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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 405/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMethDMR 1.4.0  (landing page)
Fernanda Veitzman
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/coMethDMR
git_branch: RELEASE_3_17
git_last_commit: 40e80ff
git_last_commit_date: 2023-04-25 11:35:11 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for coMethDMR on kjohnson2


To the developers/maintainers of the coMethDMR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: coMethDMR
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2023-10-17 11:09:48 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 11:27:40 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 1072.0 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/coMethDMR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMethDMR/DESCRIPTION’ ... OK
* this is package ‘coMethDMR’ version ‘1.4.0’
* 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 startup messages can be suppressed ... 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  40.197  1.279  65.868
lmmTest             34.170  1.040  56.137
SplitCpGDFbyRegion  25.058  0.781  41.565
CpGsInfoOneRegion   24.572  0.772  40.416
lmmTestAllRegions   24.390  0.606  39.547
GetCpGsInRegion     16.616  0.588  27.177
CoMethAllRegions    15.288  0.404  23.501
AnnotateResults     11.545  0.457  17.569
CloseBySingleRegion  9.838  1.061  16.721
CpGsInfoAllRegions  10.170  0.319  16.804
OrderCpGsByLocation  8.528  0.311  17.114
ImportSesameData     7.735  0.284  13.005
CreateOutputDF       7.702  0.263  12.697
* 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-3.17-bioc-mac-arm64/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
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (coMethDMR)

Tests output

coMethDMR.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.
> 
> test_check("coMethDMR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
 71.601   3.336 124.356 

Example timings

coMethDMR.Rcheck/coMethDMR-Ex.timings

nameusersystemelapsed
AnnotateResults11.545 0.45717.569
CloseBySingleRegion 9.838 1.06116.721
CoMethAllRegions15.288 0.40423.501
CoMethSingleRegion40.197 1.27965.868
CpGsInfoAllRegions10.170 0.31916.804
CpGsInfoOneRegion24.572 0.77240.416
CreateOutputDF 7.702 0.26312.697
CreateParallelWorkers1.4940.0502.352
CreateRdrop0.0040.0040.010
FindComethylatedRegions0.0170.0080.038
GetCpGsInRegion16.616 0.58827.177
GetResiduals0.3480.0120.546
ImportSesameData 7.735 0.28413.005
MarkComethylatedCpGs0.0040.0010.007
MarkMissing0.0040.0010.009
NameRegion0.0000.0000.001
OrderCpGsByLocation 8.528 0.31117.114
RegionsToRanges0.0140.0000.026
SplitCpGDFbyRegion25.058 0.78141.565
WriteCloseByAllRegions0.0480.0010.076
lmmTest34.170 1.04056.137
lmmTestAllRegions24.390 0.60639.547