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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dandelionR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dandelionR_1.1.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.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 ‘dandelionR/DESCRIPTION’ ... OK
* this is package ‘dandelionR’ version ‘1.1.4’
* 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 ‘dandelionR’ 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
miloUmap: no visible binding for global variable ‘milo_object’
Undefined global functions or variables:
  milo_object
* 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 ‘dandelionR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: markovProbability
> ### Title: Markov Chain Construction and Probability Calculation
> ### Aliases: markovProbability
> 
> ### ** Examples
> 
> data(sce_vdj)
> # downsample to first 2000 cells
> sce_vdj <- sce_vdj[, 1:2000]
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 ‘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 ‘dandelionR.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-16-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-19-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-23-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-26-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-26-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-28-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-28-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-28-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dandelionR.Rcheck/vign_test/dandelionR/vignettes/dandelionR_files/figure-html/unnamed-chunk-28-4.png" but not available.
--- finished re-building ‘dandelionR.Rmd’

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

Quitting from dandelionR_with_slingshot.Rmd:54-65 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─dandelionR::setupVdjPseudobulk(...)
  2. │ └─dandelionR:::.filterProductivity(...)
  3. │   └─base::Reduce(...)
  4. │     └─dandelionR (local) f(init, x[[i]])
  5. │       ├─data[, idx]
  6. │       └─data[, idx]
  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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Quitting from vignette_reproduce_original.rmd:72-81 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─dandelionR::setupVdjPseudobulk(...)
  2. │ └─dandelionR:::.filterProductivity(...)
  3. │   └─base::Reduce(...)
  4. │     └─dandelionR (local) f(init, x[[i]])
  5. │       ├─data[, idx]
  6. │       └─data[, idx]
  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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following files failed:
  ‘dandelionR_with_slingshot.Rmd’ ‘vignette_reproduce_original.rmd’

Error: Vignette re-building failed.
Execution halted

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

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL dandelionR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘dandelionR’ ...
** this is package ‘dandelionR’ version ‘1.1.4’
** 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 (dandelionR)

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(dandelionR)
> 
> test_check("dandelionR")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 74 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 74 ]
> 
> proc.time()
   user  system elapsed 
 48.145   3.163  51.588