##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SPIAT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SPIAT_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SPIAT.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 ‘SPIAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPIAT’ version ‘1.11.0’
* 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 ‘SPIAT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* 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 LazyData ... 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
dimensionality_reduction_plot 20.634  0.149  20.783
calculate_percentage_of_grids  7.216  0.086   7.303
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ‘SPIAT.Rmd’ using rmarkdown
--- finished re-building ‘SPIAT.Rmd’

--- re-building ‘basic_analysis.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from basic_analysis.Rmd:34-46 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─SPIAT::define_celltypes(...)
  2. │ ├─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  3. │ └─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  4. │   ├─methods::callNextMethod()
  5. │   └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
  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 'basic_analysis.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘basic_analysis.Rmd’

--- re-building ‘cell-colocalisation.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from cell-colocalisation.Rmd:37-49 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─SPIAT::define_celltypes(...)
  2. │ ├─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  3. │ └─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  4. │   ├─methods::callNextMethod()
  5. │   └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
  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 'cell-colocalisation.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘cell-colocalisation.Rmd’

--- re-building ‘data_reading-formatting.Rmd’ using rmarkdown
--- finished re-building ‘data_reading-formatting.Rmd’

--- re-building ‘neighborhood.Rmd’ using rmarkdown
--- finished re-building ‘neighborhood.Rmd’

--- re-building ‘quality-control_visualisation.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from quality-control_visualisation.Rmd:40-52 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─SPIAT::define_celltypes(...)
  2. │ ├─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  3. │ └─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  4. │   ├─methods::callNextMethod()
  5. │   └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
  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 'quality-control_visualisation.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘quality-control_visualisation.Rmd’

--- re-building ‘spatial-heterogeneity.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from spatial-heterogeneity.Rmd:43-55 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─SPIAT::define_celltypes(...)
  2. │ ├─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  3. │ └─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  4. │   ├─methods::callNextMethod()
  5. │   └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
  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 'spatial-heterogeneity.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘spatial-heterogeneity.Rmd’

--- re-building ‘tissue-structure.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from tissue-structure.Rmd:46-58 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─SPIAT::define_celltypes(...)
  2. │ ├─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  3. │ └─`*tmp*`[, spe_object[[category_colname]] == categories[i]]
  4. │   ├─methods::callNextMethod()
  5. │   └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
  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 'tissue-structure.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘tissue-structure.Rmd’

SUMMARY: processing the following files failed:
  ‘basic_analysis.Rmd’ ‘cell-colocalisation.Rmd’
  ‘quality-control_visualisation.Rmd’ ‘spatial-heterogeneity.Rmd’
  ‘tissue-structure.Rmd’

Error: Vignette re-building failed.
Execution halted

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

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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SPIAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SPIAT’ ...
** this is package ‘SPIAT’ version ‘1.11.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SPIAT)

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(SPIAT)
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("SPIAT")
[1] "Markers had been selected in minimum distance calculation: "
[1] "Immune1" "Tumour" 
[1] "Crossing of cross K function is detected for this image, indicating a potential immune ring."
[1] "The crossing happens at the 50% of the specified distance."
[1] "The alpha of Polygon is: 63.24375"
[1] "Markers had been selected in minimum distance calculation: "
[1] "Non-border" "Border"    
[1] "Tumour_marker"
[1] "Immune_marker1"
[1] "Immune_marker2"
[1] "Immune_marker3"
[1] "Immune_marker4"
[1] "Tumour_marker"
[1] "Immune_marker1"
[1] "Immune_marker2"
[1] "Immune_marker3"
[1] "Immune_marker4"
[1] "Tumour_marker  threshold intensity:  0.445450443784465"
[1] "Immune_marker1  threshold intensity:  0.116980867970434"
[1] "Immune_marker2  threshold intensity:  0.124283809517202"
[1] "Immune_marker3  threshold intensity:  0.0166413130263845"
[1] "Immune_marker4  threshold intensity:  0.00989731350898589"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 80 ]
> 
> proc.time()
   user  system elapsed 
 62.768   1.969  64.719