BioNet 1.29.0
Marcus Dittrich
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BioNet | | Last Changed Rev: 102594 / Revision: 107602 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ ERROR ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | ERROR | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### rm -rf BioNet.buildbin-libdir BioNet.Rcheck && mkdir BioNet.buildbin-libdir BioNet.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioNet.buildbin-libdir BioNet_1.29.0.tar.gz >BioNet.Rcheck\00install.out 2>&1 && cp BioNet.Rcheck\00install.out BioNet-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BioNet.buildbin-libdir --install="check:BioNet-install.out" --force-multiarch --no-vignettes --timings BioNet_1.29.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/BioNet.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.29.0'
* 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
'library' or 'require' calls in package code:
'XML' 'genefilter' 'rgl'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'Biobase' '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.destription: no visible global function definition for 'xmlNode'
.XGMML.destription: no visible global function definition for
'append.xmlNode'
.XGMML.edges: no visible binding for global variable 'xmlNode'
.XGMML.edges: no visible global function definition for 'addAttributes'
.XGMML.edges: no visible global function definition for
'append.xmlNode'
.XGMML.nodes: no visible binding for global variable 'xmlNode'
.XGMML.nodes: no visible global function definition for 'addAttributes'
.XGMML.nodes: no visible global function definition for
'append.xmlNode'
.affyID2ppiID: no visible global function definition for 'annotation'
.affyID2ppiID: no visible global function definition for 'featureNames'
.affyID2ppiID: no visible global function definition for 'nodeData'
.saveGraph.net: no visible global function definition for 'nodes'
.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 '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 'subGraph'
.subNetwork0: no visible global function definition for 'nodes'
.subNetwork1: no visible global function definition for 'adj'
.subNetwork1: no visible global function definition for 'subGraph'
.subNetwork1: no visible global function definition for 'nodes'
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'
getCompScores: no visible global function definition for 'connComp'
getCompScores: no visible global function definition for 'listLen'
getEdgeList: no visible global function definition for 'edgeMatrix'
getEdgeList: no visible global function definition for 'nodes'
largestComp: no visible global function definition for 'connectedComp'
largestComp: no visible global function definition for 'listLen'
largestComp: no visible global function definition for 'subGraph'
largestScoreComp: no visible global function definition for 'nodes'
largestScoreComp: no visible global function definition for 'subGraph'
loadNetwork.tab: no visible global function definition for 'addEdge'
makeNetwork: no visible global function definition for 'addEdge'
mapByVar: no visible global function definition for 'exprs'
permutateNodes: no visible global function definition for 'nodes<-'
permutateNodes: no visible global function definition for 'nodes'
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'
readHeinzTree: no visible global function definition for 'edgeNames'
readHeinzTree: no visible global function definition for 'removeEdge'
resamplingPvalues: no visible global function definition for
'rowttests'
rmSelfLoops: no visible global function definition for 'edgeNames'
rmSelfLoops: no visible global function definition for 'numEdges'
rmSelfLoops: no visible global function definition for 'removeEdge'
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 'append.xmlNode'
saveNetwork: no visible global function definition for 'saveXML'
scoreNodes: no visible global function definition for 'nodes'
sortedEdgeList: no visible global function definition for 'isDirected'
* 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' ... ERROR
Running examples in 'BioNet-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runFastHeinz
> ### Title: Calculate heuristically maximum scoring subnetwork
> ### Aliases: runFastHeinz
>
> ### ** Examples
>
> library(DLBCL)
> # load p-values
> data(dataLym)
> # load graph
> data(interactome)
> # get induced subnetwork for all genes contained on the chip
> interactome <- subNetwork(dataLym$label, interactome)
> p.values <- dataLym$t.pval
> names(p.values) <- dataLym$label
> bum <- fitBumModel(p.values, plot=TRUE)
> scores <- scoreNodes(network=interactome, fb=bum, fdr=0.0001)
> module <- runFastHeinz(network=interactome, scores=scores)
Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
Calls: runFastHeinz ... [ -> [.igraph.vs -> lapply -> FUN -> simple_vs_index
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'BioNet-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runFastHeinz
> ### Title: Calculate heuristically maximum scoring subnetwork
> ### Aliases: runFastHeinz
>
> ### ** Examples
>
> library(DLBCL)
> # load p-values
> data(dataLym)
> # load graph
> data(interactome)
> # get induced subnetwork for all genes contained on the chip
> interactome <- subNetwork(dataLym$label, interactome)
> p.values <- dataLym$t.pval
> names(p.values) <- dataLym$label
> bum <- fitBumModel(p.values, plot=TRUE)
> scores <- scoreNodes(network=interactome, fb=bum, fdr=0.0001)
> module <- runFastHeinz(network=interactome, scores=scores)
Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
Calls: runFastHeinz ... [ -> [.igraph.vs -> lapply -> FUN -> simple_vs_index
Execution halted
* 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 ERRORs, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/BioNet.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'BioNet' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'BioNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioNet' as BioNet_1.29.0.zip
* DONE (BioNet)