Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 414/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMethDMR 1.10.0  (landing page)
Fernanda Veitzman
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/coMethDMR
git_branch: RELEASE_3_20
git_last_commit: ea15e3a
git_last_commit_date: 2024-10-29 11:07:14 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
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  


CHECK results for coMethDMR on teran2

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.

raw results


Summary

Package: coMethDMR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings coMethDMR_1.10.0.tar.gz
StartedAt: 2024-11-20 00:45:55 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 00:58:12 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 736.1 seconds
RetCode: 0
Status:   OK  
CheckDir: coMethDMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings coMethDMR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/coMethDMR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘coMethDMR/DESCRIPTION’ ... OK
* this is package ‘coMethDMR’ version ‘1.10.0’
* 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  21.009  0.960  28.377
lmmTest             18.322  0.330  23.084
lmmTestAllRegions   12.355  1.029  16.287
CpGsInfoOneRegion   12.820  0.219  14.734
SplitCpGDFbyRegion  12.599  0.253  15.703
AnnotateResults      8.934  0.673  10.491
CoMethAllRegions     8.851  0.404  10.690
GetCpGsInRegion      7.554  0.127   9.247
CreateOutputDF       5.920  0.087   6.763
CpGsInfoAllRegions   4.841  0.196   6.683
CloseBySingleRegion  4.569  0.231   5.790
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/coMethDMR.Rcheck/00check.log’
for details.


Installation output

coMethDMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL coMethDMR
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
 48.187   2.015  58.774 

Example timings

coMethDMR.Rcheck/coMethDMR-Ex.timings

nameusersystemelapsed
AnnotateResults 8.934 0.67310.491
CloseBySingleRegion4.5690.2315.790
CoMethAllRegions 8.851 0.40410.690
CoMethSingleRegion21.009 0.96028.377
CpGsInfoAllRegions4.8410.1966.683
CpGsInfoOneRegion12.820 0.21914.734
CreateOutputDF5.9200.0876.763
CreateParallelWorkers1.5130.0101.572
CreateRdrop0.0030.0000.003
FindComethylatedRegions0.0110.0010.012
GetCpGsInRegion7.5540.1279.247
GetResiduals0.1650.0020.167
ImportSesameData3.3010.0583.797
MarkComethylatedCpGs0.0030.0000.003
MarkMissing0.0010.0010.002
NameRegion000
OrderCpGsByLocation3.6440.0584.579
RegionsToRanges0.0080.0000.008
SplitCpGDFbyRegion12.599 0.25315.703
WriteCloseByAllRegions0.0280.0010.029
lmmTest18.322 0.33023.084
lmmTestAllRegions12.355 1.02916.287