Marcus Dittrich
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/BioNet |
| git_branch: master |
| git_last_commit: 79979a9 |
| git_last_commit_date: 2021-10-26 11:56:40 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:03 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 186/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNet 1.55.0 (landing page) Marcus Dittrich
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BioNet |
| Version: 1.55.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNet.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioNet_1.55.0.tar.gz |
| StartedAt: 2022-03-17 18:34:24 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:36:35 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 131.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioNet.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNet.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioNet_1.55.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BioNet.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNet' version '1.55.0'
* 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 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runFastHeinz 8.27 0.39 8.66
* 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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/BioNet.Rcheck/00check.log'
for details.
BioNet.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BioNet
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BioNet' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BioNet'
finding HTML links ... done
BioNet-package html
aggrPvals html
bumOptim html
compareNetworks html
consensusScores html
fbum html
fbumLL html
fdrThreshold html
fitBumModel html
getCompScores html
getEdgeList html
hist.bum html
largestComp html
largestScoreComp html
loadNetwork.sif html
loadNetwork.tab html
makeNetwork html
mapByVar html
permutateNodes html
piUpper html
plot.bum html
plot3dModule html
plotLLSurface html
plotModule html
print.bum html
pvaluesExample html
readHeinzGraph html
readHeinzTree html
resamplingPvalues html
rmSelfLoops html
runFastHeinz html
runHeinz html
save3dModule html
saveNetwork html
scanFDR html
scoreFunction html
scoreNodes html
scoreOffset html
sortedEdgeList html
subNetwork html
summary.bum html
writeHeinz html
writeHeinzEdges html
writeHeinzNodes html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'goTools' is missing or broken
done
BioNet.Rcheck/BioNet-Ex.timings
| name | user | system | elapsed | |
| aggrPvals | 0.25 | 0.06 | 0.31 | |
| bumOptim | 0.57 | 0.01 | 0.58 | |
| compareNetworks | 0.59 | 0.02 | 0.61 | |
| consensusScores | 0.16 | 0.00 | 0.16 | |
| fbum | 0 | 0 | 0 | |
| fbumLL | 0.50 | 0.03 | 0.53 | |
| fdrThreshold | 0.55 | 0.00 | 0.54 | |
| fitBumModel | 0.76 | 0.09 | 0.86 | |
| getCompScores | 0.89 | 0.06 | 0.96 | |
| getEdgeList | 0.33 | 0.00 | 0.32 | |
| hist.bum | 0.86 | 0.00 | 0.86 | |
| largestComp | 0.75 | 0.06 | 0.81 | |
| largestScoreComp | 2.31 | 0.83 | 3.14 | |
| loadNetwork.sif | 0 | 0 | 0 | |
| makeNetwork | 0.02 | 0.00 | 0.02 | |
| mapByVar | 0 | 0 | 0 | |
| permutateNodes | 3.14 | 0.09 | 3.23 | |
| piUpper | 0.52 | 0.02 | 0.53 | |
| plot.bum | 0.79 | 0.00 | 0.93 | |
| plot3dModule | 1.19 | 0.01 | 1.20 | |
| plotLLSurface | 0.45 | 0.02 | 0.47 | |
| plotModule | 1.10 | 0.00 | 1.09 | |
| print.bum | 0.54 | 0.00 | 0.54 | |
| pvaluesExample | 0 | 0 | 0 | |
| readHeinzGraph | 0.16 | 0.02 | 0.18 | |
| readHeinzTree | 0.17 | 0.00 | 0.17 | |
| resamplingPvalues | 2.58 | 0.23 | 2.81 | |
| rmSelfLoops | 0.03 | 0.00 | 0.03 | |
| runFastHeinz | 8.27 | 0.39 | 8.66 | |
| save3dModule | 0.79 | 0.09 | 0.89 | |
| saveNetwork | 0.47 | 0.07 | 0.54 | |
| scanFDR | 0.55 | 0.00 | 0.54 | |
| scoreFunction | 0.56 | 0.00 | 0.56 | |
| scoreNodes | 1.22 | 0.06 | 1.28 | |
| scoreOffset | 0.56 | 0.00 | 0.56 | |
| sortedEdgeList | 1.53 | 0.03 | 1.57 | |
| subNetwork | 0.01 | 0.00 | 0.02 | |
| summary.bum | 0.52 | 0.00 | 0.51 | |
| writeHeinz | 0.75 | 0.17 | 0.92 | |
| writeHeinzEdges | 1.53 | 0.13 | 1.66 | |
| writeHeinzNodes | 1.05 | 0.12 | 1.17 | |