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BioC 2.14: CHECK report for BioNet on zin2

This page was generated on 2014-10-08 08:48:51 -0700 (Wed, 08 Oct 2014).

Package 96/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNet 1.24.1
Marcus Dittrich
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/BioNet
Last Changed Rev: 93165 / Revision: 95116
Last Changed Date: 2014-08-04 04:58:58 -0700 (Mon, 04 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: BioNet
Version: 1.24.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.24.1.tar.gz
StartedAt: 2014-10-07 22:06:28 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:08:51 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 143.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BioNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/BioNet.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.24.1’
* 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 ... [8s/8s] 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:
  ‘Biobase’ ‘RBGL’ ‘graph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [65s/65s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runFastHeinz     10.393  0.012  10.499
permutateNodes    6.160  0.004   6.179
largestScoreComp  6.061  0.012   6.080
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-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
aggrPvals0.5880.0440.633
bumOptim0.5840.0080.593
compareNetworks1.1480.0121.186
consensusScores0.2440.0000.244
fbum0.0000.0000.001
fbumLL0.5440.0080.599
fdrThreshold0.5480.0040.553
fitBumModel1.4600.0001.464
getCompScores1.5840.0161.600
getEdgeList0.6520.0080.661
hist.bum0.7280.0000.760
largestComp1.6600.0081.671
largestScoreComp6.0610.0126.080
loadNetwork.sif0.0040.0000.001
makeNetwork0.0080.0000.009
mapByVar0.0000.0000.001
permutateNodes6.1600.0046.179
piUpper0.5560.0000.558
plot.bum1.4040.0001.405
plot3dModule2.0720.0082.113
plotLLSurface0.5760.0040.584
plotModule2.3170.0042.364
print.bum0.6000.0000.626
pvaluesExample0.0080.0000.007
readHeinzGraph0.2640.0000.265
readHeinzTree0.2360.0000.236
resamplingPvalues4.7320.0444.786
rmSelfLoops0.0040.0000.006
runFastHeinz10.393 0.01210.499
save3dModule1.2400.0041.248
saveNetwork0.8320.0000.833
scanFDR0.5520.0000.552
scoreFunction0.6160.0160.631
scoreNodes2.1800.0122.198
scoreOffset0.5760.0000.616
sortedEdgeList3.5360.0003.541
subNetwork0.0280.0040.029
summary.bum0.5240.0000.523
writeHeinz1.3440.0001.346
writeHeinzEdges2.7040.0122.723
writeHeinzNodes1.7770.0081.787