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CHECK report for methInheritSim on malbec1

This page was generated on 2021-05-06 12:28:12 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the methInheritSim package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1066/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methInheritSim 1.12.0  (landing page)
Pascal Belleau
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/methInheritSim
Branch: RELEASE_3_12
Last Commit: 36e0739
Last Changed Date: 2020-10-27 11:24:40 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: methInheritSim
Version: 1.12.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:methInheritSim.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings methInheritSim_1.12.0.tar.gz
StartedAt: 2021-05-06 03:20:08 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:25:52 -0400 (Thu, 06 May 2021)
EllapsedTime: 344.0 seconds
RetCode: 0
Status:   OK  
CheckDir: methInheritSim.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:methInheritSim.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings methInheritSim_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/methInheritSim.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methInheritSim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methInheritSim’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘methInheritSim’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
samplesForChrSynthetic 23.244  0.032  23.349
runSim                 11.000  0.020  11.038
* 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-3.12-bioc/meat/methInheritSim.Rcheck/00check.log’
for details.



Installation output

methInheritSim.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL methInheritSim
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘methInheritSim’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methInheritSim)

Tests output

methInheritSim.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("methInheritSim")
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)


RUNIT TEST PROTOCOL -- Thu May  6 03:25:49 2021 
*********************************************** 
Number of test functions: 104 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
methInheritSim RUnit Tests - 104 test functions, 0 errors, 0 failures
Number of test functions: 104 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 41.416   0.408  41.942 

Example timings

methInheritSim.Rcheck/methInheritSim-Ex.timings

nameusersystemelapsed
calculateNbDiffCase0.0040.0000.003
createSampleID0.0040.0000.001
dataSimExample0.0840.0040.086
estBetaAlpha000
estBetaBeta000
fixSeed0.0000.0000.001
getDiffCase0.0000.0000.001
getDiffMeth0.0920.0200.112
getSim1.5680.0321.602
getSyntheticChr0.1680.0160.183
runOnEachSynCHR2.4000.0442.446
runSim11.000 0.02011.038
samplesForChrSynthetic23.244 0.03223.349
saveData000
simEachGeneration1.0800.0001.083
simInheritance1.3840.0001.386
testIfAlreadyDone000
validateRunSimDoubleParameters000
validateRunSimIntegerParameters000
validateRunSimLogicalParameters0.0320.0000.032
validateRunSimOtherParameters0.0400.0000.041
validateRunSimParameters0.0520.0000.052