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installation via devtools::install_github([...], build_vignettes=True, [...]) fails if 'BiocStyle' is not already installed #35

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ymahlich opened this issue Jan 7, 2025 · 0 comments

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@ymahlich
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ymahlich commented Jan 7, 2025

On a fresh install the installation via

library(devtools)
devtools::install_github('pnnl-compbio/spammR',build_vignettes = TRUE,force=TRUE)

fails with the following error message on an ARM based MacOS running R 4.4.1.

The downloaded source packages are in
	‘/private/var/folders/81/d9jch6jj21z6tg8dndtgpry00000gn/T/RtmpJdyGQX/downloaded_packages’
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/81/d9jch6jj21z6tg8dndtgpry00000gn/T/RtmpJdyGQX/remotes1273dfd4c40/PNNL-CompBio-spammR-0382c94/DESCRIPTION’ ...
─  preparing ‘spammR’:
✔  checking DESCRIPTION meta-information
─  installing the package to build vignettes
E  creating vignettes (16.4s)
   --- re-building ‘spammR.Rmd’ using rmarkdown
   Error: processing vignette 'spammR.Rmd' failed with diagnostics:
   there is no package called ‘BiocStyle’
   --- failed re-building ‘spammR.Rmd’
   
   SUMMARY: processing the following file failed:
     ‘spammR.Rmd’
   
   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'spammR' from GitHub:
  ! System command 'R' failed

After manually installing BiocStyle via BiocManager::install('BiocStyle') the installation is successful granted all other dependencies stated in the installation routine are satisfied.

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