Migrate "R Known issues" from SciComp wiki to /computing/cluster_software & overhaul ?

[ptvan]

Proposed Domain
Computing

Content Summary
There's a useful "R issues on Rhino" page (https://teams.fhcrc.org/sites/citwiki/SciComp/Pages/R%20Known%20Issues%20and%20Changes%20Omnibus.aspx) but AFAIK it's not linked anywhere. It's still being referenced/used (a postdoc in my lab found it this week), so maybe we can migrate it to https://sciwiki.fredhutch.org/computing/cluster_software/#packagesmodules-for-python-and-r and update with any additional changes ?

Local Content Expert(s)
Anyone in SciComp, really.

[vortexing]

That seems like it could go directly into a compdemo. Can we do that?!??!?! @fizwit You edited that page last. What do you think?

[ptvan]

@bmcgough or @fizwit, what do you think about merging this (and other R tidbits) into the page referenced above ?

[bmcgough]

I think a separate page for the R issues as we hope these are transitory and will be solved as bugs and workarounds are addressed. Search will be how people find these things as they will be facing error messages from R in most cases. While it is not exactly a howto or demo, it does sort of fit there. Perhaps we consider an FAQ-style page template? That seems like the place for info like this, and an FAQ would give us a place to link stuff we don't know where else to link (make up a question and link it!).

[atombaby]

One thing to keep in mind is that we really don't have transitory bugs since we keep old (i.e. buggy) versions of R around. There are, of course, other issues that may be fixed within an EB release. In the current page it's not clear which "bugs" apply to which releases.

[vortexing]

This strikes me as a twofold issue. One being "Bugs in the current Default version of R" and the other being "Bugs in historical versions of R still supported".

Perhaps we begin a Resource Library entry that is organized by R version, and under each version we list the known bugs. This would require the current Sharepoint content to be broken down by version, which may not be possible, so we may need to have at the bottom a section of "Historical bugs". And we might just have to be ok with that.

Edited to add: I'm hesitant to go down the FAQ avenue. Let's pick a theme, like "Known R Build Issues", make a compdemos page for it, and then organize within it to allow it to collect all of the random items about R that exist. We could then, as needed, make a similar page for other topics to collect thematically related FAQ's. As these evolve they could move into article content.

[vortexing]

@bmcgough and @atombaby what do you guys think about this issue? Can we resolve it in some way? What portion of known bugs do we want to document for people?

[vortexing]

@ptvan do you think moving some of this content to your R Tips and Tricks demo might be of interest?

[ptvan]

That sounds good to me !

[vortexing]

@ptvan Shall we resolve this one way or the other?

[atombaby]

We're going to track build-specific information in the index for the build description (FredHutch/easybuild-life-sciences#177)

[fizwit]

I see two types of R issues that can be documented. General issues that effect multiple versions of R and/or R issues relating to our environment. And specific issues that would only relate to a single release. To handle the case of documenting issues with a release, I have added an Know Issues
section of the software release docs in Easybuild life sciences.

More general issues with R could be documented here Available R Modules

My suggestion moves software issues out of SciWiki and puts them with the software documentation.
Scientific Software

The applies to Python and other tools.

[vortexing]

I think this is good. I like @fizwit 's solution. I'm calling it!!!!