##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scider.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scider_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scider.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 ‘scider/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scider’ version ‘1.7.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘scider’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scider-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findNbrsSNN
> ### Title: Construct a SNN neighbour list from assay.
> ### Aliases: findNbrsSNN
> 
> ### ** Examples
> 
> 
> data("xenium_bc_spe")
> spe <- runPCA(spe)
Default assay logcounts not found. Switching to counts assay instead.
Genes with 0 variance are excluded: ENSG00000135218 NegControlProbe_00002 NegControlCodeword_0504 NegControlCodeword_0509 NegControlCodeword_0510 NegControlCodeword_0511 NegControlCodeword_0512 NegControlCodeword_0516 NegControlCodeword_0517 NegControlCodeword_0518 NegControlCodeword_0519 NegControlCodeword_0520 NegControlCodeword_0522 NegControlCodeword_0526 NegControlCodeword_0527 NegControlCodeword_0530 NegControlCodeword_0536 NegControlCodeword_0537 BLANK_0030 BLANK_0163 BLANK_0165 BLANK_0212 BLANK_0221 BLANK_0230 BLANK_0237 BLANK_0311 BLANK_0361 BLANK_0365 BLANK_0382 BLANK_0384 BLANK_0387 BLANK_0388 BLANK_0391 BLANK_0393 BLANK_0397 BLANK_0399 BLANK_0404 BLANK_0406 BLANK_0410 BLANK_0411 BLANK_0418 BLANK_0425 BLANK_0432 BLANK_0447
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: runPCA ... .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:
    7. │     ├─methods::callNextMethod()
    8. │     └─SummarizedExperiment (local) .nextMethod(object = object)
    9. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
   10. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   11. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   12. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   13. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   14. └─methods:::.extendsForS3(`<chr>`)
   15.   └─methods::extends(Class, maybe = FALSE)
   16.     └─methods::getClassDef(class1)
   17.       └─methods:::.requirePackage(package)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 61 ]
  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 ‘scider_userGuide.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from scider_userGuide.Rmd:76-78 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(...)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   ├─knitr:::in_input_dir(...)
 18. │                   │ └─knitr:::in_dir(input_dir(), expr)
 19. │                   └─knitr (local) evaluate(...)
 20. │                     └─evaluate::evaluate(...)
 21. │                       ├─base::withRestarts(...)
 22. │                       │ └─base (local) withRestartList(expr, restarts)
 23. │                       │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 24. │                       │   │ └─base (local) doWithOneRestart(return(expr), restart)
 25. │                       │   └─base (local) withRestartList(expr, restarts[-nr])
 26. │                       │     └─base (local) withOneRestart(expr, restarts[[1L]])
 27. │                       │       └─base (local) doWithOneRestart(return(expr), restart)
 28. │                       ├─evaluate:::with_handlers(...)
 29. │                       │ ├─base::eval(call)
 30. │                       │ │ └─base::eval(call)
 31. │                       │ └─base::withCallingHandlers(...)
 32. │                       └─watcher$print_value(ev$value, ev$visible, envir)
 33. │                         ├─base::withVisible(handle_value(handler, value, visible, envir))
 34. │                         └─evaluate:::handle_value(handler, value, visible, envir)
 35. │                           └─handler$value(value, visible)
 36. │                             └─knitr (local) fun(x, options = options)
 37. │                               ├─base::withVisible(knit_print(x, ...))
 38. │                               ├─knitr::knit_print(x, ...)
 39. │                               └─knitr:::knit_print.default(x, ...)
 40. │                                 └─knitr::normal_print(x)
 41. │                                   ├─methods::show(x)
 42. │                                   └─methods::show(x)
 43. │                                     ├─methods::callNextMethod()
 44. │                                     └─SingleCellExperiment (local) .nextMethod(object = object)
 45. │                                       ├─S4Vectors::coolcat("reducedDimNames(%d): %s\n", reducedDimNames(object))
 46. │                                       │ └─base::ifelse(nzchar(vals), vals, "''")
 47. │                                       ├─SingleCellExperiment::reducedDimNames(object)
 48. │                                       └─SingleCellExperiment::reducedDimNames(object)
 49. │                                         └─SingleCellExperiment:::.get_internal_names(...)
 50. │                                           ├─BiocGenerics::updateObject(x)
 51. │                                           └─SingleCellExperiment::updateObject(x)
 52. │                                             ├─methods::callNextMethod()
 53. │                                             └─SummarizedExperiment (local) .nextMethod(object = object)
 54. │                                               ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 55. │                                               └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 56. │                                                 ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 57. │                                                 └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 58. │                                                   └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 59. └─methods:::.extendsForS3(`<chr>`)
 60.   └─methods::extends(Class, maybe = FALSE)
 61.     └─methods::getClassDef(class1)
 62.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scider.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scider’ ...
** this is package ‘scider’ version ‘1.7.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c C_findSNN.cpp -o C_findSNN.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c C_globalMoran.cpp -o C_globalMoran.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c C_localMoran.cpp -o C_localMoran.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o scider.so C_findSNN.o C_globalMoran.o C_localMoran.o utils.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-scider/00new/scider/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scider)

