Bioconductor style linters

[jimhester]

Add as an optional default perhaps?

http://bioconductor.org/developers/how-to/coding-style/

[mjsteinbaugh]

@jimhester Any update on this? Would love to see this feature added. I'd be happy to help contribute.

[kjohnsen]

I'd also be interested in this 😃

[jimhester]

For those interested I would gladly review a PR!

[mjsteinbaugh]

Cool thanks Jim, I'll see if I can put together a list of rules that would be helpful.

[kjohnsen]

I could use this since I'm developing a Bioconductor package now, so I'll see what I can do to help

[jimhester]

https://bioconductor.org/developers/how-to/coding-style/ would probably be a useful place to start.

[llrs]

Maybe a good way to start is using this file I could spend some time, I have also some interest on this: see https://github.com/r-lib/styler/issues/331

I understand that this is different from r-lib/styler but I don't understand if there is any relationship between these packages or not. Anyway with that file it seems that it might be easier for me to use lintr

[mjsteinbaugh]

@llrs I've been using this .lintr file in my packages, which has some additional checks

[russHyde]

Hi @mjsteinbaugh , would you be OK if I used your .lintr for basejump to define a list of bioconductor defaults within lintr?

[mjsteinbaugh]

Sure thing!

[russHyde]

There's some additional best-practices mentioned here: http://bioconductor.org/developers/package-guidelines/#rcode

• Use vapply() instead of sapply() and use the various apply functions instead of for loops.
• Use seq_len() or seq_along() instead of 1:... -Use TRUE/FALSE instead of T/F
• Avoid class()== and class()!= instead use is()
• Use system2() instead of system
• Do not use set.seed in any internal R code.
• No browser() calls should be in code
• Avoid the use of <<-.
• Avoid use of direct slot access with @ or slot(). Accessor methods should be created and utilized
• Use <- instead of = for assignment
• Function names should be camel case or utilize the underscore _ and not have a dot . which indicates S3 dispatch.
• Use dev.new() to start a graphics drive if necessary. Avoid using x11() or X11() for it can only be called on machines that have access to an X server.

[mjsteinbaugh]

Yes, refer to BiocCheck::BiocCheck() for details on additional Bioconductor checks. In particular, I run it on CI with these flags: https://github.com/acidgenomics/Rcheck/blob/master/checks/bioc-check

[mjsteinbaugh]

Also, one addition that would be particularly useful in my opinion is improved handling of internal S4 method functions, which currently return as lint errors. Here's an example: https://github.com/acidgenomics/basejump/blob/master/R/counts-methods.R#L46

counts,SummarizedExperiment will currently fail the camelCase lint check. This is similar to the S3 method lint issue reported in #223.

[MichaelChirico]

Encourage anyone that's interested to file PRs. Would especially be nice to include some for the 3.0.0 release. A lot of the points referenced in https://github.com/r-lib/lintr/issues/43#issuecomment-552857792 are already doable with existing linters; others would be straightforward adaptations of existing logic (see e.g. the linters filed in #884). We can add the bioconductor tag to allow linters_with_tags("bioconductor") to facilitate easy .lintr configs.