sketchR

[csoneson]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/fmicompbio/sketchR

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[bioc-issue-bot]

Hi @csoneson

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: sketchR
Version: 0.99.0
Date: 2024-02-01
Title: An R interface for python subsampling/sketching algorithms
Authors@R: c(
    person("Charlotte", "Soneson", email = "charlottesoneson@gmail.com",
        role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3833-2169")),
    person("Michael", "Stadler", email = "michael.stadler@fmi.ch",
 role = c("aut"), comment = c(ORCID = "0000-0002-2269-4934")))
License: MIT + file LICENSE
Description: Provides an R interface for various subsampling algorithms 
    implemented in python packages. Currently, interfaces to the geosketch 
    and scSampler python packages are implemented. In addition it also
    provides diagnostic plots to evaluate the subsampling.
Imports:
    basilisk,
    Biobase,
    DelayedArray,
    dplyr,
    ggplot2,
    methods,
    reticulate,
    rlang,
    scales,
    stats
Suggests:
    rmarkdown,
    knitr,
    testthat (>= 3.0.0),
    TENxPBMCData,
    scuttle,
    scran,
    scater,
    SingleR,
    celldex,
    cowplot,
    SummarizedExperiment,
    beachmat.hdf5,
    BiocStyle,
    BiocManager,
    SingleCellExperiment
URL: https://github.com/fmicompbio/sketchR
BugReports: https://github.com/fmicompbio/sketchR/issues
RoxygenNote: 7.3.1
Encoding: UTF-8
StagedInstall: no
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: SingleCell

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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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: "TIMEOUT, skipped". 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 22.04.3 LTS): sketchR_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 git@git.bioconductor.org:packages/sketchR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[csoneson]

I think the timeout here (on macOS only) comes from building the conda environment, which I'm not sure how to do much about - this should only have to be done once, and then things should be much faster. Is there anything that can be done to retrigger the build and let it run through (I guess that if I bump the version it will try to create a new environment)?

[hpages]

Hi Charlotte,

We've made some changes to how basilisk's cache is set up on nebbiolo1 and merida1. Now it's shared between the daily builds (BBS) and SPB. This should help a little bit with R CMD build and R CMD check timings of sketchR because the SPB will now benefit from things that are already installed by the daily builds.

Can you bump the version of the package? We'll see how it goes.

Note that there will still be a substantial amount of stuff that needs to be reinstalled over and over each time you bump the version of the package (this is how basilisk was designed, I can't think of an easy way to avoid that), but the cache also contains a significant amount of stuff that is version-independent. That part won't be reinstalled.

Best

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 01368738c25fc831dfa87529bf545215173c865d

[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: "TIMEOUT, skipped". 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 22.04.3 LTS): sketchR_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 git@git.bioconductor.org:packages/sketchR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[hpages]

hmm... :disappointed: I'll take a look...

[csoneson]

Thanks Hervé! Let me know if there's something else I should try (I can probably reduce the run time of the vignette a little by using a smaller data set to start with, but I'm not sure that has a big impact compared to the time spent building the environment).

[hpages]

Turns out that the SPB was still using the old cache location (~/Library/Caches/org.R-project.R/R/basilisk). Looks like the SPB server needs to be restarted for the new cache location (/var/cache/basilisk) to become effective, so I just did that.

Can you please try again? :crossed_fingers:

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 96ab3a4fe2e1925eaa0df8200991305d47070ae6

[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: "TIMEOUT, skipped". 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 22.04.3 LTS): sketchR_0.99.2.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 git@git.bioconductor.org:packages/sketchR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[hpages]

Bummer! :disappointed:

FWIW I was able to manually build sketchR in an interactive session on merida1 in 9m32s (see https://github.com/Bioconductor/BBS/issues/400), but that was when the daily builds were not running so I guess that gave me a small advantage.

Anyways, even though sharing the cache seems to help a little bit, it's not enough.

Let me think about what else we can do about this.

[csoneson]

Thanks again - just let me know if there's something I can do! I am also able build the package locally in less than 10 minutes, but of course there's not really anything else running on my laptop at the same time.

[vjcitn]

Hi -- when you say "build the package locally in 10 min" does that include all the miniconda activities for a version bump?

