Marcus Dittrich
| Snapshot Date: 2019-12-12 16:45:55 -0500 (Thu, 12 Dec 2019) |
| URL: https://git.bioconductor.org/packages/BioNet |
| Branch: master |
| Last Commit: 6275a14 |
| Last Changed Date: 2019-10-29 13:35:18 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2019-12-13 12:41:21 -0500 (Fri, 13 Dec 2019).
| Package 171/1808 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BioNet 1.47.0 Marcus Dittrich
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BioNet |
| Version: 1.47.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioNet_1.47.0.tar.gz |
| StartedAt: 2019-12-13 01:28:28 -0500 (Fri, 13 Dec 2019) |
| EndedAt: 2019-12-13 01:32:11 -0500 (Fri, 13 Dec 2019) |
| EllapsedTime: 223.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioNet.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioNet_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BioNet.Rcheck’ * using R Under development (unstable) (2019-11-03 r77362) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioNet’ version ‘1.47.0’ * 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 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 :: 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runFastHeinz 20.018 0.726 20.772 permutateNodes 7.649 1.619 9.268 largestScoreComp 7.366 1.662 11.127 sortedEdgeList 6.080 0.059 6.409 resamplingPvalues 4.855 0.300 5.159 * 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 ‘/Users/biocbuild/bbs-3.11-bioc/meat/BioNet.Rcheck/00check.log’ for details.
BioNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BioNet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘BioNet’ ... ** 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 | 1.040 | 0.259 | 1.352 | |
| bumOptim | 0.385 | 0.039 | 0.503 | |
| compareNetworks | 0.842 | 0.045 | 1.093 | |
| consensusScores | 0.440 | 0.014 | 0.541 | |
| fbum | 0.000 | 0.000 | 0.001 | |
| fbumLL | 0.472 | 0.020 | 0.578 | |
| fdrThreshold | 0.385 | 0.023 | 0.484 | |
| fitBumModel | 1.373 | 0.014 | 1.639 | |
| getCompScores | 3.110 | 0.072 | 3.814 | |
| getEdgeList | 0.806 | 0.021 | 0.979 | |
| hist.bum | 0.614 | 0.037 | 0.787 | |
| largestComp | 2.262 | 0.062 | 2.825 | |
| largestScoreComp | 7.366 | 1.662 | 11.127 | |
| loadNetwork.sif | 0.001 | 0.000 | 0.000 | |
| makeNetwork | 0.014 | 0.001 | 0.015 | |
| mapByVar | 0.000 | 0.001 | 0.001 | |
| permutateNodes | 7.649 | 1.619 | 9.268 | |
| piUpper | 0.330 | 0.021 | 0.352 | |
| plot.bum | 1.348 | 0.027 | 1.375 | |
| plot3dModule | 2.828 | 0.252 | 3.081 | |
| plotLLSurface | 0.421 | 0.022 | 0.445 | |
| plotModule | 2.407 | 0.258 | 2.665 | |
| print.bum | 0.411 | 0.030 | 0.440 | |
| pvaluesExample | 0.010 | 0.003 | 0.013 | |
| readHeinzGraph | 0.431 | 0.009 | 0.441 | |
| readHeinzTree | 0.413 | 0.008 | 0.423 | |
| resamplingPvalues | 4.855 | 0.300 | 5.159 | |
| rmSelfLoops | 0.067 | 0.001 | 0.068 | |
| runFastHeinz | 20.018 | 0.726 | 20.772 | |
| save3dModule | 1.580 | 0.163 | 1.873 | |
| saveNetwork | 1.301 | 0.090 | 1.401 | |
| scanFDR | 0.408 | 0.032 | 0.440 | |
| scoreFunction | 0.554 | 0.157 | 0.723 | |
| scoreNodes | 2.813 | 0.265 | 3.154 | |
| scoreOffset | 0.306 | 0.014 | 0.320 | |
| sortedEdgeList | 6.080 | 0.059 | 6.409 | |
| subNetwork | 0.053 | 0.002 | 0.078 | |
| summary.bum | 0.361 | 0.009 | 0.562 | |
| writeHeinz | 1.495 | 0.096 | 2.062 | |
| writeHeinzEdges | 3.565 | 0.153 | 4.330 | |
| writeHeinzNodes | 1.856 | 0.208 | 2.064 | |