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This page was generated on 2021-11-29 15:05:52 -0500 (Mon, 29 Nov 2021).

CHECK results for DMRcate on machv2

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 2.8.0  (landing page)
Tim Peters
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/DMRcate
git_branch: RELEASE_3_14
git_last_commit: 984cee7
git_last_commit_date: 2021-10-26 12:12:00 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: 2.8.0
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_2.8.0.tar.gz
StartedAt: 2021-11-28 15:47:37 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 15:59:58 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 740.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: DMRcate.Rcheck
Warnings: NA

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_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/DMRcate.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* this is package ‘DMRcate’ version ‘2.8.0’
* 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 ‘/Users/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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DMRcate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DMR.plot
> ### Title: Plotting DMRs
> ### Aliases: DMR.plot plot
> 
> ### ** Examples
> 
> library(ExperimentHub)
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

> library(limma)

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> eh <- ExperimentHub()
snapshotDate(): 2021-10-19
> FlowSorted.Blood.EPIC <- eh[["EH1136"]]
see ?FlowSorted.Blood.EPIC and browseVignettes('FlowSorted.Blood.EPIC') for documentation
loading from cache
> tcell <- FlowSorted.Blood.EPIC[,colData(FlowSorted.Blood.EPIC)$CD4T==100 |
+                                 colData(FlowSorted.Blood.EPIC)$CD8T==100]
> detP <- detectionP(tcell)
Loading required package: IlluminaHumanMethylationEPICmanifest
> remove <- apply(detP, 1, function (x) any(x > 0.01))
> tcell <- tcell[!remove,]
> tcell <- preprocessFunnorm(tcell)
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization
> #Subset to chr2 only
> tcell <- tcell[seqnames(tcell) == "chr2",]
> tcellms <- getM(tcell)
> tcellms.noSNPs <- rmSNPandCH(tcellms, dist=2, mafcut=0.05)
snapshotDate(): 2021-10-19
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'DMRcatedata'
Error in UseMethod("conditionMessage") : 
  no applicable method for 'conditionMessage' applied to an object of class "character"
Calls: rmSNPandCH ... tryCatchList -> tryCatchOne -> doTryCatch -> download.file
Execution halted
* 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 ERROR, 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/DMRcate.Rcheck/00check.log’
for details.


Installation output

DMRcate.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DMRcate
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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