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fmicompbio / TabulaMurisSenisData

data from the TabulaMuris Senis project
https://fmicompbio.github.io/TabulaMurisSenisData/
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Error when running TabulaMurisSenisDroplet(tissues = "All") #16

Closed flugende closed 3 years ago

flugende commented 3 years ago

Hi,

just wanted to use your package to retrieve the TabulaMurisSensisData. However, running TabulaMurisSenisDroplet(tissues = "All")results in
snapshotDate(): 2020-10-27 Error in .getHubRecord(hub = hub, host = host, tissue = ts, suffix = "_counts.h5") : (All) Error - expected a single counts.h5 file

"TabulaMurisSenisData/tabula-muris-senis-droplet" also doesn't seem to be in hub$rdatapath hub <- ExperimentHub::ExperimentHub() host <- file.path("TabulaMurisSenisData", "tabula-muris-senis-droplet") tissue <- "All" suffix = "_counts.h5" hub[hub$rdatapath == file.path(host, paste0(tissue, suffix))] ExperimentHub with 0 records snapshotDate(): 2020-10-27

and grep("muris", hub$rdatapath, value=TRUE, ignore.case = T) just shows [1] "TabulaMurisData/TabulaMurisDroplet.rds"
[2] "TabulaMurisData/TabulaMurisSmartSeq2.rds"
[3] "clustifyrdatahub/ref_tabula_muris_drop.rda" [4] "clustifyrdatahub/ref_tabula_muris_facs.rda"

csoneson commented 3 years ago

Yes, that's correct - to access the data you need to use the development version of Bioconductor (which will become the next release by the end of October).

flugende commented 3 years ago

I see, thank you. Would suggest mentioning it in the README or in the DESCRIPTION file as a dependency.

csoneson commented 3 years ago

I was about to add it to the README, but in fact the information is already there :) Here: 

Note that R version 4.1 or newer, and Bioconductor release 3.14 (current devel version) or newer are required to use the package.
flugende commented 3 years ago

Sorry, next time I should read more carefully... :)