add lintr step to PR workflow

[bernt-matthias]

also integrate latest changes (from galaxyproject/tools-devteam#560) from devteam repo.

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[bernt-matthias]

Thanks @nsoranzo . Looks quite good to me now.

Caching of the R packages seems not to work yet.

Any idea where the annotation:

No files were found for the provided path: galaxy.sha. No artifacts will be uploaded.

comes from?

[nsoranzo]

Some suggested changes to print the full relative path of the files with linting errors.

[nsoranzo]

Nice! You could now check if fixing an R script makes the linter step pass correctly.

[bernt-matthias]

Seems to work -- also the caching runs if the lint step is successful. I think the last question is if the caching of the R packages is fine as it is. Maybe it should be versioned?

[bernt-matthias]

OK. Cool. Not sure about R package management. What happens if a new version of lintr or one of its requirements is available?

[nsoranzo]

OK. Cool. Not sure about R package management. What happens if a new version of lintr or one of its requirements is available?

As it is now, the present version of lintr will be used from the cache until we change the R version in the matrix. I don't think it is a big deal, we can change that later if needed.