Processing ‘workflow_haplotyping.Rmd’ Failed

[plhm]

Hey there, J0bbie.

Working on getting scir up and running. I've installed monocle3, as well as scir without the vignettes. However, I have not been able to instsall the scir vignettes.

Here is the command and the error message:

> devtools::install_github("odomlab2/scir", build_vignettes = TRUE, force = TRUE)
Downloading GitHub repo odomlab2/scir@HEAD
Skipping 3 packages not available: SummarizedExperiment, S4Vectors, rtracklayer
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpZSpryI/remotes66360428f91da/odomlab2-scir-e0aa11e/DESCRIPTION’ ...
─  preparing ‘scir’:
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
E  creating vignettes (8.1s)
   --- re-building ‘workflow_haplotyping.Rmd’ using rmarkdown

   Quitting from lines 26-30 [load_cds] (workflow_haplotyping.Rmd)
   Error: processing vignette 'workflow_haplotyping.Rmd' failed with diagnostics:
   Assertion on 'folder' failed: '/omics/groups/OE0538/internal/projects/manuscript_scirocket/workflow/test_haplotyping/alignment/' not readable.
   --- failed re-building ‘workflow_haplotyping.Rmd’

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

   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'scir' from GitHub:
  ! System command 'R' failed

I'm wondering if you've heard of someone having this issue (of having assertion problems with the alignment file), and whether there is another way to get the vignettes, since I've been able to install scir on its own.