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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scds.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scds_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scds.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 ‘scds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scds’ version ‘1.25.0’
* 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 ‘scds’ 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 ... ERROR
Running examples in ‘scds-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bcds
> ### Title: Find doublets/multiplets in UMI scRNA-seq data;
> ### Aliases: bcds
> 
> ### ** Examples
> 
> data("sce_chcl")
> ## create small data set using only 100 cells
> sce_chcl_small = sce_chcl[, 1:100]
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: [ ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
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 ‘scds.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from scds.Rmd:73-81 [proj]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─SingleCellExperiment::`reducedDim<-`(`*tmp*`, "tsne", value = `<dbl[,2]>`)
  2. ├─SingleCellExperiment::`reducedDim<-`(`*tmp*`, "tsne", value = `<dbl[,2]>`)
  3. │ └─SingleCellExperiment:::.set_internal_character(...)
  4. │   ├─BiocGenerics::updateObject(x)
  5. │   └─SingleCellExperiment::updateObject(x)
  6. │     ├─methods::callNextMethod()
  7. │     └─SummarizedExperiment (local) .nextMethod(object = object)
  8. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
  9. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 10. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 11. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 12. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 13. └─methods:::.extendsForS3(`<chr>`)
 14.   └─methods::extends(Class, maybe = FALSE)
 15.     └─methods::getClassDef(class1)
 16.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following file failed:
  ‘scds.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/scds.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scds
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scds’ ...
** this is package ‘scds’ version ‘1.25.0’
** 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 (scds)