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BioC 3.5: CHECK report for CausalR on malbec2

This page was generated on 2017-08-16 13:16:43 -0400 (Wed, 16 Aug 2017).

Package 178/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CausalR 1.8.0
Glyn Bradley , Steven Barrett
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CausalR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CausalR
Version: 1.8.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CausalR_1.8.0.tar.gz
StartedAt: 2017-08-15 21:44:24 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:45:01 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 36.5 seconds
RetCode: 0
Status:  OK 
CheckDir: CausalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CausalR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CausalR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CausalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CausalR’ version ‘1.8.0’
* 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 ‘CausalR’ 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
* 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 loading without being on the library search path ... OK
* checking 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/CausalR.Rcheck/00check.log’
for details.


CausalR.Rcheck/00install.out:

* installing *source* package ‘CausalR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CausalR)

CausalR.Rcheck/CausalR-Ex.timings:

nameusersystemelapsed
AnalysePredictionsList0.1160.0000.118
CalculateEnrichmentPValue0.0040.0000.002
CalculateSignificance0.2920.0040.296
CalculateSignificanceUsingCubicAlgorithm0.0600.0000.061
CalculateSignificanceUsingCubicAlgorithm1b0.0400.0000.039
CalculateSignificanceUsingQuarticAlgorithm0.0440.0000.043
CompareHypothesis0.0080.0000.007
CreateCCG0.0760.0000.074
CreateCG0.0360.0000.035
GetNodeName0.0080.0000.007
GetNumberOfPositiveAndNegativeEntries0.0000.0000.001
GetShortestPathsFromCCG0.0120.0000.009
MakePredictions0.0680.0000.069
MakePredictionsFromCCG0.0080.0000.007
MakePredictionsFromCG0.260.000.26
PlotGraphWithNodeNames0.0720.0040.298
RankTheHypotheses0.3560.0200.376
ReadExperimentalData0.0400.0040.044
ScoreHypothesis0.0360.0000.035
WriteAllExplainedNodesToSifFile0.2480.0200.245
WriteExplainedNodesToSifFile0.0360.0000.040
runSCANR0.4400.0280.426