install

[cathalgking]

I am trying to install VisiumIO but am having an issue. I am running R version:

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3

I try to install with:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("VisiumIO")

And I get the Error

Error: Bioconductor version '3.19' requires R version '4.4'; use `version = '3.18'` with R version 4.3; see
  https://bioconductor.org/install

I already have R 4.3.2 and there does not seem to be a version 4.4 that exists

[lwaldron]

Hi @cathalgking , R 4.4 is referring to the unreleased devel version of R - see https://contributions.bioconductor.org/use-devel.html for some more information on using the devel version of Bioconductor and links for installing R-devel. Since VisiumIO is pre-release it hasn't been tested against the current release version of Bioconductor, but after this April's release of Bioconductor 3.19 it will become installable with a regular Bioconductor release installation. To be honest I don't know if the package would work with a current bioc-release (@LiNk-NY might have a better idea), although it's possible to try by downloading your own version of the package, changing the DESCRIPTION file, and building/installing locally (definitely voids the non-existent warranty :) ).

[LiNk-NY]

Hi @cathalgking

Thank you for your interest. VisiumIO currently doesn't work with Bioconductor 3.18 because I made updates to TENxIO in devel. Those changes are not bug fixes but feature updates and thus were not ported to the stable release. You'd have to wait until the next Bioconductor release or use Bioc-devel as Levi mentioned.

Best regards, Marcel

[cathalgking]

Ok, thanks for your work on this and the prompt replies @LiNk-NY @lwaldron Ill await the full release of VisiumIO. I mainly wanted to be able to read in a 10x Visium dataset to an SPE object with SpatialExperiment but getting an error and dont know why. Error in names(xyz) <- names(sfs) <- sids : 'names' attribute [1] must be the same length as the vector [0]

[LiNk-NY]

@cathalgking Perhaps it's a bug in SpatialExperiment. Feel free to report it with a reproducible example to our collaborator Dario Righelli at https://github.com/drighelli/SpatialExperiment/issues Thanks!