Hi,

The checks of compartmap fail on Linux due to missing Suggest declarations for csaw, BiocStyle and SingleCellExperiment:

* 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

I've opened a Pull Request with a fix.

Regards,

Martin

It tells you what the problem is, in the error message.

Error: processing vignette 'compartmap_vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'

Install BiocStyle.