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This page was generated on 2021-10-23 14:05:57 -0400 (Sat, 23 Oct 2021).

CHECK results for DMRcate on nebbiolo2

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 526/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcate 2.7.0  (landing page)
Tim Peters
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/DMRcate
git_branch: master
git_last_commit: ca23944
git_last_commit_date: 2021-05-19 12:03:06 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: DMRcate
Version: 2.7.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DMRcate_2.7.0.tar.gz
StartedAt: 2021-10-22 19:52:36 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 20:16:38 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 1442.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DMRcate.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DMRcate_2.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-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 ‘2.7.0’
* 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-3.14-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            221.237  6.908 239.367
DMRcate-package     162.277  3.887 168.130
extractRanges       150.905  2.555 154.883
rmSNPandCH          137.937  1.593 140.593
cpg.annotate        131.824  5.004 137.843
dmrcate             130.230  3.165 134.405
changeFDR            58.878  7.224  66.525
sequencing.annotate  52.912  5.983  59.202
* 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-3.14-bioc/meat/DMRcate.Rcheck/00check.log’
for details.



Installation output

DMRcate.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DMRcate
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-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.plot221.237 6.908239.367
DMRcate-package162.277 3.887168.130
changeFDR58.878 7.22466.525
cpg.annotate131.824 5.004137.843
dmrcate130.230 3.165134.405
extractRanges150.905 2.555154.883
rmSNPandCH137.937 1.593140.593
sequencing.annotate52.912 5.98359.202