BioC 3.2: CHECK report for CausalR on perceval

Package: CausalR

Version: 0.99.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CausalR_0.99.12.tar.gz

StartedAt: 2015-06-25 22:58:49 -0700 (Thu, 25 Jun 2015)

EndedAt: 2015-06-25 22:59:26 -0700 (Thu, 25 Jun 2015)

EllapsedTime: 36.5 seconds

RetCode: 0

Status:  OK

CheckDir: CausalR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CausalR_0.99.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CausalR.Rcheck’
* using R version 3.2.1 (2015-06-18)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘0.99.12’
* 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 ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘igraph’
A package should be listed in only one of these fields.
* 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 ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/5s]
 [6s/6s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.020	0.001	0.022
CalculateEnrichmentPValue	0.002	0.000	0.003
CalculateSignificance	0.171	0.001	0.172
CalculateSignificanceUsingCubicAlgorithm	0.199	0.001	0.201
CalculateSignificanceUsingCubicAlgorithm1b	0.153	0.000	0.154
CalculateSignificanceUsingQuarticAlgorithm	0.164	0.001	0.165
CompareHypothesis	0.008	0.001	0.009
CreateCCG	0.015	0.001	0.015
CreateCG	0.006	0.001	0.006
GetNodeName	0.013	0.000	0.014
GetNumberOfPositiveAndNegativeEntries	0.002	0.000	0.002
GetShortestPathsFromCCG	0.015	0.001	0.015
MakePredictions	0.013	0.000	0.014
MakePredictionsFromCCG	0.017	0.000	0.017
PlotGraphWithNodeNames	0.129	0.002	0.131
RankTheHypotheses	0.136	0.010	0.146
ReadExperimentalData	0.022	0.001	0.023
ScoreHypothesis	0.005	0.001	0.006
runSCANR	0.101	0.003	0.104