Marcus Dittrich
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/BioNet |
| Branch: RELEASE_3_6 |
| Last Commit: 5353ce7 |
| Last Changed Date: 2017-10-30 12:39:30 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:20:18 -0400 (Thu, 12 Apr 2018).
| Package 138/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BioNet 1.38.0 Marcus Dittrich
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BioNet |
| Version: 1.38.0 |
| Command: rm -rf BioNet.buildbin-libdir BioNet.Rcheck && mkdir BioNet.buildbin-libdir BioNet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioNet.buildbin-libdir BioNet_1.38.0.tar.gz >BioNet.Rcheck\00install.out 2>&1 && cp BioNet.Rcheck\00install.out BioNet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BioNet.buildbin-libdir --install="check:BioNet-install.out" --force-multiarch --no-vignettes --timings BioNet_1.38.0.tar.gz |
| StartedAt: 2018-04-11 22:31:50 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:36:00 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 249.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioNet.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf BioNet.buildbin-libdir BioNet.Rcheck && mkdir BioNet.buildbin-libdir BioNet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioNet.buildbin-libdir BioNet_1.38.0.tar.gz >BioNet.Rcheck\00install.out 2>&1 && cp BioNet.Rcheck\00install.out BioNet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BioNet.buildbin-libdir --install="check:BioNet-install.out" --force-multiarch --no-vignettes --timings BioNet_1.38.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BioNet.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.38.0'
* 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 ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
extdata 3.7Mb
* 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 'plot'
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'
plotModule: no visible global function definition for 'plot'
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 plot 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", "plot", "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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runFastHeinz 14.05 0.09 14.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runFastHeinz 16.33 0.06 16.43
largestScoreComp 5.04 0.04 5.11
* 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
'C:/Users/biocbuild/bbs-3.6-bioc/meat/BioNet.Rcheck/00check.log'
for details.
BioNet.Rcheck/00install.out
install for i386
* installing *source* package 'BioNet' ...
** R
** data
** inst
** preparing 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
In R CMD INSTALL
install for x64
* installing *source* package 'BioNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioNet' as BioNet_1.38.0.zip
* DONE (BioNet)
In R CMD INSTALL
In R CMD INSTALL
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BioNet.Rcheck/examples_i386/BioNet-Ex.timings
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BioNet.Rcheck/examples_x64/BioNet-Ex.timings
|