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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:blase.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings blase_0.99.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/blase.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 ‘blase/DESCRIPTION’ ... OK
* this is package ‘blase’ version ‘0.99.3’
* 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 ‘blase’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'plot_mapping_result.Rd':
  ‘[scater:plot_reddim]{scater::plotUMAP()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
calculate_gene_peakedness        24.890  0.348  25.494
plot_gene_peakedness             24.572  0.208  25.209
gene_peakedness_spread_selection 22.500  0.247  23.057
smooth_gene                      22.521  0.104  22.962
evaluate_parameters              13.233  0.157  13.443
plot_mapping_result               7.969  0.110   8.319
find_best_params                  6.841  0.159   7.009
plot_find_best_params_results     5.563  0.036   5.712
* 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 ‘BLASE-for-annotating-scRNA-seq.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from BLASE-for-annotating-scRNA-seq.Rmd:60-70 [sc_umaps]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─scater::plotUMAP(MCA_PF_SCE, colour_by = "STAGE_HR")
  2. │ └─scater::plotReducedDim(...)
  3. │   ├─base::as.matrix(reducedDim(object, dimred))
  4. │   ├─SingleCellExperiment::reducedDim(object, dimred)
  5. │   └─SingleCellExperiment::reducedDim(object, dimred)
  6. │     └─SingleCellExperiment (local) .local(x, type, ...)
  7. │       └─SingleCellExperiment:::.get_internal_character(...)
  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 'BLASE-for-annotating-scRNA-seq.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘BLASE-for-annotating-scRNA-seq.Rmd’

--- re-building ‘BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd:59-69 [sc_umaps]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─scater::plotUMAP(MCA_PF_SCE, colour_by = "STAGE_HR")
  2. │ └─scater::plotReducedDim(...)
  3. │   ├─base::as.matrix(reducedDim(object, dimred))
  4. │   ├─SingleCellExperiment::reducedDim(object, dimred)
  5. │   └─SingleCellExperiment::reducedDim(object, dimred)
  6. │     └─SingleCellExperiment (local) .local(x, type, ...)
  7. │       └─SingleCellExperiment:::.get_internal_character(...)
  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 'BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd’

--- re-building ‘assign-bulk-to-pseudotime.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/blase.Rcheck/vign_test/blase/vignettes/assign-bulk-to-pseudotime_files/figure-html/expressionOverPseudotimePlot-1.png" but not available.
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from assign-bulk-to-pseudotime.Rmd:135-143 [setupSCEPlot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─scater::plotUMAP(sce, text_by = "celltype", colour_by = "celltype")
  2. │ └─scater::plotReducedDim(...)
  3. │   ├─base::as.matrix(reducedDim(object, dimred))
  4. │   ├─SingleCellExperiment::reducedDim(object, dimred)
  5. │   └─SingleCellExperiment::reducedDim(object, dimred)
  6. │     └─SingleCellExperiment (local) .local(x, type, ...)
  7. │       └─SingleCellExperiment:::.get_internal_character(...)
  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 'assign-bulk-to-pseudotime.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘assign-bulk-to-pseudotime.Rmd’

SUMMARY: processing the following files failed:
  ‘BLASE-for-annotating-scRNA-seq.Rmd’
  ‘BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd’
  ‘assign-bulk-to-pseudotime.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/blase.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘blase’ ...
** this is package ‘blase’ version ‘0.99.3’
** using staged installation
** R
** data
** inst
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (blase)

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(blase)
> 
> test_check("blase")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 124 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 124 ]
> 
> proc.time()
   user  system elapsed 
 73.273   2.913  79.609