sparseMatrixStats

[const-ae]

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[bioc-issue-bot]

Hi @const-ae

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: sparseMatrixStats
Type: Package
Title: Summary Statistics for Rows and Columns of Sparse Matrices
Version: 0.99.0
Authors@R: person("Constantin", "Ahlmann-Eltze", email = "artjom31415@googlemail.com", 
        role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3762-068X"))
Description: High performance functions for row and column operations on sparse matrices.
    For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently,
    the optimizations are limited to data in the column sparse format. 
    This package is inspired by the matrixStats package by Henrik Bengtsson.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
LinkingTo: 
    Rcpp
Imports: 
    Rcpp,
    Matrix,
    MatrixGenerics,
    matrixStats,
    methods
Suggests: 
    testthat (>= 2.1.0),
    knitr,
    bench,
    rmarkdown,
    BiocStyle
SystemRequirements: C++14
VignetteBuilder: knitr
biocViews: Infrastructure, Software, DataRepresentation

[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: "skipped, ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

[lawremi]

Shouldn't this (and MatrixGenerics) go into CRAN?

[const-ae]

I don't necessarily disagree ;)

I guess the case for sparseMatrixStats being on BioConductor is that MatrixGenerics was submitted here and it makes sense to have them together. More generally, a lot of functionality around S4 is here on BioConductor (like S4Vectors), so it felt appropriate for me to submit both packages here as well.
But you are right, that the packages could be of interest for the whole R community :)

@PeteHaitch and @hpages, what would you say about this?

[PeteHaitch]

Shouldn't this (and MatrixGenerics) go into CRAN?

I also don't necessarily disagree :)
There's been a fair bit of bike-shedding and going around in circles on this package and its extensions (including very much myself in this; see Bioconductor/MatrixGenerics#2 (comment)).
It's good to have an actual implementation of it - I hope this can help clarify where it should live.

[lawremi]

Thanks for introducing me to the term "bike-shedding" and the law of triviality.

[PeteHaitch]

@lawremi I didn't mean that to dismiss your suggestion or concerns, which are well-placed. This really reflects my frustrations with myself for not being able to nail down the implementation

[mtmorgan]

@hpages has advocated for (initial) submission to Bioconductor, where it is much easier to mature packages, pointing to rhdf5 as an example

[lshep]

I'll do some behinds the scenes stuff too to have this be able to build without waiting for MartrixGenerics to be accepted and without submitting under the other issue. hand tight and I'll kick off a new build when I have it set up so I can move forward with the review

[lawremi]

I recognize that Bioconductor wins in terms of developer convenience, but our community should be more proactive about sharing our general solutions and distributing through CRAN. Otherwise, only we will benefit.

[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: "skipped, ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

[lshep]

It is our understanding that R doesn't support C++14 on Windows yet. Please update to C++11

[const-ae]

Hi Lori,
thanks for kicking of another build and "do some behinds the scenes stuff". That's highly appreciated :)

It is our understanding that R doesn't support C++14 on Windows yet

Oh, that is unfortunate. I thought that R 4.0 also meant Rtools 40 and thus finally a modern compiler on windows.
If not, I will see that I how I can rewrite the internals to avoid the C++14 features.

[PeteHaitch]

I thought that R 4.0 also meant Rtools 40 and thus finally a modern compiler on windows.

It seems like its still being decided; see https://stat.ethz.ch/pipermail/r-devel/2020-April/079253.html

[lshep]

We are ready to go with the Rtools40 whenever CRAN decides to switch over but as far as we are aware it is still being discussed. @hpages Do you know if this is truly the case when we switch to the new toolchain?

[hpages]

Yep, we should be ready to switch (we have set up builds with the new toolchain for a small subset of packages).

As for whether or not R core is going to switch in time for the R 4.0.0 release, I don't know more about this than what's being currently discussed on the R-devel mailing list. The thing is that we can't switch before they switch, which means that for now the SPB still has to use the old toolchain. So no C++14 features yet.

So here you go: all the cards are on the table and I let you guys decide the strategy for getting sparseMatrixStats into Bioconductor in time for the release.

[lshep]

We can wait to see when/if R 4.0.0 gives the official word that they will use the new toolchain. Until then it is up to you if you decide to modify the code to work in the meantime or temporarily mark as unsupported on windows until the switch happens.

The package is generally well written and I only have the few minor comments:

General

• are duplicate copies of the license and readme necessary?

README

• Include Bioconductor installation instructions

vignette

• If the set.seed is required for users to reproduce the output in the vignette then this should be shown.

I won't be able to accept this package until MatrixGenerics gets accepted first.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

3c0ea53 Remove all C++14 feature I mainly used generic la...
a81ef6a Bump version

[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".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

cbf1b0a Bump version

[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".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

[const-ae]

I have adapted the C++ code in a way that the C++14 features are not used anymore and it should now build on Windows with Rtools 35.

I have also added the Bioconductor installation instructions to the README and made sure the set.seed(1) is visible in the vignette. Thank you for the comments.

are duplicate copies of the license and readme necessary?

I have deleted the LICENSE.md file as it was not necessary. The two README files, I would say, are necessary, because the .Rmd file generates the .md file that is then displayed on GitHub.

---

However, the BiocCheck() is now failing for my package, but I don't understand why:

* Checking package NEWS...
Error in file.path(pkgdir, pkg, c("inst", "inst", "inst", ".", "."), c("NEWS.Rd",  : 
  object 'pkg' not found
Calls: <Anonymous> -> BiocCheck -> checkNEWS -> file.path
Execution halted

I don't remember that is was an issue before. Is it related to the fact that MatrixGenerics is not yet accepted?

[const-ae]

Ah I see the NEWS error was already fixed with Bioconductor/BiocCheck@27ea5e2.
I will just wait and bump the version tomorrow to see if the fix has propagated until then :)

[lshep]

The NEWS file ERROR is on our end. We have a fix implemented in linux and there will be a fix on windows by later this afternoon. I will kick off a manual build so there is at least an accurate linux build. it should post shortly.

[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: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

[lshep]

Great as soon as MatrixGenerics is accepted I will accept this package. Cheers

[PeteHaitch]

@const-ae I know you already changed the code, but it looks like the migration to rtools40 is happening: https://twitter.com/opencpu/status/1250452381403398149 and https://community-bioc.slack.com/archives/CEQ04GKEC/p1586999356141000

[const-ae]

Hi, thanks for the links :)
In that case, I am wondering if I should just revert commit const-ae/sparseMatrixStats@3c0ea53.

@lori, the MatrixGenerics package has been accepted tonight (#1448 (comment)) :)

[lshep]

Yes we updated the R and tool chain on windows last night. Up to you if you want to revert code. accepting the package regardless.

[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!

[mtmorgan]

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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("sparseMatrixStats"). The package 'landing page' will be created at

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