BioC 3.5: CHECK report for CausalR on malbec2

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: 2017-10-17 21:47:46 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:48:21 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 34.9 seconds

RetCode: 0

Status:  OK

CheckDir: CausalR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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 3.4.2 (2017-09-28)
* 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.

* 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)

name	user	system	elapsed
AnalysePredictionsList	0.116	0.004	0.122
CalculateEnrichmentPValue	0.004	0.000	0.003
CalculateSignificance	0.344	0.004	0.352
CalculateSignificanceUsingCubicAlgorithm	0.056	0.000	0.059
CalculateSignificanceUsingCubicAlgorithm1b	0.04	0.00	0.04
CalculateSignificanceUsingQuarticAlgorithm	0.040	0.000	0.042
CompareHypothesis	0.004	0.000	0.006
CreateCCG	0.060	0.000	0.059
CreateCG	0.032	0.000	0.032
GetNodeName	0.004	0.000	0.006
GetNumberOfPositiveAndNegativeEntries	0.000	0.000	0.001
GetShortestPathsFromCCG	0.008	0.000	0.008
MakePredictions	0.068	0.000	0.070
MakePredictionsFromCCG	0.008	0.000	0.008
MakePredictionsFromCG	0.260	0.000	0.258
PlotGraphWithNodeNames	0.080	0.000	0.105
RankTheHypotheses	0.260	0.004	0.283
ReadExperimentalData	0.036	0.004	0.041
ScoreHypothesis	0.032	0.000	0.032
WriteAllExplainedNodesToSifFile	0.300	0.044	0.306
WriteExplainedNodesToSifFile	0.044	0.000	0.045
runSCANR	0.436	0.036	0.435