beachmat.tiledb

[LTLA]

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• Repository: https://github.com/tatami-inc/beachmat.tiledb

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[bioc-issue-bot]

Hi @LTLA

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: beachmat.tiledb
Version: 0.99.0
Date: 2024-11-07
Title: beachmat bindings for TileDB-backed matrices
Description: 
    Extends beachmat to initialize tatami matrices from TileDB-backed arrays.
    This allows C++ code in downstream packages to directly call the TileDB C/C++ library to access array data,
    without the need for block processing via DelayedArray.
    Developers only need to import this package to automatically extend the capabilities of beachmat::initializeCpp to TileDBArray instances.
Authors@R: person("Aaron", "Lun", role = c("aut", "cre"), email = "[email protected]")
Imports: 
    methods,
    beachmat,
    tiledb,
    TileDBArray,
    DelayedArray,
    Rcpp
Suggests: 
    testthat,
    BiocStyle,
    knitr,
    rmarkdown,
    Matrix
LinkingTo: 
    Rcpp, 
    assorthead,
    beachmat
biocViews:
    DataRepresentation,
    DataImport,
    Infrastructure
License: GPL-3
NeedsCompilation: yes
VignetteBuilder: knitr
SystemRequirements: C++17
RoxygenNote: 7.3.2
Encoding: UTF-8

[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 the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): beachmat.tiledb_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/beachmat.tiledb to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.

[PeteHaitch]

Hi Aaron,

All looks good with only a few requests and queries.

Cheers,
Pete

---

Queries

• R_ENVIRON_USER=~/.Renviron.bioc R CMD check beachmat.tiledb_0.99.0.tar.gz reports the following. Frankly I don't know exactly what this means or requires, but can it be avoided/quietened?

* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.

• BiocCheck() reports ! WARNING: Package files exceed the 5MB size limit.. I'm guessing this is unavoidable?

---

Required

• Please devtools::document() to ensure documentation is up-to-date.

---

Recommended

• Consider adding BugReports to DESCRIPTION.
• Consider adding a NEWS file.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ddcfd81ade5274bd581ff8eb0ebb82ffca57ef1c

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): beachmat.tiledb_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/beachmat.tiledb to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LTLA]

Done with the exception of the the install size. The binaries produced by GCC with R's defaults come with loads of unnecessary symbols and I don't know how to reliably remove them on a per-package level. I think one would need to enable LTO in the R installation.

[PeteHaitch]

Thanks, Aaron.

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

[LTLA]

Can someone add this to the build system? Normally I'd get the 3b notification by now.

[PeteHaitch]

I can't and assume it'll have to be once someone from @Bioconductor/core is back online

[vjcitn]

Noted.

[lshep]

sorry I was away for the holiday for a week and half. I'll look at processing accepted packages today or tomorrow at the absolute latest.

[lshep]

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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("beachmat.tiledb"). The package 'landing page' will be created at

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