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This page was generated on 2022-01-26 11:08:06 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for methInheritSim on riesling1


To the developers/maintainers of the methInheritSim package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methInheritSim.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1109/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methInheritSim 1.17.1  (landing page)
Pascal Belleau
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/methInheritSim
git_branch: master
git_last_commit: ea580fb
git_last_commit_date: 2021-11-21 00:32:40 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'methylKit' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: methInheritSim
Version: 1.17.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methInheritSim.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings methInheritSim_1.17.1.tar.gz
StartedAt: 2022-01-25 19:25:25 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 19:29:23 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 238.0 seconds
RetCode: 0
Status:   OK  
CheckDir: methInheritSim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methInheritSim.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings methInheritSim_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/methInheritSim.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methInheritSim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methInheritSim' version '1.17.1'
* 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 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 8.53   0.01    8.55
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/methInheritSim.Rcheck/00check.log'
for details.



Installation output

methInheritSim.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL methInheritSim
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'methInheritSim'
    finding HTML links ... done
    calculateNbDiffCase                     html  
    createSampleID                          html  
    dataSimExample                          html  
    estBetaAlpha                            html  
    estBetaBeta                             html  
    fixSeed                                 html  
    getDiffCase                             html  
    getDiffMeth                             html  
    getSim                                  html  
    getSyntheticChr                         html  
    methInheritSim-package                  html  
    runOnEachSynCHR                         html  
    runSim                                  html  
    samplesForChrSynthetic                  html  
    saveData                                html  
    simEachGeneration                       html  
    simInheritance                          html  
    testIfAlreadyDone                       html  
    validateRunSimDoubleParameters          html  
    validateRunSimIntegerParameters         html  
    validateRunSimLogicalParameters         html  
    validateRunSimOtherParameters           html  
    validateRunSimParameters                html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'regsplice' is missing or broken
 done

Tests output

methInheritSim.Rcheck/tests/runTests.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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 -- Tue Jan 25 19:29:12 2022 
*********************************************** 
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 
  24.15    1.00   25.11 

Example timings

methInheritSim.Rcheck/methInheritSim-Ex.timings

nameusersystemelapsed
calculateNbDiffCase0.010.000.01
createSampleID000
dataSimExample0.020.040.06
estBetaAlpha000
estBetaBeta000
fixSeed000
getDiffCase000
getDiffMeth0.030.060.09
getSim0.970.000.97
getSyntheticChr0.130.050.17
runOnEachSynCHR1.420.191.61
runSim4.620.064.69
samplesForChrSynthetic8.530.018.55
saveData000
simEachGeneration0.330.020.34
simInheritance0.550.000.55
testIfAlreadyDone000
validateRunSimDoubleParameters000
validateRunSimIntegerParameters000
validateRunSimLogicalParameters0.010.020.03
validateRunSimOtherParameters0.040.000.03
validateRunSimParameters0.030.000.03