##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SpaNorm.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SpaNorm_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SpaNorm.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpaNorm/DESCRIPTION’ ... OK
* this is package ‘SpaNorm’ version ‘1.3.0’
* 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 ‘SpaNorm’ 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 ... NOTE
plotSpatial: no visible binding for global variable ‘x’
plotSpatial: no visible binding for global variable ‘y’
plotSpatial: no visible binding for global variable ‘colour’
plotSpatial: no visible binding for global variable ‘r’
Undefined global functions or variables:
  colour r x y
* 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 ‘SpaNorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fastSizeFactors
> ### Title: Filter genes based on expression
> ### Aliases: fastSizeFactors fastSizeFactors,SpatialExperiment-method
> 
> ### ** Examples
> 
> data(HumanDLPFC)
> HumanDLPFC <- fastSizeFactors(HumanDLPFC)
Loading required namespace: SpatialExperiment
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: fastSizeFactors ... .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:
   17. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   18. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   19. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   20. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   21. ├─methods:::.extendsForS3(`<chr>`)
   22. │ └─methods::extends(Class, maybe = FALSE)
   23. │   └─methods::getClassDef(class1)
   24. │     └─methods:::.requirePackage(package)
   25. │       └─base::stop(...)
   26. └─base::.handleSimpleError(...)
   27.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 80 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SpaNorm.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SpaNorm
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘SpaNorm’ ...
** this is package ‘SpaNorm’ version ‘1.3.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘fastSizeFactors’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
in method for ‘filterGenes’ with signature ‘"SpatialExperiment","ANY"’: no definition for class “SpatialExperiment”
in method for ‘filterGenes’ with signature ‘"Seurat","ANY"’: no definition for class “Seurat”
in method for ‘SpaNorm’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
** 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 (SpaNorm)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(SpaNorm)
> 
> test_check("SpaNorm")
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''
Loading required namespace: GenomeInfoDb
Failed with error:  'there is no package called 'GenomeInfoDb''
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 80 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-fastSizeFactors.R:5:3'): fastSizeFactors works ─────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'spe' in selecting a method for function 'filterGenes': unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_error(filterGenes(HumanDLPFC[, 0]), "ncol") at test-fastSizeFactors.R:5:3
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. ├─SpaNorm::filterGenes(HumanDLPFC[, 0])
  8. ├─HumanDLPFC[, 0]
  9. ├─HumanDLPFC[, 0]
 10. │ ├─methods::callNextMethod()
 11. │ └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
 12. │   ├─BiocGenerics::updateObject(x)
 13. │   └─SingleCellExperiment::updateObject(x)
 14. │     ├─methods::callNextMethod()
 15. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 16. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 17. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 18. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 19. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 20. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 21. ├─methods:::.extendsForS3(`<chr>`)
 22. │ └─methods::extends(Class, maybe = FALSE)
 23. │   └─methods::getClassDef(class1)
 24. │     └─methods:::.requirePackage(package)
 25. │       └─base::stop(...)
 26. └─base::.handleSimpleError(...)
 27.   └─base (local) h(simpleError(msg, call))
── Error ('test-filterGenes.R:13:3'): check SpatialExperiment works ────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_error(checkSPE(HumanDLPFC[0, 0]), "nrow.+ncol") at test-filterGenes.R:13:3
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. ├─SpaNorm:::checkSPE(HumanDLPFC[0, 0])
  8. │ ├─base::stopifnot(is(spe, "SpatialExperiment"))
  9. │ └─methods::is(spe, "SpatialExperiment")
 10. ├─HumanDLPFC[0, 0]
 11. ├─HumanDLPFC[0, 0]
 12. │ ├─methods::callNextMethod()
 13. │ └─SingleCellExperiment (local) .nextMethod(x = x, i = i, j = j)
 14. │   ├─BiocGenerics::updateObject(x)
 15. │   └─SingleCellExperiment::updateObject(x)
 16. │     ├─methods::callNextMethod()
 17. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 18. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 19. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 20. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 21. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 22. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 23. └─methods:::.extendsForS3(`<chr>`)
 24.   └─methods::extends(Class, maybe = FALSE)
 25.     └─methods::getClassDef(class1)
 26.       └─methods:::.requirePackage(package)
── Error ('test-filterGenes.R:22:3'): check Seurat works ───────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─base::suppressWarnings(Seurat::as.Seurat(HumanDLPFC)) at test-filterGenes.R:22:3
  2. │ └─base::withCallingHandlers(...)
  3. ├─Seurat::as.Seurat(HumanDLPFC)
  4. ├─Seurat:::as.Seurat.SingleCellExperiment(HumanDLPFC)
  5. │ ├─SingleCellExperiment::altExpNames(x = x)
  6. │ └─SingleCellExperiment::altExpNames(x = x)
  7. │   └─SingleCellExperiment (local) .local(x, ...)
  8. │     └─SingleCellExperiment:::.get_internal_names(...)
  9. │       ├─BiocGenerics::updateObject(x)
 10. │       └─SingleCellExperiment::updateObject(x)
 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-filterGenes.R:44:3'): check filterGenes works ──────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'spe' in selecting a method for function 'filterGenes': unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_error(filterGenes(HumanDLPFC[, 0]), "ncol") at test-filterGenes.R:44:3
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. ├─SpaNorm::filterGenes(HumanDLPFC[, 0])
  8. ├─HumanDLPFC[, 0]
  9. ├─HumanDLPFC[, 0]
 10. │ ├─methods::callNextMethod()
 11. │ └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
 12. │   ├─BiocGenerics::updateObject(x)
 13. │   └─SingleCellExperiment::updateObject(x)
 14. │     ├─methods::callNextMethod()
 15. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 16. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 17. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 18. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 19. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 20. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 21. ├─methods:::.extendsForS3(`<chr>`)
 22. │ └─methods::extends(Class, maybe = FALSE)
 23. │   └─methods::getClassDef(class1)
 24. │     └─methods:::.requirePackage(package)
 25. │       └─base::stop(...)
 26. └─base::.handleSimpleError(...)
 27.   └─base (local) h(simpleError(msg, call))

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 80 ]
Error: Test failures
Execution halted