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This page was generated on 2022-12-09 11:06:04 -0500 (Fri, 09 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4449
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4194
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4237
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 nebbiolo1


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? 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 1147/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methInheritSim 1.21.0  (landing page)
Pascal Belleau
Snapshot Date: 2022-12-08 14:00:20 -0500 (Thu, 08 Dec 2022)
git_url: https://git.bioconductor.org/packages/methInheritSim
git_branch: master
git_last_commit: 0f2cecc
git_last_commit_date: 2022-11-01 11:15:46 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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  NO, package depends on 'methylKit' which is not available

Summary

Package: methInheritSim
Version: 1.21.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methInheritSim.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings methInheritSim_1.21.0.tar.gz
StartedAt: 2022-12-08 21:30:28 -0500 (Thu, 08 Dec 2022)
EndedAt: 2022-12-08 21:35:43 -0500 (Thu, 08 Dec 2022)
EllapsedTime: 314.9 seconds
RetCode: 0
Status:   OK  
CheckDir: methInheritSim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methInheritSim.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings methInheritSim_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/methInheritSim.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘methInheritSim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methInheritSim’ version ‘1.21.0’
* 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 10.339  0.128  10.467
runSim                  5.377  0.088   5.465
* 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 ...
  ‘methInheritSim.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/methInheritSim.Rcheck/00check.log’
for details.



Installation output

methInheritSim.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL methInheritSim
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 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

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, aperm, 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
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 Dec  8 21:35:06 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 
 28.263   1.061  29.315 

Example timings

methInheritSim.Rcheck/methInheritSim-Ex.timings

nameusersystemelapsed
calculateNbDiffCase0.0020.0000.002
createSampleID0.0020.0000.002
dataSimExample0.0640.0120.076
estBetaAlpha0.0000.0010.001
estBetaBeta0.0000.0010.000
fixSeed000
getDiffCase0.0000.0010.000
getDiffMeth0.0650.0320.097
getSim0.4760.0080.484
getSyntheticChr0.2030.0120.215
runOnEachSynCHR2.6460.1562.803
runSim5.3770.0885.465
samplesForChrSynthetic10.339 0.12810.467
saveData000
simEachGeneration0.4670.0000.468
simInheritance0.7470.0080.755
testIfAlreadyDone0.0000.0000.001
validateRunSimDoubleParameters000
validateRunSimIntegerParameters0.0010.0000.000
validateRunSimLogicalParameters0.0260.0040.030
validateRunSimOtherParameters0.0260.0040.030
validateRunSimParameters0.0300.0000.031