Marcus Dittrich
| Snapshot Date: 2025-11-03 13:40 -0500 (Mon, 03 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BioNet |
| git_branch: devel |
| git_last_commit: 9742714 |
| git_last_commit_date: 2025-10-29 10:05:29 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-04 11:32 -0500 (Tue, 04 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4788 |
| 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 217/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNet 1.71.0 (landing page) Marcus Dittrich
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
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. |
| Package: BioNet |
| Version: 1.71.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BioNet.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BioNet_1.71.0.tar.gz |
| StartedAt: 2025-11-03 21:18:18 -0500 (Mon, 03 Nov 2025) |
| EndedAt: 2025-11-03 21:21:39 -0500 (Mon, 03 Nov 2025) |
| EllapsedTime: 201.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioNet.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BioNet.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BioNet_1.71.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BioNet.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BioNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNet’ version ‘1.71.0’
* 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 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 loading without being on the library search path ... 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’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runFastHeinz 20.226 0.074 20.302
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/BioNet.Rcheck/00check.log’
for details.
BioNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BioNet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BioNet’ ... ** this is package ‘BioNet’ version ‘1.71.0’ ** 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)
BioNet.Rcheck/BioNet-Ex.timings
| name | user | system | elapsed | |
| aggrPvals | 0.481 | 0.087 | 0.567 | |
| bumOptim | 0.166 | 0.018 | 0.184 | |
| compareNetworks | 0.976 | 0.012 | 0.989 | |
| consensusScores | 0.231 | 0.019 | 0.253 | |
| fbum | 0 | 0 | 0 | |
| fbumLL | 0.190 | 0.005 | 0.195 | |
| fdrThreshold | 0.167 | 0.004 | 0.172 | |
| fitBumModel | 0.538 | 0.052 | 0.591 | |
| getCompScores | 1.226 | 0.045 | 1.271 | |
| getEdgeList | 0.447 | 0.012 | 0.459 | |
| hist.bum | 0.556 | 0.002 | 0.558 | |
| largestComp | 1.066 | 0.001 | 1.067 | |
| largestScoreComp | 3.412 | 0.020 | 3.433 | |
| loadNetwork.sif | 0 | 0 | 0 | |
| makeNetwork | 0.008 | 0.000 | 0.010 | |
| mapByVar | 0.000 | 0.001 | 0.000 | |
| permutateNodes | 4.083 | 0.084 | 4.167 | |
| piUpper | 0.181 | 0.000 | 0.181 | |
| plot.bum | 0.551 | 0.004 | 0.555 | |
| plot3dModule | 1.581 | 0.008 | 1.589 | |
| plotLLSurface | 0.190 | 0.005 | 0.195 | |
| plotModule | 1.541 | 0.029 | 1.570 | |
| print.bum | 0.175 | 0.000 | 0.175 | |
| pvaluesExample | 0.006 | 0.001 | 0.006 | |
| readHeinzGraph | 0.258 | 0.001 | 0.259 | |
| readHeinzTree | 0.238 | 0.002 | 0.240 | |
| resamplingPvalues | 2.609 | 0.134 | 2.743 | |
| rmSelfLoops | 0.028 | 0.002 | 0.030 | |
| runFastHeinz | 20.226 | 0.074 | 20.302 | |
| save3dModule | 1.129 | 0.057 | 1.186 | |
| saveNetwork | 0.802 | 0.006 | 0.808 | |
| scanFDR | 0.190 | 0.006 | 0.196 | |
| scoreFunction | 0.211 | 0.083 | 0.294 | |
| scoreNodes | 1.578 | 0.036 | 1.614 | |
| scoreOffset | 0.191 | 0.000 | 0.192 | |
| sortedEdgeList | 1.954 | 0.030 | 1.984 | |
| subNetwork | 0.103 | 0.002 | 0.104 | |
| summary.bum | 0.190 | 0.001 | 0.191 | |
| writeHeinz | 1.286 | 0.003 | 1.289 | |
| writeHeinzEdges | 2.478 | 0.011 | 2.489 | |
| writeHeinzNodes | 1.818 | 0.079 | 1.898 | |