Closed csoneson closed 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
tagging coauthors @machlabd, @federicomarini and @StefaniAstrologo
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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?
2.2 GB and counting...
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?
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: aa2b1745f3d2f95af1c058a92f142e9e5202d492
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 - 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.
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
It looks like the EHub snapshot is too old - I think I uploaded the data only in June.
Confirm @csoneson's impression - I have a machine running the release version, and that is exactly the snapshot date reported
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