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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GloScope.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GloScope_1.99.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GloScope.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 ‘GloScope/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GloScope’ version ‘1.99.1’
* 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 ‘GloScope’ 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getMetrics 20.729  0.130  20.860
plotCI      9.620  0.072   9.692
* 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:
   21. │                               └─SummarizedExperiment (local) .nextMethod(object = object)
   22. │                                 ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
   23. │                                 └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   24. │                                   ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   25. │                                   └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   26. │                                     └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   27. ├─methods:::.extendsForS3(`<chr>`)
   28. │ └─methods::extends(Class, maybe = FALSE)
   29. │   └─methods::getClassDef(class1)
   30. │     └─methods:::.requirePackage(package)
   31. │       └─base::stop(...)
   32. └─base::.handleSimpleError(...)
   33.   └─testthat (local) h(simpleError(msg, call))
   34.     └─rlang::abort(...)
  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 ‘GloScopeTutorial.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from GloScopeTutorial.Rmd:79-82 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─utils::head(...)
  2. ├─SingleCellExperiment::reducedDim(example_SCE, "PCA")
  3. ├─SingleCellExperiment::reducedDim(example_SCE, "PCA")
  4. │ └─SingleCellExperiment (local) .local(x, type, ...)
  5. │   └─SingleCellExperiment:::.get_internal_character(...)
  6. │     ├─BiocGenerics::updateObject(x)
  7. │     └─SingleCellExperiment::updateObject(x)
  8. │       ├─methods::callNextMethod()
  9. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 10. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 11. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 12. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 13. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 14. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 15. └─methods:::.extendsForS3(`<chr>`)
 16.   └─methods::extends(Class, maybe = FALSE)
 17.     └─methods::getClassDef(class1)
 18.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GloScopeTutorial.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘GloScopeTutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GloScope.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GloScope
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GloScope’ ...
** this is package ‘GloScope’ version ‘1.99.1’
** using staged installation
** R
** data
** 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 (GloScope)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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(GloScope)
> 
> test_check("GloScope")
Loading required namespace: GenomeInfoDb
Failed with error:  'there is no package called 'GenomeInfoDb''
Error in `FUN()`:
! In path: "/home/biocbuild/bbs-3.22-bioc/meat/GloScope.Rcheck/tests/testthat/setup_data.R"
Caused by error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::test_check("GloScope")
  2. │ └─testthat::test_dir(...)
  3. │   └─testthat:::test_files(...)
  4. │     └─testthat:::test_files_serial(...)
  5. │       └─testthat:::test_files_setup_state(...)
  6. │         └─testthat::source_test_setup(".", env)
  7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
  8. │             └─base::lapply(...)
  9. │               └─testthat (local) FUN(X[[i]], ...)
 10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
 11. │                   ├─base::withCallingHandlers(...)
 12. │                   └─base::eval(exprs, env)
 13. │                     └─base::eval(exprs, env)
 14. │                       ├─SingleCellExperiment::reducedDim(example_SCE, "PCA") at tests/testthat/setup_data.R:7:1
 15. │                       └─SingleCellExperiment::reducedDim(example_SCE, "PCA")
 16. │                         └─SingleCellExperiment (local) .local(x, type, ...)
 17. │                           └─SingleCellExperiment:::.get_internal_character(...)
 18. │                             ├─BiocGenerics::updateObject(x)
 19. │                             └─SingleCellExperiment::updateObject(x)
 20. │                               ├─methods::callNextMethod()
 21. │                               └─SummarizedExperiment (local) .nextMethod(object = object)
 22. │                                 ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 23. │                                 └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 24. │                                   ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 25. │                                   └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 26. │                                     └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 27. ├─methods:::.extendsForS3(`<chr>`)
 28. │ └─methods::extends(Class, maybe = FALSE)
 29. │   └─methods::getClassDef(class1)
 30. │     └─methods:::.requirePackage(package)
 31. │       └─base::stop(...)
 32. └─base::.handleSimpleError(...)
 33.   └─testthat (local) h(simpleError(msg, call))
 34.     └─rlang::abort(...)
Execution halted