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This page was generated on 2024-03-28 11:32:19 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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Package 581/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcate 2.16.1  (landing page)
Tim Peters
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/DMRcate
git_branch: RELEASE_3_18
git_last_commit: 4cd2397
git_last_commit_date: 2023-12-04 22:28:28 -0400 (Mon, 04 Dec 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for DMRcate on kjohnson1


To the developers/maintainers of the DMRcate 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: DMRcate
Version: 2.16.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DMRcate_2.16.1.tar.gz
StartedAt: 2024-03-27 11:40:42 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 12:11:25 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 1843.2 seconds
RetCode: 0
Status:   OK  
CheckDir: DMRcate.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DMRcate_2.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/DMRcate.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* this is package ‘DMRcate’ version ‘2.16.1’
* 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 ‘DMRcate’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    DSS dependency removed
  Cannot process chunk/lines:
    CITATION updated.
  Cannot process chunk/lines:
    BUG FIXES
    •	annotate() renamed to cpg.annotate to avoid clashes with same-named function in ggplot2
  Cannot process chunk/lines:
    NEW FEATURES
    •	Kernel estimator has been rewritten from scratch without the need for ks:::kde. Now only takes moderated t-values as cpg weights, as required by the chi-square transformation. 
    •	Now allows for multi-level factor experiments, as allowed by limma. Contrasts should be specified with a contrast matrix, otherwise the design matrix MUST have an intercept. (Thanks to Tim Triche Jr. and David Martino for their advice).
    •	A GRanges object can be produced from the results.
    •	XY probes can also be filtered out using rmSNPandCH().
    •	DMR.plot() allows group median lines to be plotted to better visualise distances between groups (Thanks to Susan van Dijk and Magnus Tobiasson for their advice).
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
DMR.plot            251.948 12.502 280.580
DMRcate-package     195.347 10.374 211.516
extractRanges       168.293 11.065 184.620
rmSNPandCH          164.993  9.680 178.747
cpg.annotate        161.338 10.694 176.123
dmrcate             162.622  8.790 175.299
changeFDR            79.549  4.712  86.942
sequencing.annotate  59.775  3.762  65.071
* 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-3.18-bioc-mac-arm64/meat/DMRcate.Rcheck/00check.log’
for details.



Installation output

DMRcate.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DMRcate
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘DMRcate’ ...
** using staged installation
** R
** 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 (DMRcate)

Tests output


Example timings

DMRcate.Rcheck/DMRcate-Ex.timings

nameusersystemelapsed
DMR.plot251.948 12.502280.580
DMRcate-package195.347 10.374211.516
changeFDR79.549 4.71286.942
cpg.annotate161.338 10.694176.123
dmrcate162.622 8.790175.299
extractRanges168.293 11.065184.620
rmSNPandCH164.993 9.680178.747
sequencing.annotate59.775 3.76265.071