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amc-heme / scExploreR

Shiny app for single cell omics data visualization
https://amc-heme.github.io/scExploreR/
MIT License
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scExploreR errors when trying to install Bioconductor dependencies #256

Closed jairav closed 1 month ago

jairav commented 3 months ago

To reproduce: on a fresh install of R, run remotes::install_github("amc-heme/scExploreR")

Error:

ERROR: dependencies ‘HDF5Array’, ‘SCUBA’ are not available for package ‘scExploreR’
* removing ‘/home/jairav.desai/R/x86_64-pc-linux-gnu-library/4.3/scExploreR’
Warning messages:
1: packages ‘SummarizedExperiment’, ‘HDF5Array’, ‘SingleCellExperiment’ are not available for this version of R

To repair: This is a known issue - with a fix and references discussed here https://bioinformatics.stackexchange.com/a/3375

We should just be able to add the line biocViews: to the DESCRIPTION file.

jairav commented 1 month ago

There appears to be no reliable way to automatically install bioconductor dependences by modifying the DESCRIPTION file. There is an ongoing discussion - could potentially switch to pak in future.

For now, an update to the ReadMe will suffice.