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BioC 2.12: CHECK report for BioNet on george2

This page was generated on 2013-10-09 09:37:39 -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: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.18.0.tar.gz
StartedAt: 2013-10-09 00:28:09 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:33:42 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 333.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BioNet.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/BioNet.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.18.0’
* 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 ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  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 installed files from ‘inst/doc’ ... OK
* checking examples ... [156s/159s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    22.689  0.052  23.413
largestScoreComp  16.425  0.056  16.881
runFastHeinz      13.773  0.048  13.990
resamplingPvalues  9.545  0.096  10.188
largestComp        6.873  0.032   6.905
writeHeinzEdges    6.773  0.004   6.775
sortedEdgeList     6.356  0.004   6.518
plot3dModule       6.081  0.072   6.156
* 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
  ‘/home/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
aggrPvals0.6960.0480.743
bumOptim1.4120.0161.472
compareNetworks3.5720.1123.951
consensusScores0.4760.0040.479
fbum0.0280.0000.027
fbumLL1.5360.0041.540
fdrThreshold1.7130.0001.713
fitBumModel1.5480.0281.574
getCompScores3.5520.0323.620
getEdgeList2.3760.0082.514
hist.bum2.6560.0162.674
largestComp6.8730.0326.905
largestScoreComp16.425 0.05616.881
loadNetwork.sif0.0680.0000.070
makeNetwork0.0880.0000.091
mapByVar0.0400.0000.039
permutateNodes22.689 0.05223.413
piUpper1.5800.0121.593
plot.bum2.4480.0042.459
plot3dModule6.0810.0726.156
plotLLSurface2.3000.0122.649
plotModule4.8080.0004.811
print.bum2.1320.0002.132
pvaluesExample0.0600.0040.066
readHeinzGraph0.5600.0080.565
readHeinzTree1.3080.0001.312
resamplingPvalues 9.545 0.09610.188
rmSelfLoops0.0080.0080.016
runFastHeinz13.773 0.04813.990
save3dModule3.2120.0083.585
saveNetwork1.7720.0081.785
scanFDR1.2120.0001.214
scoreFunction1.2440.0561.299
scoreNodes3.9690.0163.984
scoreOffset1.4880.0001.489
sortedEdgeList6.3560.0046.518
subNetwork0.2400.0040.249
summary.bum1.7360.0001.920
writeHeinz3.4960.0043.555
writeHeinzEdges6.7730.0046.775
writeHeinzNodes3.7640.0003.766