Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:15 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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? 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 188/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNet 1.54.0  (landing page)
Marcus Dittrich
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/BioNet
git_branch: RELEASE_3_14
git_last_commit: 09b4d2f
git_last_commit_date: 2021-10-26 11:56:40 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.54.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioNet_1.54.0.tar.gz
StartedAt: 2022-04-12 16:25:40 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:29:42 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 241.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioNet_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BioNet.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.54.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
runFastHeinz 10.28   0.06   10.35
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
runFastHeinz 11.2      0    11.2
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/BioNet.Rcheck/00check.log'
for details.



Installation output

BioNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BioNet_1.54.0.tar.gz && rm -rf BioNet.buildbin-libdir && mkdir BioNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioNet.buildbin-libdir BioNet_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BioNet_1.54.0.zip && rm BioNet_1.54.0.tar.gz BioNet_1.54.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 41 1016k   41  417k    0     0   796k      0  0:00:01 --:--:--  0:00:01  797k
100 1016k  100 1016k    0     0  1049k      0 --:--:-- --:--:-- --:--:-- 1049k

install for i386

* 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

install for x64

* installing *source* package 'BioNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioNet' as BioNet_1.54.0.zip
* DONE (BioNet)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BioNet' successfully unpacked and MD5 sums checked

Tests output


Example timings

BioNet.Rcheck/examples_i386/BioNet-Ex.timings

nameusersystemelapsed
aggrPvals0.380.010.39
bumOptim0.470.060.53
compareNetworks0.840.001.45
consensusScores0.270.020.28
fbum000
fbumLL0.790.020.82
fdrThreshold0.430.010.43
fitBumModel0.790.010.81
getCompScores1.520.111.80
getEdgeList0.440.020.45
hist.bum0.540.040.60
largestComp1.000.021.01
largestScoreComp3.130.023.14
loadNetwork.sif000
makeNetwork000
mapByVar000
permutateNodes3.210.003.20
piUpper0.480.000.49
plot.bum0.940.000.93
plot3dModule1.360.011.38
plotLLSurface0.510.000.51
plotModule1.330.001.33
print.bum0.530.000.53
pvaluesExample0.010.000.01
readHeinzGraph0.280.000.29
readHeinzTree0.270.000.26
resamplingPvalues3.830.033.86
rmSelfLoops0.030.000.03
runFastHeinz10.28 0.0610.35
save3dModule0.780.070.84
saveNetwork0.580.000.58
scanFDR0.480.000.48
scoreFunction0.470.040.52
scoreNodes1.430.081.50
scoreOffset0.450.000.45
sortedEdgeList2.120.002.13
subNetwork0.050.020.06
summary.bum0.720.000.72
writeHeinz1.000.041.04
writeHeinzEdges1.800.051.85
writeHeinzNodes1.200.051.25

BioNet.Rcheck/examples_x64/BioNet-Ex.timings

nameusersystemelapsed
aggrPvals0.380.060.44
bumOptim0.730.060.79
compareNetworks0.800.020.82
consensusScores0.40.00.4
fbum000
fbumLL0.910.030.94
fdrThreshold0.830.000.83
fitBumModel1.120.051.19
getCompScores1.570.061.62
getEdgeList0.420.020.43
hist.bum1.050.001.05
largestComp0.840.010.86
largestScoreComp3.190.003.19
loadNetwork.sif000
makeNetwork000
mapByVar000
permutateNodes3.750.023.76
piUpper0.80.00.8
plot.bum1.30.01.3
plot3dModule1.730.011.75
plotLLSurface0.660.020.67
plotModule1.290.011.31
print.bum0.770.000.77
pvaluesExample000
readHeinzGraph0.230.000.23
readHeinzTree0.240.000.24
resamplingPvalues3.360.033.39
rmSelfLoops0.030.000.03
runFastHeinz11.2 0.011.2
save3dModule0.810.080.89
saveNetwork0.630.000.63
scanFDR0.720.000.72
scoreFunction0.80.00.8
scoreNodes1.530.021.54
scoreOffset0.740.000.74
sortedEdgeList2.370.002.37
subNetwork0.020.000.02
summary.bum0.760.000.76
writeHeinz1.350.011.36
writeHeinzEdges1.620.021.64
writeHeinzNodes1.050.001.05