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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:RepViz.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings RepViz_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/RepViz.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘RepViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RepViz’ version ‘1.27.0’
* 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 ‘RepViz’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES IN VERSION 0.99.26
      RELEASE
      + Correction of a visual bug that appeared when there is low signal. This was due to the fact that the coverage was stopping at the last read instead of at the end of the window. As the result the lines of signal on the plot appeared cutted.
* 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 ... NOTE
unitTest: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'RepViz.Rd':
RepViz
  Code: function(region, genome = c("hg19", "hg38", "mm10"), BAM =
                 NULL, BED = NULL, avgTrack = TRUE, geneTrack = TRUE,
                 max = NULL, verbose = TRUE, cex = 1, col = NULL)
  Docs: function(region, genome = c("hg19", "hg38", "mm10"), BAM =
                 NULL, BED = NULL, avgTrack = TRUE, geneTrack = TRUE,
                 max = NULL, verbose = TRUE, cex = 1)
  Argument names in code not in docs:
    col

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'RepViz.Rd':
  ‘col’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RepViz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RepViz
> ### Title: Plot a genomic region
> ### Aliases: RepViz
> 
> ### ** Examples
> 
> region <- GRanges('chr12:110938000-110940000')
> setwd(tempdir())
> #Copying the files to the user working directory
> file.copy(from = list.files(system.file('extdata', package = 'RepViz'), full.names = TRUE),
+     to = tempdir())
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> #Generate the visualization of the given region
> RepViz::RepViz(region = region,
+     genome = 'hg19',
+     BAM = 'BAM_input.csv',
+     BED = 'BED_input.csv',
+     avgTrack = TRUE,
+     geneTrack = TRUE)
loading the BAM related data from BAM_input.csv

loading the BED related data from BED_input.csv

plotting the coverages 

plotting the BED files 

overlapping peaks with region 

load the peak files 

plotting the gene track 

Error: Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
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 ‘RepViz.Rmd’ using rmarkdown

Quitting from RepViz.Rmd:80-93 [plot_plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
---
Backtrace:
    ▆
 1. └─RepViz::RepViz(...)
 2.   └─RepViz:::getBiomaRt(region, genome)
 3.     └─biomaRt::useMart(...)
 4.       └─biomaRt:::.useMart(...)
 5.         └─biomaRt:::.listMarts(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RepViz.Rmd' failed with diagnostics:
Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
--- failed re-building ‘RepViz.Rmd’

SUMMARY: processing the following file failed:
  ‘RepViz.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/RepViz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL RepViz
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘RepViz’ ...
** this is package ‘RepViz’ version ‘1.27.0’
** 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 (RepViz)