Bioconductor / Contributions

Contribute Packages to Bioconductor
134 stars 33 forks source link

TabulaMurisSenisData #2179

Closed csoneson closed 3 years ago

csoneson commented 3 years ago

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

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 3 years ago

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: TabulaMurisSenisData
Type: Package
Title: Bulk and single-cell RNA-seq data from the Tabula Muris Senis project
Version: 0.99.0
Authors@R: c(person("Charlotte", "Soneson", role = c("aut", "cre"), 
          email = "charlottesoneson@gmail.com", 
          comment = c(ORCID = "0000-0003-3833-2169")),
   person("Dania", "Machlab", role = c("aut"),
          email = "dania.machlab@gmail.com",
          comment = c(ORCID = "0000-0002-2578-6930")),
   person("Federico", "Marini", role = c("aut"), 
          email = "marinif@uni-mainz.de", 
          comment = c(ORCID = "0000-0003-3252-7758")),
   person("Stefania", "Astrologo", role = c("aut"), 
          email = "stefania.astrologo@gmail.com", 
          comment = c(ORCID = "0000-0002-4845-2802"))
 )
Description: This package provides access to RNA-seq data generated by the 
    Tabula Muris Senis project via the Bioconductor project. The data is made 
    available without restrictions by the Chan Zuckerberg Biohub. It is 
    provided here without further processing, collected in the form of 
    SingleCellExperiment objects. 
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.1
Imports: 
    ExperimentHub,
    SingleCellExperiment,
    HDF5Array,
    SummarizedExperiment
URL: https://github.com/fmicompbio/TabulaMurisSenisData
BugReports: https://github.com/fmicompbio/TabulaMurisSenisData/issues
VignetteBuilder: knitr
biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub
Suggests: 
    ggplot2,
    testthat,
    knitr,
    rmarkdown,
    iSEE,
    BiocStyle
csoneson commented 3 years ago

tagging coauthors @machlabd, @federicomarini and @StefaniAstrologo

bioc-issue-bot commented 3 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

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

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

Please see the build report for more details. This link will be 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/TabulaMurisSenisData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

vjcitn commented 3 years ago

It would be nice to indicate the volume of HDF5 that will be transmitted to the ExperimentHub cache.

Just curious -- have you had any opportunity to try out the rhdf5 capability to interrogate HDF5 in AWS S3?

vjcitn commented 3 years ago

2.2 GB and counting...

vjcitn commented 3 years ago

I think section 4 of the vignette would be better with a screenshot. Do we really expect the user to set or reset some of the parameters in 'initial', or read them as displayed in vignette?

csoneson commented 3 years ago

Thanks Vince - we're updating the package to allow users to see the size of the download before starting (the largest file - the processed count matrix for the droplet data set - is roughly 4GB, the total amount of data for all three data sets and tissue subsets is ~16GB). We didn't actually try out the rhdf5 capabilities of interrogating HDF5 in AWS S3.

We'll also cut down section 4 of the vignette. Will push an updated version shortly.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: aa2b1745f3d2f95af1c058a92f142e9e5202d492

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

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

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

Please see the build report for more details. This link will be 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/TabulaMurisSenisData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

csoneson commented 3 years ago

👋🏻 @vjcitn - sorry for the delay (holiday time...). We've now added an argument (infoOnly) to all the data access functions. If this is set to TRUE, the function will only print out the total size of the objects that will be downloaded/loaded from cache. If FALSE (default), the data will be returned. We also cut down on section 4 in the vignette.

vjcitn commented 3 years ago

Sorry for delays. I can't tell why, in trying to run code in vignette, I am hitting

> tmp <- TabulaMurisSenisBulk(infoOnly = FALSE)
snapshotDate(): 2021-05-18
Error in .getHubRecord(hub = hub, host = host, tissue = "", suffix = "counts.rds") : 
  () Error - expected a single counts.rds file
csoneson commented 3 years ago

It looks like the EHub snapshot is too old - I think I uploaded the data only in June.

federicomarini commented 3 years ago

Confirm @csoneson's impression - I have a machine running the release version, and that is exactly the snapshot date reported

federicomarini commented 3 years ago
image
bioc-issue-bot commented 3 years ago

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.

vjcitn commented 3 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/csoneson.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

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

https://bioconductor.org/packages/TabulaMurisSenisData

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.