Back to Multiple platform build/check report for BioC 3.18:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-27 11:37:25 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 213/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNet 1.62.0  (landing page)
Marcus Dittrich
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/BioNet
git_branch: RELEASE_3_18
git_last_commit: 760e83d
git_last_commit_date: 2023-10-24 09:44:29 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for BioNet on merida1


To the developers/maintainers of the BioNet package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BioNet
Version: 1.62.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNet_1.62.0.tar.gz
StartedAt: 2024-03-25 23:48:32 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 23:53:44 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 312.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNet_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/BioNet.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNet’ version ‘1.62.0’
* 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 ... 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 ... NOTE
checkRd: (-1) writeHeinz.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) writeHeinzEdges.Rd:23: Escaped LaTeX specials: \$
* 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      35.847  0.787  40.367
permutateNodes     7.915  0.474   8.902
largestScoreComp   6.715  0.483   7.644
sortedEdgeList     6.008  0.067   6.374
resamplingPvalues  5.668  0.246   6.067
* 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-3.18-bioc/meat/BioNet.Rcheck/00check.log’
for details.



Installation output

BioNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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
aggrPvals1.1200.2551.508
bumOptim0.3930.0180.425
compareNetworks1.4340.0601.613
consensusScores0.4730.0230.504
fbum0.0000.0010.000
fbumLL0.4120.0170.439
fdrThreshold0.3940.0120.421
fitBumModel1.5450.1601.743
getCompScores2.9570.1913.348
getEdgeList0.8330.0220.910
hist.bum0.8340.0460.914
largestComp1.8190.0421.963
largestScoreComp6.7150.4837.644
loadNetwork.sif0.0010.0010.001
makeNetwork0.0160.0010.047
mapByVar0.0000.0010.001
permutateNodes7.9150.4748.902
piUpper0.3780.0040.396
plot.bum1.4650.0201.585
plot3dModule2.5990.1062.862
plotLLSurface0.4370.0170.484
plotModule2.6590.0852.870
print.bum0.4150.0160.434
pvaluesExample0.0110.0030.015
readHeinzGraph0.5000.0090.519
readHeinzTree0.4830.0080.495
resamplingPvalues5.6680.2466.067
rmSelfLoops0.0690.0020.077
runFastHeinz35.847 0.78740.367
save3dModule1.5630.0741.699
saveNetwork1.4890.0371.556
scanFDR0.3860.0110.453
scoreFunction0.5160.2450.767
scoreNodes2.4580.1632.680
scoreOffset0.3770.0050.403
sortedEdgeList6.0080.0676.374
subNetwork0.1330.0030.137
summary.bum0.3770.0040.384
writeHeinz1.5810.0621.671
writeHeinzEdges3.5090.1383.897
writeHeinzNodes2.1850.0832.604