##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:derfinderPlot.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings derfinderPlot_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/derfinderPlot.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘derfinderPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinderPlot’ version ‘1.43.0’
* package encoding: UTF-8
* 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 ‘derfinderPlot’ 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 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'plotCluster.Rd':
  ‘[ggbio:plotSingleChrom]{plotIdeogram}’

Non-topic package-anchored link(s) in Rd file 'plotOverview.Rd':
  ‘[ggplot2:element]{element_text}’

Non-topic package-anchored link(s) in Rd file 'vennRegions.Rd':
  ‘[limma:venn]{vennDiagram}’ ‘[limma:venn]{vennCounts}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ‘derfinderPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotRegionCoverage
> ### Title: Makes plots for every region while summarizing the annotation
> ### Aliases: plotRegionCoverage
> 
> ### ** Examples
> 
> ## Load data
> library("derfinder")
> 
> ## Annotate regions, first two regions only
> regions <- genomeRegions$regions[1:2]
> annotatedRegions <- annotateRegions(
+     regions = regions,
+     genomicState = genomicState$fullGenome, minoverlap = 1
+ )
2025-07-23 20:26:08.135589 annotateRegions: counting
2025-07-23 20:26:08.244808 annotateRegions: annotating
> 
> ## Find nearest annotation with bumphunter::matchGenes()
> library("bumphunter")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.12 	 2025-03-05
> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene)
No annotationPackage supplied. Trying org.Hs.eg.db.
Loading required package: org.Hs.eg.db
Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
> nearestAnnotation <- matchGenes(x = regions, subject = genes)
> 
> ## Obtain fullCov object
> fullCov <- list("21" = genomeDataRaw$coverage)
> 
> ## Assign chr lengths using hg19 information
> library("GenomicRanges")
> seqlengths(regions) <- seqlengths(getChromInfoFromUCSC("hg19",
+     as.Seqinfo = TRUE
+ ))[
+     mapSeqlevels(names(seqlengths(regions)), "UCSC")
+ ]
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'seqlengths': could not find function "getChromInfoFromUCSC"
Calls: seqlengths -> .handleSimpleError -> h
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plotCluster 62.588  1.154  64.075
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/derfinderPlot.Rcheck/00check.log’
for details.