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BioC 3.4: CHECK report for CausalR on zin1

This page was generated on 2016-09-21 03:39:56 -0700 (Wed, 21 Sep 2016).

Package 161/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CausalR 1.5.2
Glyn Bradley , Steven Barrett , Bhushan Bonde
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: CausalR
Version: 1.5.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CausalR_1.5.2.tar.gz
StartedAt: 2016-09-20 04:08:41 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:09:06 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 25.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CausalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CausalR_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CausalR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.5.2’
* 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 files look like leftovers/mistakes:
  ‘CausalR.bbl’, ‘CausalR.blg’
Please remove them from your package.
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-3.4-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
AnalysePredictionsList0.0160.0000.015
CalculateEnrichmentPValue0.0000.0000.002
CalculateSignificance0.1080.0000.108
CalculateSignificanceUsingCubicAlgorithm0.1200.0000.122
CalculateSignificanceUsingCubicAlgorithm1b0.0960.0000.096
CalculateSignificanceUsingQuarticAlgorithm0.1040.0000.104
CompareHypothesis0.0080.0000.006
CreateCCG0.0080.0000.009
CreateCG0.0040.0000.006
GetNodeName0.0120.0000.011
GetNumberOfPositiveAndNegativeEntries0.0000.0000.002
GetShortestPathsFromCCG0.0120.0000.012
MakePredictions0.0120.0000.011
MakePredictionsFromCCG0.0120.0000.012
PlotGraphWithNodeNames0.0800.0000.078
RankTheHypotheses0.1000.0000.122
ReadExperimentalData0.0240.0000.024
ScoreHypothesis0.0040.0000.003
WriteExplainedNodesToSifFile0.0680.0040.074
runSCANR0.1400.0240.119