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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RegionalST_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RegionalST.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 ‘RegionalST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RegionalST’ version ‘1.7.0’
* 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 ‘RegionalST’ 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
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  ‘OneRegOut1’
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  ‘twoCenter’
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  ‘OneRegOut2’
Undefined global functions or variables:
  OneRegOut1 OneRegOut2 twoCenter
* 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 ‘RegionalST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetCellTypeSpecificDE_withProp
> ### Title: Identify cross-regional cell type-specific differential analysis
> ###   with proportion
> ### Aliases: GetCellTypeSpecificDE_withProp
> 
> ### ** Examples
> 
> data("example_sce")
> example_sce <- mySpatialPreprocess(example_sce, platform="Visium")
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: mySpatialPreprocess ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
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:
   11. │           ├─methods::callNextMethod()
   12. │           └─SummarizedExperiment (local) .nextMethod(object = object)
   13. │             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
   14. │             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   15. │               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   16. │               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   17. │                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   18. └─methods:::.extendsForS3(`<chr>`)
   19.   └─methods::extends(Class, maybe = FALSE)
   20.     └─methods::getClassDef(class1)
   21.       └─methods:::.requirePackage(package)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  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 ‘RegionalST.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from RegionalST.Rmd:118-129 [pre1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─example_sce[, colSums(counts(example_sce)) > 0]
  2. ├─example_sce[, colSums(counts(example_sce)) > 0]
  3. │ ├─BiocGenerics::updateObject(x)
  4. │ └─SingleCellExperiment::updateObject(x)
  5. │   ├─methods::callNextMethod()
  6. │   └─SummarizedExperiment (local) .nextMethod(object = object)
  7. │     ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
  8. │     └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
  9. │       ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 10. │       └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 11. │         └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 12. └─methods:::.extendsForS3(`<chr>`)
 13.   └─methods::extends(Class, maybe = FALSE)
 14.     └─methods::getClassDef(class1)
 15.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/RegionalST.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RegionalST
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘RegionalST’ ...
** this is package ‘RegionalST’ version ‘1.7.0’
** 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 (RegionalST)

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(RegionalST)
> 
> test_check("RegionalST")
Loading required namespace: GenomeInfoDb
Failed with error:  'there is no package called 'GenomeInfoDb''
Loading required namespace: GenomeInfoDb
Failed with error:  'there is no package called 'GenomeInfoDb''
Loading required namespace: GenomeInfoDb
Failed with error:  'there is no package called 'GenomeInfoDb''
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-GetCrossRegionalDE_raw.R:5:5'): GetCrossRegionalDE_raw works ───
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─RegionalST::mySpatialPreprocess(example_sce, platform = "Visium") at test-GetCrossRegionalDE_raw.R:5:5
  2. │ ├─scater::logNormCounts(sce)
  3. │ └─scater::logNormCounts(sce)
  4. │   └─scuttle (local) .local(x, ...)
  5. │     ├─scuttle:::.replace(size.factors, size_factors)
  6. │     ├─BiocGenerics::sizeFactors(x)
  7. │     └─SingleCellExperiment::sizeFactors(x)
  8. │       └─SingleCellExperiment (local) .local(object, ...)
  9. │         ├─BiocGenerics::updateObject(object)
 10. │         └─SingleCellExperiment::updateObject(object)
 11. │           ├─methods::callNextMethod()
 12. │           └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)
── Error ('test-GetOneRadiusEntropy.R:13:5'): GetOneRadiusEntropy works ────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─RegionalST::mySpatialPreprocess(example_sce, platform = "Visium") at test-GetOneRadiusEntropy.R:13:5
  2. │ ├─scater::logNormCounts(sce)
  3. │ └─scater::logNormCounts(sce)
  4. │   └─scuttle (local) .local(x, ...)
  5. │     ├─scuttle:::.replace(size.factors, size_factors)
  6. │     ├─BiocGenerics::sizeFactors(x)
  7. │     └─SingleCellExperiment::sizeFactors(x)
  8. │       └─SingleCellExperiment (local) .local(object, ...)
  9. │         ├─BiocGenerics::updateObject(object)
 10. │         └─SingleCellExperiment::updateObject(object)
 11. │           ├─methods::callNextMethod()
 12. │           └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)
── Error ('test-PlotOneSelectCenter.R:4:1'): (code run outside of `test_that()`) ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─RegionalST::mySpatialPreprocess(example_sce, platform = "Visium") at test-PlotOneSelectCenter.R:4:1
  2. │ ├─scater::logNormCounts(sce)
  3. │ └─scater::logNormCounts(sce)
  4. │   └─scuttle (local) .local(x, ...)
  5. │     ├─scuttle:::.replace(size.factors, size_factors)
  6. │     ├─BiocGenerics::sizeFactors(x)
  7. │     └─SingleCellExperiment::sizeFactors(x)
  8. │       └─SingleCellExperiment (local) .local(object, ...)
  9. │         ├─BiocGenerics::updateObject(object)
 10. │         └─SingleCellExperiment::updateObject(object)
 11. │           ├─methods::callNextMethod()
 12. │           └─SummarizedExperiment (local) .nextMethod(object = object)
 13. │             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 16. │               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 17. │                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 18. └─methods:::.extendsForS3(`<chr>`)
 19.   └─methods::extends(Class, maybe = FALSE)
 20.     └─methods::getClassDef(class1)
 21.       └─methods:::.requirePackage(package)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]
Error: Test failures
Execution halted