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BioC 3.6: CHECK report for CausalR on veracruz1

This page was generated on 2017-08-16 13:47:13 -0400 (Wed, 16 Aug 2017).

Package 179/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CausalR 1.9.0
Glyn Bradley , Steven Barrett
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CausalR
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CausalR_1.9.0.tar.gz
StartedAt: 2017-08-16 00:48:35 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:49:14 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 38.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CausalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CausalR_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CausalR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.6-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
AnalysePredictionsList0.1150.0040.121
CalculateEnrichmentPValue0.0020.0000.002
CalculateSignificance0.3160.0040.331
CalculateSignificanceUsingCubicAlgorithm0.0630.0010.064
CalculateSignificanceUsingCubicAlgorithm1b0.0560.0010.057
CalculateSignificanceUsingQuarticAlgorithm0.0560.0000.060
CompareHypothesis0.0070.0000.007
CreateCCG0.0770.0010.081
CreateCG0.0370.0000.039
GetNodeName0.0060.0000.006
GetNumberOfPositiveAndNegativeEntries0.0020.0000.002
GetShortestPathsFromCCG0.0140.0010.014
MakePredictions0.0720.0000.074
MakePredictionsFromCCG0.0060.0000.006
MakePredictionsFromCG0.2960.0010.300
PlotGraphWithNodeNames0.0600.0020.061
RankTheHypotheses0.2390.0210.268
ReadExperimentalData0.0450.0040.050
ScoreHypothesis0.0490.0010.050
WriteAllExplainedNodesToSifFile0.2830.0810.313
WriteExplainedNodesToSifFile0.0590.0010.064
runSCANR0.5460.0740.609