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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LOLA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LOLA_1.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/LOLA.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 ‘LOLA/DESCRIPTION’ ... OK
* this is package ‘LOLA’ 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 ‘LOLA’ 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 ... 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘LOLA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildRestrictedUniverse
> ### Title: If you want to test for differential enrichment within your
> ###   usersets, you can restrict the universe to only regions that are
> ###   covered in at least one of your sets. This function helps you build
> ###   just such a restricted universe
> ### Aliases: buildRestrictedUniverse
> 
> ### ** Examples
> 
> data("sample_input", package="LOLA") # load userSets
> restrictedUniverse = buildRestrictedUniverse(userSets)
Error in S4Vectors:::load_package_gracefully("XVector", "by the range() method ",  : 
  Could not load package XVector. Is it installed?

  Note that the XVector package is required by the range() method for
  CompressedIRangesList objects. Please install it with:

    BiocManager::install("XVector")
Calls: buildRestrictedUniverse ... .local -> .range_CompressedIRangesList -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6.       │ └─base::eval(call, parent.frame())
    7.       │   └─base::eval(call, parent.frame())
    8.       ├─IRanges::disjoin(rgl, with.revmap = with.revmap)
    9.       └─IRanges::disjoin(rgl, with.revmap = with.revmap)
   10.         └─IRanges (local) .local(x, ...)
   11.           ├─methods (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
   12.           └─IRanges (local) range(`<S4: CompressedIRangesList>`, na.rm = FALSE)
   13.             └─IRanges (local) .local(x, ..., na.rm = na.rm)
   14.               └─IRanges:::.range_CompressedIRangesList(x, with.revmap = with.revmap)
   15.                 └─S4Vectors:::load_package_gracefully(...)
  
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 27 ]
  Error:
  ! Test failures.
  Execution halted
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/LOLA.Rcheck/00check.log’
for details.