alabaster.schemas

[LTLA]

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[lshep]

All the package should now be in git.bioconductor.org . Please push changes to fix dependency error's.

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[LiNk-NY]

Hi Aaron, @LTLA

OK, maybe there's a bug in BiocCheck... @LiNk-NY ? Anyway the pre-check is passed, it will be in the single-package builder soon.

alabaster.spatial has luna@gene.com which is not registered on the support site: https://github.com/ArtifactDB/alabaster.spatial/blob/30ad7a45460359685dbf11245339df7df386dad6/DESCRIPTION#L11

See also: https://support.bioconductor.org/api/email/luna@gene.com/

cc: @vjcitn

[lshep]

I was afraid my comments might get lost in the build report messages so moving them to the end here: -

1. just FYI alabaster.string and alabaster.spatial use luna@gene.com as maintainer email while the rest are infinite.monkeys.with.keyboards@gmail.com (also pointed out with support site registration)
2. alabater.ranges http://staging.bioconductor.org:8000/job/18413/ : there is no package called ‘jsonvalidate’ -- I think you need to declare in your DESCRIPTION of alabaster.ranges -- I assume this is why the error's propagate through the rest of the build reports for the subsequent packages
3. 'chihaya-R' http://staging.bioconductor.org:8000/job/18416/ Its a requirement of the BBS that the repo name and the package name in the DESCRIPTION match.

[hpages]

Hi @LTLA ,

This is a big stack of packages. I wonder if it couldn't be broken down into groups to try to make the review process a little bit easier to manage. For example into 4 groups (I guess there are other ways to break this down, this is just one possibility):

1. Not really part of the alabaster stack:

• chihaya (it's only suggested by alabaster.matrix)

2. Bottom half of the alabaster stack:

• alabaster.schemas
• alabaster.base
• alabaster.matrix
• alabaster.ranges
• alabaster.bumpy
• alabaster.string

3. Top half of the alabaster stack:

• alabaster.se
• alabaster.sce
• alabaster.spatial
• alabaster.mae
• alabaster.vcf

4. Sitting at the top of the stack (umbrella package):

• alabaster

Each group could be done in a separate submission. Of course group N+1 cannot be submitted until group N is accepted, so the entire process might take slightly longer (but hopefully not too much).

Do you think this could make the submission process somehow easier to manage? Or does this split feel too artificial?

H.

[lshep]

@hpages @vjcitn suggested they all be submitted together in a private slack thread and now that they are in git and in the spb database it might be a bit of a mess to try to separate out and re-add

[hpages]

Ah ok, seems like I'm late to the party :grinning: Nevermind.

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[LTLA]

Thanks all, responses below.

1. just FYI alabaster.string and alabaster.spatial use luna@gene.com as maintainer email while the rest are infinite.monkeys.with.keyboards@gmail.com (also pointed out with support site registration)

Fixed.

2. alabater.ranges http://staging.bioconductor.org:8000/job/18413/ : there is no package called ‘jsonvalidate’ -- I think you need to declare in your DESCRIPTION of alabaster.ranges -- I assume this is why the error's propagate through the rest of the build reports for the subsequent packages

There should already be a Suggests dependency on jsonvalidate in alabaster.base. Surely I don't have to list transitive dependencies? Otherwise I've got a whole bunch of packages that would need to Suggests: statmod when pulling in edgeR and using the QL functions, and I don't recall having to do that.

I'll note that I deliberately set jsonvalidate as a Suggests as (i) it is only needed for writing objects, so people who are only reading from existing databases don't need it, and (ii) it's a minor pain to install, as it depends on the V8 package and thus the system libraries of the same name.

3. 'chihaya-R' http://staging.bioconductor.org:8000/job/18416/ Its a requirement of the BBS that the repo name and the package name in the DESCRIPTION match.

This is mildly problematic because https://github.com/LTLA/chihaya is already in use; it's the underlying C++ library that feeds into various interfaces (e.g., R, Javascript). I can't rename that one, either, because various CMake scripts are fetching from that URL to build other things. Renaming the R package to the "expected" repo URL would break those scripts.

What does the repo name matter? It's not like BioC is syncing to the GitHub repo anyway.

This is a big stack of packages. I wonder if it couldn't be broken down into groups to try to make the review process a little bit easier to manage. For example into 4 groups (I guess there are other ways to break this down, this is just one possibility):

Yes, on hindsight that would probably have been a better idea. I also forgot about chihaya until I had started the process, so I just had to throw it in to get artificer.matrix to CHECK.

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[vjcitn]

Please use chihayaR as the name of repo and of package. We need congruency between package name and repo name, it is in the guidelines. Additionally the declarations have to be sufficient for the build system to report OK. We appreciate the contributions but have to work within the current parameters of the build system, we cannot introduce new exceptions.

[vjcitn]

Of course if you prefer some other name, that is fine, but repo name and package name must agree and be valid.

[LTLA]

Hm. Well, for the time being, maybe you can switch it to https://github.com/ArtifactDB/chihaya instead.

[lshep]

Can you please use the additonalpackages format so we can process everything correctly. I will work on removing chihaya-R in the meantime

[LTLA]

AdditionalPackage: https://github.com/ArtifactDB/chihaya

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[vjcitn]

Apropos jsonvalidate, if it is not installed, a user of the package will not be able to run the vignette code in alabaster.string. So I think jsonvalidate should be declared in alabaster.string and in any package that will fail check when it is not declared.

[vjcitn]

The argument concerning burden of installing jsonvalidate is, I think, nugatory for mac and windows users, and for linux the difficulties will be mitigated when the r2u discipline is adopted for bioc packages ... stay tuned.

[LTLA]

So I think jsonvalidate should be declared in alabaster.string and in any package that will fail check when it is not declared.

Which would basically be every alabaster package. Seems unreasonable to ask all the other alabaster packages to break alabaster.base's abstraction by meddling in the implementation details of how the validation is done.

For submission purposes, I don't mind moving jsonvalidate to an Imports in alabaster.base, but I can't guarantee that it'll stay there - the installation burden of V8 system libraries is not insignificant in my experience. It's likely that I will eventually move it back to a Suggests and just add a nicer error message to instruct users to install jsonvalidate if they attempt to stage an object without that package being installed.

The argument concerning burden of installing jsonvalidate is, I think, nugatory for mac and windows users

Well, to provide a counterexample: I don't install binaries on my mac, I always build from source. I don't think I've ever used the binaries when I was working on a mac in the past 8 years.

More generally - while the binaries (and r2u) could be treated as a mitigation for the installation burden, that's all it is, a mitigation. Better to just solve it at the source by not requiring installation in the first place.

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