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This page was generated on 2021-09-22 15:04:50 -0400 (Wed, 22 Sep 2021).

CHECK results for DMRcate on nebbiolo1

To the developers/maintainers of the DMRcate package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DMRcate.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 517/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcate 2.6.0  (landing page)
Tim Peters
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/DMRcate
git_branch: RELEASE_3_13
git_last_commit: d7de4ca
git_last_commit_date: 2021-05-19 12:03:06 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: DMRcate
Version: 2.6.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DMRcate_2.6.0.tar.gz
StartedAt: 2021-09-21 09:40:32 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 10:04:43 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 1451.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DMRcate.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DMRcate_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/DMRcate.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* this is package ‘DMRcate’ version ‘2.6.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
See ‘/home/biocbuild/bbs-3.13-bioc/meat/DMRcate.Rcheck/00install.out’ for details.
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
DMR.plot            225.235  7.442 244.400
DMRcate-package     164.105  6.232 172.228
extractRanges       144.958  2.920 149.317
rmSNPandCH          143.346  3.053 147.433
cpg.annotate        131.587  6.319 138.998
dmrcate             127.702  3.573 132.339
changeFDR            58.961  7.238  66.742
sequencing.annotate  50.275  5.203  55.904
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/DMRcate.Rcheck/00check.log’
for details.



Installation output

DMRcate.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DMRcate
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘DMRcate’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** testing if installed package keeps a record of temporary installation path
* DONE (DMRcate)

Tests output


Example timings

DMRcate.Rcheck/DMRcate-Ex.timings

nameusersystemelapsed
DMR.plot225.235 7.442244.400
DMRcate-package164.105 6.232172.228
changeFDR58.961 7.23866.742
cpg.annotate131.587 6.319138.998
dmrcate127.702 3.573132.339
extractRanges144.958 2.920149.317
rmSNPandCH143.346 3.053147.433
sequencing.annotate50.275 5.20355.904