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This page was generated on 2023-04-12 11:06:03 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 coMethDMR on lconway


To the developers/maintainers of the coMethDMR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coMethDMR.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 390/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMethDMR 1.2.0  (landing page)
Fernanda Veitzman
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/coMethDMR
git_branch: RELEASE_3_16
git_last_commit: 366ee96
git_last_commit_date: 2022-11-01 11:26:14 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: coMethDMR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMethDMR_1.2.0.tar.gz
StartedAt: 2023-04-10 19:31:56 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:40:33 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 517.1 seconds
RetCode: 0
Status:   OK  
CheckDir: coMethDMR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMethDMR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/coMethDMR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMethDMR/DESCRIPTION’ ... OK
* this is package ‘coMethDMR’ version ‘1.2.0’
* 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 ‘coMethDMR’ 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 ... NOTE
File ‘coMethDMR/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("Checking for cached SeSAMe data.")
    packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.")

See section ‘Good practice’ in '?.onAttach'.
* 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
CoMethSingleRegion  27.102  0.953  29.425
lmmTest             21.328  0.737  23.039
SplitCpGDFbyRegion  17.044  0.628  18.315
lmmTestAllRegions   16.771  0.514  17.966
CpGsInfoOneRegion   14.921  0.581  16.166
CoMethAllRegions    12.489  0.453  13.260
GetCpGsInRegion     10.222  0.353  10.983
AnnotateResults      9.637  0.462  10.113
CloseBySingleRegion  7.667  0.975   9.110
ImportSesameData     7.133  0.257   7.603
CpGsInfoAllRegions   6.655  0.261   7.112
CreateOutputDF       6.033  0.291   6.537
OrderCpGsByLocation  4.762  0.167   5.160
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/coMethDMR.Rcheck/00check.log’
for details.



Installation output

coMethDMR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL coMethDMR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘coMethDMR’ ...
** 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
snapshotDate(): 2022-10-31
** testing if installed package can be loaded from final location
snapshotDate(): 2022-10-31
** testing if installed package keeps a record of temporary installation path
* DONE (coMethDMR)

Tests output

coMethDMR.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> library(testthat)
> library(coMethDMR)
Checking for cached SeSAMe data.
snapshotDate(): 2022-10-31
> 
> test_check("coMethDMR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
 57.756   2.967  62.746 

Example timings

coMethDMR.Rcheck/coMethDMR-Ex.timings

nameusersystemelapsed
AnnotateResults 9.637 0.46210.113
CloseBySingleRegion7.6670.9759.110
CoMethAllRegions12.489 0.45313.260
CoMethSingleRegion27.102 0.95329.425
CpGsInfoAllRegions6.6550.2617.112
CpGsInfoOneRegion14.921 0.58116.166
CreateOutputDF6.0330.2916.537
CreateParallelWorkers0.0090.0010.009
CreateRdrop0.0020.0020.005
FindComethylatedRegions0.0130.0030.016
GetCpGsInRegion10.222 0.35310.983
GetResiduals0.2210.0080.231
ImportSesameData7.1330.2577.603
MarkComethylatedCpGs0.0030.0030.006
MarkMissing0.0020.0000.003
NameRegion0.0000.0000.001
OrderCpGsByLocation4.7620.1675.160
RegionsToRanges0.0090.0010.009
SplitCpGDFbyRegion17.044 0.62818.315
WriteCloseByAllRegions0.0300.0010.031
lmmTest21.328 0.73723.039
lmmTestAllRegions16.771 0.51417.966