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Bioconductor / MatrixGenerics

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
https://bioconductor.org/packages/MatrixGenerics
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BioConductor Submission #7

Closed const-ae closed 4 years ago

const-ae commented 4 years ago

I believe the package is now almost ready for submission.

I ran checks with winbuilder and rhub, which were fine. However, BiocCheck complained about the following things:

  1. NOTE: Consider adding these automatically suggested biocViews: DataImport
  2. NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements.
  3. Consider shorter lines; 473 lines (7%) are > 80 characters long.
  4. NOTE: Consider multiples of 4 spaces for line indents, 1066 lines(17%) are not.
  5. Cannot determine whether maintainer is subscribed to the bioc-devel mailing list

I would tend to ignore NOTE 1, 3, 4, and 5. About 2, I am not quite sure what to put into a NEWS for a new submission.

Two additional things, that we should think about:

  1. There is no vignette at the moment for this package. Does it makes sense for such a package to have one. And if yes, what would we put in there?
  2. @PeteHaitch, you are at the moment listed as the cre role in the DESCRIPTION. This would mean, that you would have to take care of the submission process, I believe. I can also take care of the submission, but am not sure what the appropriate role would then be.

Best, Constantin

PeteHaitch commented 4 years ago

I would tend to ignore NOTE 1, 3, 4, and 5. About 2, I am not quite sure what to put into a NEWS for a new submission.

My 2 cents: NOTE 1 seems a false-positive, 2 I think we should have (it might just be a skeleton for future releases), 3 is nice to have but not essential, 4 I also ignore because I use 2-space tabs, 5 is easily fixed (my email in the DESCRIPTION is subscribed to bioc-devel, perhaps yours isnt'?)

  1. There is no vignette at the moment for this package. Does it makes sense for such a package to have one. And if yes, what would we put in there?

The vignette would be developer-focused I think. It could conceivably give some examples of writing some methods for a novel matrix-like class. I don't think this is essential for the first submission but others may disagree.

  1. @PeteHaitch, you are at the moment listed as the cre role in the DESCRIPTION. This would mean, that you would have to take care of the submission process, I believe. I can also take care of the submission, but am not sure what the appropriate role would then be.

Okay, I will submit this by the end of this week. I will tag you in the issue and add a brief note to the submission that you may also respond to reviewer's comments etc. I will also work on a branch of DelayedMatrixStats that uses MatrixGenerics so I can add it to devel as soon as MatrixGenerics is accepted. Thank you for leading the charge on this, @const-ae!

const-ae commented 4 years ago

Okay, I will submit this by the end of this week.

Great! Thank you for your support.

I will then shift my focus and will try to get sparseMatrixStats ready as well :)

LTLA commented 4 years ago

I, too, am looking forward to this.

Note that DelayedMatrixStats will probably need to re-export MatrixGenerics generics so as to provide a smooth transition for packages that currently importFrom(DelayedMatrixStats, ...).

FYI my initial NEWS files are usually just "Added new package BLAH to Bioconductor.".

PeteHaitch commented 4 years ago

Have started on this but my week has been sidetracked by bigger things. Will continue next week, still time to get in for next release

const-ae commented 4 years ago

Sure, no problem. If you need help with anything, let me know :)

const-ae commented 4 years ago

Hi Pete, I just wanted to ping you about the status of the submission and if there is anything I can help you with it? I would like to submit sparseMatrixStats to BioConductor this release cycle as well. But I cannot go ahead as long as MatrixGenerics is not submitted.

PeteHaitch commented 4 years ago

Almost there. Just ironing out some bugs in MatrixGenerics I found when I tried integrating it into DelayedMatrixStats.

const-ae commented 4 years ago

It looks great. Thank you so much :)

const-ae commented 4 years ago

I guess we can close this one now (https://github.com/Bioconductor/Contributions/issues/1448#issuecomment-614401206). Thank you @PeteHaitch for taking care of the submission :)

And thank you all for the great collaboration, I am looking forward to to integrate MatrixGenerics in my packages and support all kinds of different matrices :)