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BioC 3.1: CHECK report for BioNet on petty

This page was generated on 2015-10-09 09:34:11 -0700 (Fri, 09 Oct 2015).

Package 102/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNet 1.29.1
Marcus Dittrich
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BioNet
Last Changed Rev: 108433 / Revision: 109384
Last Changed Date: 2015-09-11 08:19:39 -0700 (Fri, 11 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.29.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioNet_1.29.1.tar.gz
StartedAt: 2015-10-08 21:42:50 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 21:47:27 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 277.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BioNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioNet_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/BioNet.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.29.1’
* 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 ... [12s/12s] 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:
  ‘graph’ ‘RBGL’
  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
.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’
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 ‘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’
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’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [149s/150s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runFastHeinz      49.577  0.372  50.015
largestScoreComp  10.704  1.099  11.823
permutateNodes    10.217  1.064  11.281
sortedEdgeList     8.673  0.038   8.720
resamplingPvalues  6.751  0.233   6.994
writeHeinzEdges    5.204  0.262   5.473
* 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-3.1-bioc/meat/BioNet.Rcheck/00check.log’
for details.


BioNet.Rcheck/00install.out:

* installing *source* package ‘BioNet’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (BioNet)

BioNet.Rcheck/BioNet-Ex.timings:

nameusersystemelapsed
aggrPvals0.7700.0810.860
bumOptim0.6950.0080.704
compareNetworks1.6890.0361.804
consensusScores0.6710.0130.684
fbum0.0010.0000.001
fbumLL0.7610.0110.772
fdrThreshold0.7630.0020.766
fitBumModel2.2470.0262.278
getCompScores2.7940.0432.857
getEdgeList1.0040.0161.022
hist.bum1.0550.0261.086
largestComp2.5480.0242.573
largestScoreComp10.704 1.09911.823
loadNetwork.sif0.0010.0000.002
makeNetwork0.0170.0000.016
mapByVar0.0010.0010.001
permutateNodes10.217 1.06411.281
piUpper1.0250.0141.041
plot.bum2.1450.0302.179
plot3dModule4.5360.0274.571
plotLLSurface0.9360.0070.945
plotModule3.5990.0133.614
print.bum0.6660.0010.666
pvaluesExample0.0130.0010.014
readHeinzGraph0.6810.0060.688
readHeinzTree0.6530.0050.659
resamplingPvalues6.7510.2336.994
rmSelfLoops0.0090.0010.009
runFastHeinz49.577 0.37250.015
save3dModule2.5190.0932.614
saveNetwork2.4280.0592.487
scanFDR0.8540.0410.895
scoreFunction0.8580.0900.950
scoreNodes4.1400.2384.381
scoreOffset0.7320.0100.743
sortedEdgeList8.6730.0388.720
subNetwork0.1060.0010.108
summary.bum0.6600.0020.662
writeHeinz3.0850.0153.109
writeHeinzEdges5.2040.2625.473
writeHeinzNodes3.0890.0873.178