BioC 3.5: CHECK report for methylInheritance on veracruz2

Package: methylInheritance

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylInheritance_1.0.0.tar.gz

StartedAt: 2017-10-18 06:00:13 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:09:31 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 558.4 seconds

RetCode: 0

Status:  OK

CheckDir: methylInheritance.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 methylInheritance_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/methylInheritance.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylInheritance/DESCRIPTION’ ... OK
* this is package ‘methylInheritance’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘methylInheritance’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
runObservation                      75.853  0.654  78.502
samplesForTransgenerationalAnalysis 20.978  1.720  46.488
runOnePermutationOnAllGenerations   20.591  1.556  17.318
demoForTransgenerationalAnalysis    11.340  0.944   8.681
runPermutation                       9.120  0.664 107.933
* 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: OK

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

name	user	system	elapsed
createDataStructure	0.193	0.010	0.208
createOutputDir	0.002	0.001	0.002
demoForTransgenerationalAnalysis	11.340	0.944	8.681
extractInfo	0.553	0.004	0.575
getGRangesFromMethylDiff	0.099	0.003	0.112
interGeneration	0.886	0.006	0.915
isInterGenerationResults	0.002	0.000	0.002
loadAllRDSResults	0.332	0.002	0.343
mergePermutationAndObservation	0.006	0.001	0.006
methylInheritanceAllResults	0.053	0.003	0.056
methylInheritanceResults	0.080	0.005	0.085
plotGraph	2.146	0.016	2.213
readInterGenerationResults	0.163	0.003	0.175
runObservation	75.853	0.654	78.502
runOnePermutationOnAllGenerations	20.591	1.556	17.318
runPermutation	9.120	0.664	107.933
samplesForTransgenerationalAnalysis	20.978	1.720	46.488
saveInterGenerationResults	0.738	0.007	0.758
validateExtractInfo	0.003	0.002	0.005
validateMergePermutationAndObservation	0.003	0.000	0.003
validateRunObservation	0.118	0.017	0.139
validateRunPermutation	0.113	0.016	0.134