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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CHETAH.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CHETAH_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CHETAH.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 ‘CHETAH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CHETAH’ 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 ‘CHETAH’ 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 ‘CHETAH-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CHETAHclassifier
> ### Title: Identification of cell types aided by hierarchical clustering
> ### Aliases: CHETAHclassifier
> 
> ### ** Examples
> 
> data('input_mel')
> data('headneck_ref')
> ## Melanoma data from Tirosh et al. (2016) Science
> input_mel
class: SingleCellExperiment 
dim: 7943 150 
metadata(0):
assays(1): counts
rownames(7943): ELMO2 PNMA1 ... SLC39A6 CTSC
rowData names(0):
colnames(150): mel_cell1 mel_cell2 ... mel_cell149 mel_cell150
colData names(1): celltype_CHETAH
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: <Anonymous> ... .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:
   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)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  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 ‘CHETAH_introduction.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from CHETAH_introduction.Rmd:131-159 [prepare_examp]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─SingleCellExperiment::reducedDim(input_mel)
  2. ├─SingleCellExperiment::reducedDim(input_mel)
  3. │ └─SingleCellExperiment (local) .local(x, type = type, ...)
  4. │   └─SingleCellExperiment:::.get_internal_missing(...)
  5. │     ├─SingleCellExperiment (local) namefun(x)
  6. │     └─SingleCellExperiment (local) namefun(x)
  7. │       └─SingleCellExperiment:::.get_internal_names(...)
  8. │         ├─BiocGenerics::updateObject(x)
  9. │         └─SingleCellExperiment::updateObject(x)
 10. │           ├─methods::callNextMethod()
 11. │           └─SummarizedExperiment (local) .nextMethod(object = object)
 12. │             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 13. │             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 14. │               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 15. │               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 16. │                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 17. └─methods:::.extendsForS3(`<chr>`)
 18.   └─methods::extends(Class, maybe = FALSE)
 19.     └─methods::getClassDef(class1)
 20.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted

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

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

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

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(CHETAH)
Loading required package: ggplot2
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

> library(vdiffr)
> Sys.unsetenv("R_TESTS")
> test_check("CHETAH")
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''
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_classifier.R:5:1'): (code run outside of `test_that()`) ────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'assay': unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─CHETAH::CHETAHclassifier(input = input_mel, ref_cells = headneck_ref) at test_classifier.R:5:1
  2. │ └─CHETAH:::MeanRef(...)
  3. │   ├─base::apply(...)
  4. │   ├─SummarizedExperiment::assay(...)
  5. │   ├─ref[, ref[[ref_ct]] == type_sl]
  6. │   └─ref[, ref[[ref_ct]] == type_sl]
  7. │     ├─BiocGenerics::updateObject(x)
  8. │     └─SingleCellExperiment::updateObject(x)
  9. │       ├─methods::callNextMethod()
 10. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 11. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 12. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 13. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 14. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 15. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 16. ├─methods:::.extendsForS3(`<chr>`)
 17. │ └─methods::extends(Class, maybe = FALSE)
 18. │   └─methods::getClassDef(class1)
 19. │     └─methods:::.requirePackage(package)
 20. │       └─base::stop(...)
 21. └─base::.handleSimpleError(...)
 22.   └─base (local) h(simpleError(msg, call))
── Error ('test_plots.R:5:5'): return colors ───────────────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_is(...) at test_plots.R:5:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─CHETAH::PlotCHETAH(input_mel, return_col = TRUE)
  5. │ └─CHETAH::PlotTSNE(...)
  6. │   └─CHETAH:::TestCHETAH(input = input, redD = redD)
  7. │     └─CHETAH:::TestInput(...)
  8. │       ├─SingleCellExperiment (local) assessor(input)
  9. │       └─SingleCellExperiment (local) assessor(input)
 10. │         └─SingleCellExperiment (local) .local(x, ...)
 11. │           └─SingleCellExperiment:::.get_internal_all(...)
 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)
── Error ('test_plots.R:8:5'): plotchetah output ───────────────────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─vdiffr::expect_doppelganger("plot: standard chetah", PlotCHETAH(input_mel)) at test_plots.R:8:5
  2. │ └─vdiffr (local) writer(fig, testcase, title)
  3. │   └─vdiffr:::print_plot(plot, title)
  4. ├─CHETAH::PlotCHETAH(input_mel)
  5. │ └─CHETAH::PlotTSNE(...)
  6. │   └─CHETAH:::TestCHETAH(input = input, redD = redD)
  7. │     └─CHETAH:::TestInput(...)
  8. │       ├─SingleCellExperiment (local) assessor(input)
  9. │       └─SingleCellExperiment (local) assessor(input)
 10. │         └─SingleCellExperiment (local) .local(x, ...)
 11. │           └─SingleCellExperiment:::.get_internal_all(...)
 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)

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