Multiple platform build/check report for BioC 3.20 - CHECK results for BioNet on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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*

CHECK results for BioNet on kjohnson3

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: 1.66.0

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_1.66.0.tar.gz

StartedAt: 2024-11-08 21:30:39 -0500 (Fri, 08 Nov 2024)

EndedAt: 2024-11-08 21:35:14 -0500 (Fri, 08 Nov 2024)

EllapsedTime: 274.6 seconds

RetCode: 0

Status: OK

CheckDir: BioNet.Rcheck

Warnings: 0

Command output

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### 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_1.66.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BioNet.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNet’ version ‘1.66.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 5.067  0.259   5.325
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/BioNet.Rcheck/00check.log’
for details.

Installation output

BioNet.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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

name	user	system	elapsed
aggrPvals	0.117	0.022	0.139
bumOptim	0.098	0.006	0.105
compareNetworks	0.323	0.011	0.335
consensusScores	0.087	0.003	0.090
fbum	0	0	0
fbumLL	0.068	0.007	0.074
fdrThreshold	0.064	0.004	0.068
fitBumModel	0.180	0.015	0.195
getCompScores	0.434	0.033	0.467
getEdgeList	0.163	0.003	0.166
hist.bum	0.216	0.014	0.231
largestComp	0.323	0.016	0.338
largestScoreComp	1.158	0.188	1.345
loadNetwork.sif	0	0	0
makeNetwork	0.004	0.000	0.004
mapByVar	0	0	0
permutateNodes	1.346	0.184	1.529
piUpper	0.084	0.003	0.088
plot.bum	0.202	0.006	0.207
plot3dModule	0.700	0.057	0.756
plotLLSurface	0.068	0.003	0.071
plotModule	0.524	0.047	0.570
print.bum	0.066	0.005	0.071
pvaluesExample	0.003	0.001	0.003
readHeinzGraph	0.087	0.001	0.089
readHeinzTree	0.089	0.002	0.091
resamplingPvalues	1.183	0.039	1.222
rmSelfLoops	0.009	0.002	0.010
runFastHeinz	5.067	0.259	5.325
save3dModule	0.365	0.037	0.402
saveNetwork	0.261	0.012	0.273
scanFDR	0.060	0.004	0.064
scoreFunction	0.082	0.027	0.109
scoreNodes	0.447	0.048	0.494
scoreOffset	0.075	0.003	0.078
sortedEdgeList	0.675	0.008	0.683
subNetwork	0.019	0.001	0.020
summary.bum	0.059	0.003	0.063
writeHeinz	0.423	0.043	0.466
writeHeinzEdges	0.707	0.060	0.767
writeHeinzNodes	0.481	0.015	0.496