staging: patch r-sleuth NAMESPACE

[mschilli87]

This is a workaround for pachterlab/sleuth#259 (effectively applying pachterlab/sleuth#260 after unpacking the package sources).
Without it, r-sleuth cannot be installed with Guix.

[rekado]

FYI: we no longer need #T at the end of build phases. On the master branch it still prints a warning, but on core-updates-frozen (to be merged today, hopefully) it's all fine.

Long ago we used booleans to indicate success or failure for build phases. Then we switched to using exceptions for failures. With core-updates-frozen the build systems are finally fully aware of this change.

[rekado]

Could you please add a link to the upstream discussion above this build phase. It's always good to keep a record right in the code.

[mschilli87]

Thanks for the feedback. Much appreciated. I tried to address both points. Please double-check though since I did not test actually building sleuth using this latest iteration. 😉

[rekado]

I'm confused by the discussion around r-sleuth. Is this change a workaround for an upstream problem or a fix? Will sleuth not only build fine but also be usable?

IIUC upstream essentially abandoned sleuth. If that is so, perhaps we should just remove the package. Or is it worth keeping?

Sorry for being so dense. (It's heavy bones.)

[mschilli87]

r-sleuth imports a function from r-rhdf5 that used to be exported nut was depricated and later removed in newer versions. However, r-sleuth doesn't use this function at all. My guess is it used to be used (didn't check) and was replaced at some point (maybe even as a response to the deprication notice by upstream, just guessing) without removing the import.
So it definitely is not just a weird build-issue workaround but r-sleuth is fully functional with this test. I used it myself after submitting this PR. I think it has value and is worth keeping. The creators are scientists and I guess none of the original authors (but the PI) are working in that lab anymore. That said, at least for kallisto I have seen maintainers taking over and I am hopeful r-sleuth will receive more love again in the future as well. As long as it is not officially dead, I'd like to keep it around if possible.
I am not aware of an alternative offering the same features so it certainly remains useful for my research.
That said, I'd argue the issues should be fixed upstream (which is why I opened a PR there) so I'd consider this a (hopefully temporary) workaround for what one could call upstream packaging bug (since only metadata require patching).

Hope this helps, sorry for not being dense at all (as usual). 😉

[rekado]

Thank you, this sounds all reasonable.

I've applied and pushed your patch. Thanks!

[mschilli87]

In the meantime the upstream bug has been fixed. So with the next version bump, these changes should be undone.