MatrixGenerics

[PeteHaitch]

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[bioc-issue-bot]

Hi @PeteHaitch

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: MatrixGenerics
Title: S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
Description: S4 generic functions modeled after the 'matrixStats' API
    for alternative matrix implementations. Packages with alternative matrix
    implementation can depend on this package and implement the generic 
    functions that are defined here for a useful set of row and column
    summary statistics. Other package developers can import this package
    and handle a different matrix implementations without worrying
    about incompatibilities.
Version: 0.99.0
Authors@R: c(person("Constantin", "Ahlmann-Eltze", email = "artjom31415@googlemail.com", 
        role = c("aut"), comment = c(ORCID = "0000-0002-3762-068X")),
   person("Peter", "Hickey", role = c("aut", "cre"),
          email = "peter.hickey@gmail.com"))
Imports: methods
Depends: matrixStats (>= 0.56.0)
License: Artistic-2.0
Encoding: UTF-8
URL: https://github.com/Bioconductor/MatrixGenerics
BugReports: https://github.com/Bioconductor/MatrixGenerics/issues
RoxygenNote: 7.1.0
Roxygen: list(markdown = TRUE, old_usage = TRUE)
Suggests: 
    testthat (>= 2.1.0)
biocViews: Infrastructure, Software

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[PeteHaitch]

We've discussed this package a bit over the years and it's thanks to @const-ae we've got something concrete to submit 🎉

I think the aim will be for DelayedMatrixStats to depend on MatrixGenerics in the next release (I've got a branch ready to go; https://github.com/PeteHaitch/DelayedMatrixStats/tree/MatrixGenerics).
Ultimately, I think it may be best to deprecate DelayedMatrixStats by incorporating it directly into DelayedArray (and perhaps HDF5Array if there are HDF5Matrix-specific methods).
@const-ae is also working on sparseMatrixStats but I'm not sure I've left him enough time to have that prepared for the next release ...

Pinging @hpages who will likely want to run an eye over it, and @HenrikBengtsson since this builds on matrixStats.

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR".
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[PeteHaitch]

In the DESCRIPTION we have:

biocViews: Infrastructure, Software

Because it's an 'infrastructure' package I think this should mean that a vignette is not required.
Indeed, in the build report we see:

* Checking vignette directory...
    This is a software package
  Infrastructure package, vignette not required.

But then we immediately get an ERROR:

* Checking whether vignette is built with 'R CMD build'...
    * ERROR: Vignette must be built by 'R CMD build'. Please see the
      `Vignette Checks` section of the BiocCheck vignette.

And so the build fails.

Should we only have

biocViews: Infrastructure

in the DESCRIPTION?

[lshep]

Probably needs an adjustment in BiocCheck -- can you open an issue there for me to look into it? @dvantwisk ignore the vignette ERROR for now.

[dvantwisk]

I'll have a review of this package done soon.

[PeteHaitch]

👋@dvantwisk - I totally understand that you're all busy right now, just wanted to make a gentle inquiry about the review status here given that the deadline is approaching. Thanks!
The current build error is due to a false-positive in BiocCheck, I believe.

[dvantwisk]

Hi,

I apologize for the delay. I've reviewed your package and I am happy to say that I don't have anything significant to add to it. It is very well written as is and I will accept it as is.

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor Git repository and nightly builds. Additional
information will be posed to this issue in the next several
days.

Thank you for contributing to Bioconductor!

[PeteHaitch]

No worries at all, @dvantwisk, I appreciate how busy you must be.
Thank you!

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