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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylPipe_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/methylPipe.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylPipe’ version ‘1.41.0’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BSdata-class.Rd: GRanges
  GEcollection-class.Rd: RangedSummarizedExperiment, GRanges
  consolidateDMRs.Rd: GRanges
  extractBinGRanges.Rd: GRanges
  findDMR.Rd: GRanges
  getCpos.Rd: GRanges, DNAString
  getCposDensity.Rd: GRanges
  mapBSdata2GRanges.Rd: GRanges
  meth.call.Rd: GRanges
  plotMeth.Rd: GRanges, GRangesList
  process.hmc.Rd: GRanges, coverage, GenomicRanges
  profileDNAmetBin.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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
> 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)
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Error in errorHandler(responseError) : Internal Server Error
Calls: plotMeth ... doTryCatch -> <Anonymous> -> handleResponse -> errorHandler
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
findDMR   0.366  0.614  10.873
methstats 0.289  0.069   8.007
findPMDs  0.057  0.054   8.210
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/methylPipe.Rcheck/00check.log’
for details.