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This page was generated on 2024-05-04 11:40:23 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 414/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMethDMR 1.8.0  (landing page)
Fernanda Veitzman
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/coMethDMR
git_branch: RELEASE_3_19
git_last_commit: 0588fe1
git_last_commit_date: 2024-04-30 11:39:34 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for coMethDMR on kunpeng2


To the developers/maintainers of the coMethDMR package:
- 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 Troubleshooting Build Report for more information.
- 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: coMethDMR
Version: 1.8.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings coMethDMR_1.8.0.tar.gz
StartedAt: 2024-05-04 06:12:23 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 06:26:42 -0000 (Sat, 04 May 2024)
EllapsedTime: 859.5 seconds
RetCode: 0
Status:   OK  
CheckDir: coMethDMR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings coMethDMR_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/coMethDMR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMethDMR/DESCRIPTION’ ... OK
* this is package ‘coMethDMR’ version ‘1.8.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether 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 ... NOTE
checkRd: (-1) AnnotateResults.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AnnotateResults.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AnnotateResults.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CoMethSingleRegion.Rd:55-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CoMethSingleRegion.Rd:61-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateRdrop.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateRdrop.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkComethylatedCpGs.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkComethylatedCpGs.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkComethylatedCpGs.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkComethylatedCpGs.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkMissing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkMissing.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkMissing.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkMissing.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
* 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  37.998  3.057  54.883
lmmTest             31.861  2.270  45.318
lmmTestAllRegions   23.032  1.109  30.008
SplitCpGDFbyRegion  22.456  1.684  32.484
CpGsInfoOneRegion   21.309  1.720  31.862
CoMethAllRegions    17.041  1.640  21.457
GetCpGsInRegion     15.518  1.483  22.450
AnnotateResults     14.005  1.261  15.307
CreateOutputDF      10.670  1.214  14.942
CpGsInfoAllRegions   9.007  0.722  12.605
CloseBySingleRegion  8.027  0.846  12.356
OrderCpGsByLocation  7.710  0.690  11.150
ImportSesameData     6.597  0.660  10.103
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/coMethDMR.Rcheck/00check.log’
for details.


Installation output

coMethDMR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL coMethDMR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
 71.744   2.488  87.625 

Example timings

coMethDMR.Rcheck/coMethDMR-Ex.timings

nameusersystemelapsed
AnnotateResults14.005 1.26115.307
CloseBySingleRegion 8.027 0.84612.356
CoMethAllRegions17.041 1.64021.457
CoMethSingleRegion37.998 3.05754.883
CpGsInfoAllRegions 9.007 0.72212.605
CpGsInfoOneRegion21.309 1.72031.862
CreateOutputDF10.670 1.21414.942
CreateParallelWorkers1.9970.1472.148
CreateRdrop0.0040.0000.004
FindComethylatedRegions0.0280.0000.028
GetCpGsInRegion15.518 1.48322.450
GetResiduals0.3070.0120.320
ImportSesameData 6.597 0.66010.103
MarkComethylatedCpGs0.0060.0000.006
MarkMissing0.0060.0000.006
NameRegion0.0010.0000.001
OrderCpGsByLocation 7.71 0.6911.15
RegionsToRanges0.0190.0000.019
SplitCpGDFbyRegion22.456 1.68432.484
WriteCloseByAllRegions0.0620.0040.067
lmmTest31.861 2.27045.318
lmmTestAllRegions23.032 1.10930.008