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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DMRcate_3.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DMRcate.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* this is package ‘DMRcate’ version ‘3.2.1’
* 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 ... 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 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 ... ERROR
Running examples in ‘DMRcate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DMRcate-package
> ### Title: DMR calling from bisulfite sequencing and Illumina array data
> ### Aliases: DMRcate-package DMRcate
> 
> ### ** Examples
> 
> library(ExperimentHub)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> library(limma)

Attaching package: 'limma'

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

    plotMA

> eh <- ExperimentHub()
> 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 <- minfi::detectionP(tcell)
Loading required package: IlluminaHumanMethylationEPICmanifest
> remove <- apply(detP, 1, function (x) any(x > 0.01))
> tcell <- tcell[!remove,]
> tcell <- minfi::preprocessFunnorm(tcell)
[preprocessFunnorm] Background and dye bias correction with noob
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization
> #Subset to chr2 only
> tcell <- tcell[seqnames(tcell) == "chr2",]
> tcellms <- minfi::getM(tcell)
> tcellms.noSNPs <- rmSNPandCH(tcellms, dist=2, mafcut=0.05)
Probe IDs from EPICv1 or earlier detected. Proceeding...
see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation
loading from cache
see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation
loading from cache
> tcell$Replicate[tcell$Replicate==""] <- tcell$Sample_Name[tcell$Replicate==""]
> tcellms.noSNPs <- avearrays(tcellms.noSNPs, tcell$Replicate)
> tcell <- tcell[,!duplicated(tcell$Replicate)]
> tcell <- tcell[rownames(tcellms.noSNPs),]
> colnames(tcellms.noSNPs) <- colnames(tcell)
> assays(tcell)[["M"]] <- tcellms.noSNPs
> assays(tcell)[["Beta"]] <- minfi::ilogit2(tcellms.noSNPs)
> type <- factor(tcell$CellType)
> design <- model.matrix(~type) 
> myannotation <- cpg.annotate("array", tcell, 
+                              arraytype = "EPICv1", analysis.type="differential",
+                              design=design, coef=2)
Your contrast returned 2694 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
> dmrcoutput <- dmrcate(myannotation, lambda=1000, C=2)
Fitting chr2...
Demarcating regions...
Done!
> results.ranges <- extractRanges(dmrcoutput, genome = "hg19")
see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation
loading from cache
> groups <- c(CD8T="magenta", CD4T="forestgreen")
> cols <- groups[as.character(type)]
> DMR.plot(ranges=results.ranges, dmr=1, 
+          CpGs=minfi::getBeta(tcell), what="Beta", 
+          arraytype = "EPICv1", phen.col=cols, genome="hg19")
Error in errorHandler(responseError) : Internal Server Error
Calls: DMR.plot ... doTryCatch -> <Anonymous> -> handleResponse -> errorHandler
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘EPICv1_and_450K.Rnw’ using knitr
--- finished re-building ‘EPICv1_and_450K.Rnw’

--- re-building ‘EPICv2.Rnw’ using knitr

Quitting from EPICv2.Rnw:127-132 [plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
     x
  1. \-DMRcate::DMR.plot(...)
  2.   \-Gviz::IdeogramTrack(genome = genome, chromosome = as.character(seqnames(ranges.inplot)))
  3.     \-methods::new(...)
  4.       +-methods::initialize(value, ...)
  5.       \-Gviz::initialize(value, ...)
  6.         \-Gviz (local) .local(.Object, ...)
  7.           \-Gviz:::.cacheGenomes(genome = genome)
  8.             +-Gviz::.doCache(...)
  9.             | +-BiocGenerics::eval(expression, envir = callEnv)
 10.             | \-base::eval(expression, envir = callEnv)
 11.             |   \-base::eval(expression, envir = callEnv)
 12.             +-rtracklayer::getTable(query)
 13.             \-rtracklayer::getTable(query)
 14.               \-rtracklayer (local) .local(object, ...)
 15.                 +-restfulr::read(url$getData$track, query)
 16.                 \-restfulr::read(url$getData$track, query)
 17.                   +-base::tryCatch(...)
 18.                   | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 19.                   |   \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 20.                   |     \-base (local) doTryCatch(return(expr), name, parentenv, handler)
 21.                   \-x@protocol$read(x, cacheInfo)
 22.                     \-restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 23.                       \-restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'EPICv2.Rnw' failed with diagnostics:
Internal Server Error

--- failed re-building ‘EPICv2.Rnw’

--- re-building ‘sequencing.Rnw’ using knitr

Quitting from sequencing.Rnw:122-132 [seqDMRplot1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
     x
  1. \-DMRcate::DMR.plot(...)
  2.   \-Gviz::IdeogramTrack(genome = genome, chromosome = as.character(seqnames(ranges.inplot)))
  3.     \-methods::new(...)
  4.       +-methods::initialize(value, ...)
  5.       \-Gviz::initialize(value, ...)
  6.         \-Gviz (local) .local(.Object, ...)
  7.           \-Gviz:::.cacheGenomes(genome = genome)
  8.             +-Gviz::.doCache(...)
  9.             | +-BiocGenerics::eval(expression, envir = callEnv)
 10.             | \-base::eval(expression, envir = callEnv)
 11.             |   \-base::eval(expression, envir = callEnv)
 12.             +-rtracklayer::getTable(query)
 13.             \-rtracklayer::getTable(query)
 14.               \-rtracklayer (local) .local(object, ...)
 15.                 +-restfulr::read(url$getData$track, query)
 16.                 \-restfulr::read(url$getData$track, query)
 17.                   +-base::tryCatch(...)
 18.                   | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 19.                   |   \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 20.                   |     \-base (local) doTryCatch(return(expr), name, parentenv, handler)
 21.                   \-x@protocol$read(x, cacheInfo)
 22.                     \-restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 23.                       \-restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sequencing.Rnw' failed with diagnostics:
Internal Server Error

--- failed re-building ‘sequencing.Rnw’

SUMMARY: processing the following files failed:
  ‘EPICv2.Rnw’ ‘sequencing.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/DMRcate.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DMRcate
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)