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(scider)
> 
> test_check("scider")
Assigning cells to ROIs defined by Breast cancer 

No contour detected. Proceed without contour.
Using bins = 10 to draw contours with equal cell numbers.
Assigning cells to ROIs defined by Breast cancer 

Assigning cells to contour levels of Breast cancer 

Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE
Using bins = 10 to draw contours with equal cell numbers.
cell_typess is not a column of the colData. Skipping cell_typess
Using bins = 10 to draw contours with equal cell numbers.
Assigning cells to ROIs defined by Breast cancer fibroblasts 

Assigning cells to contour levels of Breast cancer 

Using bins = 10 to draw contours with equal cell numbers.
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Loading required namespace: GenomeInfoDb
Failed with error:  'there is no package called 'GenomeInfoDb''
Assigning cells to ROIs defined by Breast cancer 

No contour detected. Proceed without contour.
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 61 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotContour.R:7:5'): plotContour works ─────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'spatialCoords': unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_silent(plotContour(spe, coi = coi)) at test-plotContour.R:7:5
  2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ ├─withr::with_output_sink(...)
  5. │   │ │ └─base::force(code)
  6. │   │ ├─base::withCallingHandlers(...)
  7. │   │ └─base::withVisible(code)
  8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  9. ├─scider::plotContour(spe, coi = coi)
 10. │ ├─scider::plotSpatial(spe[, sub], reverseY = reverseY, ...)
 11. │ │ ├─base::as.data.frame(SpatialExperiment::spatialCoords(spe))
 12. │ │ └─SpatialExperiment::spatialCoords(spe)
 13. │ ├─spe[, sub]
 14. │ └─spe[, sub]
 15. │   ├─methods::callNextMethod()
 16. │   └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
 17. │     ├─BiocGenerics::updateObject(x)
 18. │     └─SingleCellExperiment::updateObject(x)
 19. │       ├─methods::callNextMethod()
 20. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 21. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 22. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 23. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 24. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 25. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 26. ├─methods:::.extendsForS3(`<chr>`)
 27. │ └─methods::extends(Class, maybe = FALSE)
 28. │   └─methods::getClassDef(class1)
 29. │     └─methods:::.requirePackage(package)
 30. │       └─base::stop(...)
 31. └─base::.handleSimpleError(...)
 32.   └─base (local) h(simpleError(msg, call))
── Error ('test-plotROI.R:9:5'): plotROI works ─────────────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_silent(...) at test-plotROI.R:9:5
  2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ ├─withr::with_output_sink(...)
  5. │   │ │ └─base::force(code)
  6. │   │ ├─base::withCallingHandlers(...)
  7. │   │ └─base::withVisible(code)
  8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  9. ├─scider::plotROI(spe, roi = coi, pt.size = 0.3, pt.alpha = 0.2)
 10. │ ├─spe[, spe@colData[, id] %in% roi]
 11. │ └─spe[, spe@colData[, id] %in% roi]
 12. │   ├─methods::callNextMethod()
 13. │   └─SingleCellExperiment (local) .nextMethod(x = x, 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-selectRegion.R:3:5'): selectRegion works ───────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─spe[, SummarizedExperiment::colData(spe)$cell_type == "B cells"] at test-selectRegion.R:3:5
  2. ├─spe[, SummarizedExperiment::colData(spe)$cell_type == "B cells"]
  3. │ ├─methods::callNextMethod()
  4. │ └─SingleCellExperiment (local) .nextMethod(x = x, i = , j = j)
  5. │   ├─BiocGenerics::updateObject(x)
  6. │   └─SingleCellExperiment::updateObject(x)
  7. │     ├─methods::callNextMethod()
  8. │     └─SummarizedExperiment (local) .nextMethod(object = object)
  9. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 10. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 11. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 12. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 13. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 14. └─methods:::.extendsForS3(`<chr>`)
 15.   └─methods::extends(Class, maybe = FALSE)
 16.     └─methods::getClassDef(class1)
 17.       └─methods:::.requirePackage(package)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 61 ]
Error: Test failures
Execution halted