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R CMD check fails on Linux for Bioconductor builds #25

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martin-g opened this issue Aug 2, 2023 · 1 comment · Fixed by #26
Closed

R CMD check fails on Linux for Bioconductor builds #25

martin-g opened this issue Aug 2, 2023 · 1 comment · Fixed by #26

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@martin-g
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martin-g commented Aug 2, 2023

Hello,

I am not sure whether you are aware that the Bioconductor check fails on Linux x86_64 and aarch64 with:

* checking data for non-ASCII characters ... WARNING
  Error loading dataset 'k562_scatac_chr14':
   Error in .requirePackage(package) : 
    unable to find required package 'csaw'
  
  Error loading dataset 'ss3_umi_sce':
   Error in .requirePackage(package) : 
    unable to find required package 'SingleCellExperiment'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* 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
scCompartments    81.621  1.832  83.454
getDenoisedMatrix  7.197  0.272   7.468
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘compartmap_vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘compartmap_vignette.Rmd’ using rmarkdown

Quitting from lines 2-16 (compartmap_vignette.Rmd)
Error: processing vignette 'compartmap_vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘compartmap_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
@martin-g
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martin-g commented Aug 2, 2023

A Pull Request is coming!

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