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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:LOLA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings LOLA_1.41.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/LOLA.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.41.0’
* 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 ‘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:
    5.       ├─methods::callGeneric(rgl, with.revmap = with.revmap)
    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-3.23-bioc/meat/LOLA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL LOLA
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘LOLA’ ...
** this is package ‘LOLA’ version ‘1.41.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (LOLA)

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(LOLA)
> 
> test_check("LOLA")
[ FAIL 1 | WARN 6 | SKIP 0 | PASS 27 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_all.R:31:2'): loadRegionDB ─────────────────────────────────────
Error in `S4Vectors:::load_package_gracefully("XVector", "by the range() method ", 
    "for CompressedIRangesList objects")`: 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")
Backtrace:
     ▆
  1. └─LOLA::buildRestrictedUniverse(GRangesList(userSet[1:50], userSet[51:100])) at test_all.R:31:9
  2.   ├─IRanges::disjoin(unlist(userSets))
  3.   └─GenomicRanges::disjoin(unlist(userSets))
  4.     └─GenomicRanges (local) .local(x, ...)
  5.       ├─methods::callGeneric(rgl, with.revmap = with.revmap)
  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