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BioC 2.12: CHECK report for BioNet on petty

This page was generated on 2013-10-09 09:39:53 -0700 (Wed, 09 Oct 2013).

Package 79/671HostnameOS / ArchBUILDCHECKBUILD BIN
BioNet 1.18.0
Marcus Dittrich
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/BioNet
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: BioNet
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.18.0.tar.gz
StartedAt: 2013-10-08 21:44:44 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:50:05 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 320.5 seconds
RetCode: 0
Status:  OK 
CheckDir: BioNet.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BioNet.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BioNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNet' version '1.18.0'
* 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 ... [16s/16s] OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.7Mb
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 examples ... [148s/152s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    17.968  1.450  20.185
largestScoreComp  14.847  1.361  16.588
runFastHeinz      13.336  0.631  14.036
resamplingPvalues  9.903  0.349  10.298
sortedEdgeList     6.869  0.066   6.990
writeHeinzEdges    6.409  0.416   6.880
largestComp        5.903  0.065   6.238
plot3dModule       4.781  0.171   5.077
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/BioNet.Rcheck/00check.log'
for details.

BioNet.Rcheck/00install.out:

* 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
* DONE (BioNet)

BioNet.Rcheck/BioNet-Ex.timings:

nameusersystemelapsed
aggrPvals0.9480.0791.099
bumOptim1.4150.0791.618
compareNetworks2.4300.0362.691
consensusScores0.9500.0121.020
fbum0.0150.0020.019
fbumLL1.3320.0431.486
fdrThreshold1.2350.0321.347
fitBumModel1.7560.0421.960
getCompScores4.2650.0794.725
getEdgeList1.9750.0372.200
hist.bum1.5470.0611.685
largestComp5.9030.0656.238
largestScoreComp14.847 1.36116.588
loadNetwork.sif0.0390.0030.042
makeNetwork0.0600.0030.063
mapByVar0.0210.0030.025
permutateNodes17.968 1.45020.185
piUpper1.1910.0871.326
plot.bum1.9820.0842.171
plot3dModule4.7810.1715.077
plotLLSurface1.4210.0311.564
plotModule4.3980.2134.777
print.bum1.1530.0731.238
pvaluesExample0.0140.0050.020
readHeinzGraph0.5220.0110.534
readHeinzTree0.5900.0120.611
resamplingPvalues 9.903 0.34910.298
rmSelfLoops0.0300.0150.045
runFastHeinz13.336 0.63114.036
save3dModule2.7370.2933.046
saveNetwork2.1350.0762.223
scanFDR1.2620.1321.397
scoreFunction1.7530.1851.941
scoreNodes4.0310.4764.569
scoreOffset1.0480.1411.202
sortedEdgeList6.8690.0666.990
subNetwork0.1210.0190.140
summary.bum1.3330.1501.499
writeHeinz3.9240.2304.220
writeHeinzEdges6.4090.4166.880
writeHeinzNodes4.1210.2724.414