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BioC 3.4: CHECK report for BioNet on moscato1

This page was generated on 2016-09-21 03:43:07 -0700 (Wed, 21 Sep 2016).

Package 121/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNet 1.33.0
Marcus Dittrich
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BioNet
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BioNet
Version: 1.33.0
Command: rm -rf BioNet.buildbin-libdir BioNet.Rcheck && mkdir BioNet.buildbin-libdir BioNet.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioNet.buildbin-libdir BioNet_1.33.0.tar.gz >BioNet.Rcheck\00install.out 2>&1 && cp BioNet.Rcheck\00install.out BioNet-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BioNet.buildbin-libdir --install="check:BioNet-install.out" --force-multiarch --no-vignettes --timings BioNet_1.33.0.tar.gz
StartedAt: 2016-09-20 04:46:16 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:50:58 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 282.2 seconds
RetCode: 0
Status:  OK  
CheckDir: BioNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BioNet.buildbin-libdir BioNet.Rcheck && mkdir BioNet.buildbin-libdir BioNet.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioNet.buildbin-libdir BioNet_1.33.0.tar.gz >BioNet.Rcheck\00install.out 2>&1 && cp BioNet.Rcheck\00install.out BioNet-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BioNet.buildbin-libdir --install="check:BioNet-install.out" --force-multiarch --no-vignettes --timings BioNet_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/BioNet.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.33.0'
* 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 '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     28.61   0.06   28.68
largestScoreComp  4.98   0.03    5.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
runFastHeinz     31.81   0.08   31.98
largestScoreComp  6.13   0.00    6.13
permutateNodes    5.56   0.03    5.59
* 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:/biocbld/bbs-3.4-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
** 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_1.33.0.zip
* DONE (BioNet)

BioNet.Rcheck/examples_i386/BioNet-Ex.timings:

nameusersystemelapsed
aggrPvals0.220.020.23
bumOptim0.570.010.59
compareNetworks0.770.003.16
consensusScores0.290.000.31
fbum000
fbumLL0.710.001.76
fdrThreshold0.560.000.56
fitBumModel1.250.001.25
getCompScores1.570.022.26
getEdgeList0.70.00.7
hist.bum0.740.000.74
largestComp1.480.001.48
largestScoreComp4.980.035.00
loadNetwork.sif000
makeNetwork000
mapByVar0.020.000.02
permutateNodes4.990.004.99
piUpper0.590.000.60
plot.bum1.330.001.32
plot3dModule2.660.002.67
plotLLSurface0.830.000.84
plotModule1.870.031.91
print.bum0.600.000.59
pvaluesExample0.000.020.01
readHeinzGraph0.310.010.33
readHeinzTree0.290.020.31
resamplingPvalues3.740.033.77
rmSelfLoops000
runFastHeinz28.61 0.0628.68
save3dModule1.360.021.37
saveNetwork1.230.001.23
scanFDR0.580.000.58
scoreFunction0.640.010.65
scoreNodes2.150.032.19
scoreOffset0.580.000.58
sortedEdgeList2.440.002.43
subNetwork0.030.000.03
summary.bum0.570.000.58
writeHeinz1.360.001.36
writeHeinzEdges2.720.022.73
writeHeinzNodes1.790.011.80

BioNet.Rcheck/examples_x64/BioNet-Ex.timings:

nameusersystemelapsed
aggrPvals0.270.020.28
bumOptim0.890.000.89
compareNetworks0.890.001.46
consensusScores0.330.000.33
fbum000
fbumLL1.060.001.06
fdrThreshold0.910.000.91
fitBumModel1.790.001.79
getCompScores1.730.011.75
getEdgeList0.750.000.75
hist.bum1.010.001.01
largestComp1.910.021.92
largestScoreComp6.130.006.13
loadNetwork.sif000
makeNetwork0.010.000.01
mapByVar000
permutateNodes5.560.035.59
piUpper1.110.001.11
plot.bum2.060.002.06
plot3dModule2.070.022.09
plotLLSurface0.770.030.80
plotModule2.200.012.21
print.bum0.860.020.88
pvaluesExample000
readHeinzGraph0.280.000.28
readHeinzTree0.30.00.3
resamplingPvalues4.040.004.04
rmSelfLoops000
runFastHeinz31.81 0.0831.98
save3dModule1.460.001.47
saveNetwork1.330.001.32
scanFDR0.870.030.91
scoreFunction0.940.010.95
scoreNodes2.360.022.37
scoreOffset0.880.000.88
sortedEdgeList3.020.003.02
subNetwork0.060.000.06
summary.bum0.870.000.87
writeHeinz1.470.041.50
writeHeinzEdges2.860.002.86
writeHeinzNodes1.950.001.95