compareSingleCell

[LTLA]

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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: compareSingleCell 
Title: Comparative Analyses of Single-Cell RNA-seq Data with Bioconductor
Version: 0.99.0
Date: 2019-05-04
Authors@R: c(
    person(role=c("aut", "cre"), "Aaron", "Lun", email = "infinite.monkeys.with.keyboards@gmail.com"),
    person(role=c("aut"), "Jonathan", "Griffiths"))
Description: Describes a comparative analysis of scRNA-seq data using scran, scater and other Bioconductor packages.
    This uses a multi-condition replicated data set from a study of early mammalian development. It demonstrates how 
    merge sample together to test for differential abundance and differential expression between conditions.
Imports: BiocStyle, callr, rmarkdown
Suggests: knitr,
        SingleCellExperiment,
        scater,
        scran,
        DropletUtils,
        batchelor,
        BiocSingular,
        BiocFileCache,
        TxDb.Mmusculus.UCSC.mm10.ensGene,
        pheatmap,
        igraph,
        edgeR,
        Matrix
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
biocViews: Workflow, SingleCellWorkflow
NeedsCompilation: no
URL: https://www.bioconductor.org/help/workflows/compareSingleCell/ 
RoxygenNote: 6.1.1

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[bioc-issue-bot]

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IMPORTANT: Please read the instructions for setting
up a push hook on your repository, or further changes to your
repository will NOT trigger a new build.

[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, TIMEOUT".
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:

f1982de Bumped version, date.

[LTLA]

Bumping in the hope that some of the resources got cached after the first TIMEOUT, so they don't have to get re-downloaded. Downloading seems to be by far the longest, at least locally.

[LTLA]

Incidentally, I can't help but feel @hpages may be more interested in reviewing #1114, while @lshep may be more interested in reviewing this one!

[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, TIMEOUT".
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.

[LTLA]

Not quite sure what's going on here... looks like it's not getting detected as a workflow.

[lshep]

Workflow: True in the DESCRIPTION

[bioc-issue-bot]

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

b28942e Specify workflow for longer BioC compilation.

[LTLA]

Thanks @lshep. I think this is the third time I've asked this question and you've given this answer! Looks like my strategy of copying a DESCRIPTION from a previous workflow was insufficient - simpleSingleCell doesn't even have a Workflow: section.

[lshep]

Can you check the build time locally for the package? I kicked off this manually thinking it stalled but there are two triggers that never finished building the package - I'm wondering if I need to check the timeout flag on the build process or if something more is going on...

[LTLA]

The downloads are very slow. Took me hours to download them - which doesn't really make sense to me, the files are not particularly big. The servers are in the UK, but still... maybe it's Brexit.

Once cached, the actual computation should be fast - no more than half an hour, but I'd have to go and time it properly. Will get back to you with some more concrete numbers.

[bioc-issue-bot]

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

74cbeb9 Use global cache for downloads instead.

[LTLA]

I realized I was caching the downloads locally - ostensibly to check that they could be re-downloaded at every build - but any locally cached results would be killed when the SPB times out and deletes the working directory of the build-in-progress. So, I've switched to the global cache, assuming that it persists on the SPB. My suspicion is that it will still TIMEOUT, though; each download is just very slow.

Might be worth considering EHub packages for this data - I'll prod a student on my end.

[lshep]

Just wanted to follow up on this - is there a better solution for downloading the data ? How many different files are we talking about - I could always download them manually on the builders so they are there but if files are updated that would probably require a manual redownload then - This also doesnt help the user who may suffer through long download times. Is it an issue that the files are large or the site they are being downloaded from? It made it seem like these weren't particularly big but could be a server issue? If thats the case maybe EH versions would be the way to go?

[LTLA]

The files are somewhat big (500 MB, give or take) and the server is a lab-specific resource that isn't really powered up; I suspect that these two factors combined are probably causing the slow download. I've been nagging someone on the UK end to make an EHub package for this data, but they're taking too long to do this, so I think I will just make one myself over the weekend.

[lshep]

Should I close this issue for now or do you think there will be an accompanied data package soon?

[LTLA]

We're almost ready to go with the data package, just a few more checks and then we can submit. Can I re-use the credentials you sent me earlier for this new package?

[lshep]

Yes those credentials have not expired yet and it should be okay to use. If there is an issue let me know

[LTLA]

I'm going to close this for the time being, as I might absorb the content here into Rob's book instead of having a separate series of workflows.