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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings methylPipe_1.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/methylPipe.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 ‘methylPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylPipe’ version ‘1.40.0’
* 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 ‘methylPipe’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 whether startup messages can be suppressed ... 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 ... NOTE
findPMDs,BSdata : PMDchr: no visible global function definition for
  'segmentPMDs'
show,BSdata: no visible global function definition for 'organism'
show,BSdataSet: no visible global function definition for 'organism'
Undefined global functions or variables:
  organism segmentPMDs
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'BSdataSet,ANY,ANY,ANY'
  generic '[' and siglist 'GElist,ANY,ANY,ANY'
  generic '[[<-' and siglist 'BSdataSet,ANY,ANY,ANY'
  generic '[[<-' and siglist 'GElist,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘methylPipe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMeth
> ### Title: Plot DNA methylation together with other omics, or annotation
> ###   data for a genomic region
> ### Aliases: plotMeth
> 
> ### ** Examples
> 
> require(TxDb.Hsapiens.UCSC.hg18.knownGene)
Loading required package: TxDb.Hsapiens.UCSC.hg18.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
> txdb <- TxDb.Hsapiens.UCSC.hg18.knownGene
> require(BSgenome.Hsapiens.UCSC.hg18)
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

> gecH1_file <- system.file('extdata', 'gec.H1.Rdata', package='methylPipe')
> load(gecH1_file)
> gecIMR_file <- system.file('extdata', 'gec.IMR90.Rdata', package='methylPipe')
> load(gecIMR_file)
> gel <- GElist(gecH1=gec.H1, gecIMR90=gec.IMR90)
> uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
> H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
> H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
> IMR90data <- system.file('extdata', 'IMR90_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
> IMR90.db <- BSdata(file=IMR90data, uncov=uncov_GR, org=Hsapiens)
> H1.IMR90.set <- list(H1=H1.db, IMR90=IMR90.db)
> plotMeth(gel, colors=c("red","blue"), datatype=c("mC","mC"), yLim=c(.025, .025), brmeth=H1.IMR90.set, mcContext="CG", transcriptDB=txdb, chr="chr20", start=14350 , end=474481, org=Hsapiens)
Error in errorHandler(responseError) : Internal Server Error
Calls: plotMeth ... 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 ‘methylPipe.rnw’ using knitr
Warning in in_dir(input_dir(), expr) :
  You changed the working directory to /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpFIG3go (probably via setwd()). It will be restored to /home/biocbuild/bbs-3.20-bioc/meat/methylPipe.Rcheck/vign_test/methylPipe/vignettes. See the Note section in ?knitr::knit

Quitting from methylPipe.rnw:239-245 [pmeth]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
     x
  1. \-methylPipe::plotMeth(...)
  2.   \-Gviz::IdeogramTrack(genome = gen, chromosome = chr)
  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 'methylPipe.rnw' failed with diagnostics:
Internal Server Error

--- failed re-building ‘methylPipe.rnw’

SUMMARY: processing the following file failed:
  ‘methylPipe.rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/methylPipe.Rcheck/00check.log’
for details.