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josefin-werme / LAVA

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installation problem #43

Closed biostat0903 closed 1 year ago

biostat0903 commented 1 year ago

Dear Werme, When I installed the LAVA, I met an error:

> devtools::install_github("https://github.com/josefin-werme/LAVA.git", build_vignettes=TRUE)Downloading GitHub repo josefin-werme/LAVA@HEADSkipping 1 packages not available: snpStats
── R CMD build ────────────────────────────────────────────────────
   checking for file ‘/tmp/RtmpAwwqjU/remotes129f718bc4062/josefin-✔  checking for file ‘/tmp/RtmpAwwqjU/remotes129f718bc4062/josefin-werme-LAVA-3ad57c8/DESCRIPTION’ (347ms)
─  preparing ‘LAVA’:
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes (393ms)E  creating vignettes (5.2s)
   --- re-building ‘sample_overlap.Rmd’ using rmarkdown   Error: processing vignette 'sample_overlap.Rmd' failed with diagnostics:
   Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
   --- failed re-building ‘sample_overlap.Rmd’

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

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

Could you tell how I can solve it. Thanks!

Best, Sheng

cadeleeuw commented 1 year ago

Hi,

It looks like there is an issue with your installation of the devtools package. You could try reinstalling that, or manually installing the latest version of the pandoc package (which seems to be causing the issue, ultimately). Alternatively, you could also run the install_github with build_vignettes=FALSE, since this is the part of the installation where the issue arises.

Best, Christiaan