addEdge adj axis colorRampPalette connComp connectedComp eWV
  edgeMatrix edgeNames filled.contour heat.colors hist is isDirected
  legend lines na.omit new nodeData nodes nodes<- numEdges numNodes
  optim par par3d pbeta points pt read.table removeEdge rgl.bg rgl.open
  rgl.postscript rgl.texts rowttests runif strheight subGraph text
  uniroot var write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "heat.colors")
  importFrom("graphics", "abline", "axis", "filled.contour", "hist",
             "legend", "lines", "par", "points", "strheight", "text")
  importFrom("methods", "is", "new")
  importFrom("stats", "na.omit", "optim", "pbeta", "pt", "runif",
             "uniroot", "var")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
runFastHeinz     12.367  0.202  12.589
largestScoreComp  6.643  0.379   7.348
permutateNodes    6.546  0.417   6.969
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/BioNet.Rcheck/00check.log’
for details.



Installation output

BioNet.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BioNet
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BioNet’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BioNet)

Tests output


Example timings

BioNet.Rcheck/BioNet-Ex.timings

nameusersystemelapsed
aggrPvals0.7160.1150.863
bumOptim0.4190.0160.436
compareNetworks0.9610.0281.022
consensusScores0.3980.0150.412
fbum0.0000.0010.001
fbumLL0.3240.0090.335
fdrThreshold0.3310.0160.347
fitBumModel1.1320.0481.182
getCompScores2.0610.1002.165
getEdgeList0.9320.0150.948
hist.bum0.3540.0120.367
largestComp1.8200.0451.918
largestScoreComp6.6430.3797.348
loadNetwork.sif0.0010.0000.001
makeNetwork0.0140.0000.014
mapByVar000
permutateNodes6.5460.4176.969
piUpper0.3560.0060.363
plot.bum1.1950.0401.238
plot3dModule2.1500.0962.249
plotLLSurface0.3170.0120.329
plotModule1.9570.0742.033
print.bum0.3070.0060.314
pvaluesExample0.0110.0030.014
readHeinzGraph0.3600.0070.366
readHeinzTree0.3740.0050.380
resamplingPvalues3.8870.1204.015
rmSelfLoops0.0350.0000.036
runFastHeinz12.367 0.20212.589
save3dModule1.3260.0731.400
saveNetwork0.8800.0280.909
scanFDR0.3580.0120.371
scoreFunction0.3610.1000.461
scoreNodes1.6300.1551.786
scoreOffset0.2990.0020.302
sortedEdgeList3.8070.0203.830
subNetwork0.0220.0010.023
summary.bum0.2480.0020.249
writeHeinz1.0910.0581.149
writeHeinzEdges2.7630.0972.863
writeHeinzNodes1.6900.0701.763