##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:regionReport.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings regionReport_1.43.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/regionReport.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘regionReport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regionReport’ version ‘1.43.1’
* 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 ‘regionReport’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘DESeq2:::pvalueAdjustment’
  See the note in ?`:::` about the use of this operator.
* 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 'derfinderReport.Rd':
  ‘[ggbio:plotSingleChrom]{plotIdeogram}’

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 ‘regionReport-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: derfinderReport
> ### Title: Generate a HTML/PDF report exploring the basic results from
> ###   derfinder
> ### Aliases: derfinderReport
> 
> ### ** Examples
> 
> 
> ## Load derfinder
> library("derfinder")
> 
> ## The output will be saved in the 'derfinderReport-example' directory
> dir.create("derfinderReport-example", showWarnings = FALSE, recursive = TRUE)
> 
> ## For convenience, the derfinder output has been pre-computed
> file.copy(system.file(file.path("extdata", "chr21"),
+     package = "derfinder",
+     mustWork = TRUE
+ ), "derfinderReport-example", recursive = TRUE)
[1] TRUE
> ## Not run: 
> ##D ## If you prefer, you can generate the output from derfinder
> ##D initialPath <- getwd()
> ##D setwd(file.path(initialPath, "derfinderReport-example"))
> ##D 
> ##D ## Collapse the coverage information
> ##D collapsedFull <- collapseFullCoverage(list(genomeData$coverage),
> ##D     verbose = TRUE
> ##D )
> ##D 
> ##D ## Calculate library size adjustments
> ##D sampleDepths <- sampleDepth(collapsedFull,
> ##D     probs = c(0.5), nonzero = TRUE,
> ##D     verbose = TRUE
> ##D )
> ##D 
> ##D ## Build the models
> ##D group <- genomeInfo$pop
> ##D adjustvars <- data.frame(genomeInfo$gender)
> ##D models <- makeModels(sampleDepths, testvars = group, adjustvars = adjustvars)
> ##D 
> ##D ## Analyze chromosome 21
> ##D analyzeChr(
> ##D     chr = "21", coverageInfo = genomeData, models = models,
> ##D     cutoffFstat = 1, cutoffType = "manual", seeds = 20140330, groupInfo = group,
> ##D     mc.cores = 1, writeOutput = TRUE, returnOutput = FALSE
> ##D )
> ##D 
> ##D ## Change the directory back to the original one
> ##D setwd(initialPath)
> ## End(Not run)
> 
> ## Merge the results from the different chromosomes. In this case, there's
> ## only one: chr21
> mergeResults(
+     chrs = "21", prefix = "derfinderReport-example",
+     genomicState = genomicState$fullGenome
+ )
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
2025-09-16 03:19:14.307485 mergeResults: Saving options used
2025-09-16 03:19:14.308307 Loading chromosome chr21
Neither 'cutoffFstatUsed' nor 'optionsStats' were supplied, so the FWER calculation step will be skipped.
2025-09-16 03:19:14.37859 mergeResults: Saving fullNullSummary
2025-09-16 03:19:14.379188 mergeResults: Re-calculating the p-values
2025-09-16 03:19:14.476374 mergeResults: Saving fullRegions
2025-09-16 03:19:14.477479 mergeResults: assigning genomic states
2025-09-16 03:19:14.59893 annotateRegions: counting
2025-09-16 03:19:14.688613 annotateRegions: annotating
2025-09-16 03:19:14.718809 mergeResults: Saving fullAnnotatedRegions
2025-09-16 03:19:14.719727 mergeResults: Saving fullFstats
2025-09-16 03:19:14.720374 mergeResults: Saving fullTime
> 
> ## Load the options used for calculating the statistics
> load(file.path("derfinderReport-example", "chr21", "optionsStats.Rdata"))
> 
> ## Generate the HTML report
> report <- derfinderReport(
+     prefix = "derfinderReport-example", browse = FALSE,
+     nBestRegions = 15, makeBestClusters = TRUE,
+     fullCov = list("21" = genomeDataRaw$coverage), optionsStats = optionsStats
+ )
Writing 9 Bibtex entries ... OK
Results written to file 'derfinderReport-example/basicExploration/basicExploration.bib'
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens


processing file: basicExploration.Rmd
Error in validObject(.Object) : 
  invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
Calls: derfinderReport ... <Anonymous> -> initialize -> initialize -> validObject

Quitting from basicExploration.Rmd:358-360 [genomeOverview1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
     ▆
  1. └─regionReport::derfinderReport(...)
  2.   ├─regionReport:::with_wd(...)
  3.   │ └─base::eval(expr, envir = parent.frame())
  4.   ├─rmarkdown::render(...)
  5.   │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  6.   │   └─knitr:::process_file(text, output)
  7.   │     ├─xfun:::handle_error(...)
  8.   │     ├─base::withCallingHandlers(...)
  9.   │     └─knitr:::process_group(group)
 10.   │       └─knitr:::call_block(x)
 11.   │         └─knitr:::block_exec(params)
 12.   │           └─knitr:::eng_r(options)
 13.   │             ├─knitr:::in_input_dir(...)
 14.   │             │ └─knitr:::in_dir(input_dir(), expr)
 15.   │             └─knitr (local) evaluate(...)
 16.   │               └─evaluate::evaluate(...)
 17.   │                 ├─base::withRestarts(...)
 18.   │                 │ └─base (local) withRestartList(expr, restarts)
 19.   │                 │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 20.   │                 │   │ └─base (local) doWithOneRestart(return(expr), restart)
 21.   │                 │   └─base (local) withRestartList(expr, restarts[-nr])
 22.   │                 │     └─base (local) withOneRestart(expr, restarts[[1L]])
 23.   │                 │       └─base (local) doWithOneRestart(return(expr), restart)
 24.   │                 ├─evaluate:::with_handlers(...)
 25.   │                 │ ├─base::eval(call)
 26.   │                 │ │ └─base::eval(call)
 27.   │                 │ └─base::withCallingHandlers(...)
 28.   │                 ├─base::withVisible(eval(expr, envir))
 29.   │                 └─base::eval(expr, envir)
 30.   │                   └─base::eval(expr, envir)
 31.   └─derfinderPlot::plotOverview(...)
 32.     ├─ggplot2::autoplot(seqinfo(regions))
 33.     └─ggbio::autoplot(seqinfo(regions))
 34.       └─ggbio (local) .local(object, ...)
 35.         └─ggbio::GGbio(p, data = object)
 36.           ├─BiocGenerics::do.call(...)
 37.           ├─base::do.call(...)
 38.           └─methods (local) `<fn>`(...)
 39.             ├─methods::initialize(value, ...)
 40.             └─methods::initialize(value, ...)
 41.               └─methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
DESeq2Report 26.2  0.789  26.978
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/regionReport.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL regionReport
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘regionReport’ ...
** this is package ‘regionReport’ version ‘1.43.1’
** 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 (regionReport)