[hpages]

when you say "build the package locally in 10 min" does that include all the miniconda activities for a version bump?

For me when I did it on merida1 it did include all the miniconda activities, yes.

Anyways, it doesn't seem fair to take into account the time it takes to set up the basilisk environment. This is just a one-time overhead and doesn't reflect the efficiency of the code in the package itself.

One way to ignore the overhead would be to have the SPB (and BBS) run R CMD build twice on the package. The first time would be behind the scene and with more time allowed, and only the second time would "count" and be reported. This would be done only for a small subset of packages that are manually enrolled via some flag that they add to their .BBSoptions file. However, this would require some substantial changes to the SPB and BBS code base (unfortunately the two build systems don't share as much code as they could). So this is something that we might consider doing in the future.

In the meantime, I'm going to manually restart a build. If it passes R CMD build on merida1 in time, hopefully we can give it the green light for ingestion.

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): sketchR_0.99.2.tar.gz macOS 12.7.1 Monterey: sketchR_0.99.2.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 git@git.bioconductor.org:packages/sketchR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[hpages]

Build and check each took about 2 min on nebbiolo1 and merida1. Yeah!

[csoneson]

Hi -- when you say "build the package locally in 10 min" does that include all the miniconda activities for a version bump?

Yes, I think so (at least as far as I can tell), and it was rebuilding the environment (but may potentially have used some previously downloaded and cached packages rather than re-downloading them, I didn't actually check that in detail).

Build and check each took about 2 min on nebbiolo1 and merida1. Yeah!

Yay!!

[hpages]

Can we clear sketchR for ingestion @vjcitn @lshep?

[lshep]

A reviewer hasn't looked at the package yet. I can take a more in depth look this week.

[lshep]

When I'm trying to build locally I'm getting the following ERROR is there something I should do to resolve?

lorikern@jbcj433:~/PkgReview$ R CMD build sketchR 
* checking for file 'sketchR/DESCRIPTION' ... OK
* preparing 'sketchR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘sketchR.Rmd’ using rmarkdown

Quitting from lines 60-89 [unnamed-chunk-2] (sketchR.Rmd)
Error: processing vignette 'sketchR.Rmd' failed with diagnostics:
function 'as_cholmod_sparse' not provided by package 'Matrix'
--- failed re-building ‘sketchR.Rmd’

SUMMARY: processing the following file failed:
  ‘sketchR.Rmd’

Error: Vignette re-building failed.
Execution halted

[csoneson]

I've seen this happening when some packages needed to be reinstalled (from source) since Matrix changed their ABI in v1.6-2. For me, reinstalling the packages mentioned in https://stat.ethz.ch/pipermail/r-package-devel/2023q4/010051.html (plus TFBSTools, but that's not used here) has been enough.

[lshep]

hmm... I just tried re-instaling Matrix from source but it still didnt work. Maybe I'll try re-installing R ...

[csoneson]

I think reinstalling Matrix itself is not enough, also the packages linking to it must be reinstalled (the ones in the linked post).

[lshep]

tried both Matrix and TFBSTools and still same...

[csoneson]

What about irlba and/or lme4?

[lshep]

I deleted out and re-installed Matrix, TFBSTools, lme4, and irlba .... and that seemed to work. I'll try to have a review by tomorrow

[lshep]

A few quick comments: LICENSE

• [ ] Is it meant to be 2022?

vignette

• [ ] Can the abstract more distinctly describe the "main functionalities" of sketchR? Why its important to add to bioconductor/what is novel about the package.

man

• [ ] Can you provide a package level man page so when a naive user tries ?sketchR it suggests functionality or where to start with the package.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 42162d80e81623fdf816638722ea1581828b2355

[csoneson]

Thanks! We've addressed the comments here: https://github.com/fmicompbio/sketchR/pull/13/files

Is it meant to be 2022?

Actually yes - from what we understand the copyright year should be when the software was first made available to the public, and in this case the package has been on GitHub since 2022.

Can the abstract more distinctly describe the "main functionalities" of sketchR?

We've expanded the introduction to cover these aspects.

Can you provide a package level man page?

Yep, good catch, I forgot that - added.

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): sketchR_0.99.3.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 git@git.bioconductor.org:packages/sketchR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[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.

[lshep]

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If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.