Call to deprecated Matrix function in calcNhoodDistance()

[mdeea]

Call to deprecated Matrix function in calcNhoodDistance()

[MikeDMorgan]

Hi @mdeea we have introduced an alternative to computing the nhood distance matrix, which has superior scaling performance. Could you re-run the makeNhoods with refinement_scheme="graph" - this dispenses with the need to run calcNhoodDistances - you will also need to adjust testNhoods with fdr.weighting="graph-overlap".

I'll flag this deprecated syntax in the next Bioc release (April).

[MikeDMorgan]

Hi @mihem - you can also access these updates by installing from the devel branch devtools::github_install("MarioniLab/miloR", ref="devel").

[mdeea]

Thanks, I did manage to get the tute running using a singularity instance of R built on Bioconductor 3.16, R 4.2 prior to the Matrix package update to 1.5.
However your workaround worked also and was much easier to use. Thanks!

[mihem]

This is very helpful, but should be mentioned in the vignette IMO, because right now the vignette leads to an error because of this Matrix issue.

[MikeDMorgan]

Hi @mihem This seems to be heavily dependent on the R version - updating to R4.3 indicates this is not an issue - can you confirm which R and package versions you are using?

[mihem]

Thanks for the swift reponse. I work on Ubuntu LTS and still work with R 4.2.1, and use miloR 1.7.1 (master branch from github).

[MikeDMorgan]

Hi @mihem the recommended installation pathway is through Bioconductor. I'd recommend to upgrade to R4.3 and Bioc 3.17 to get the updates.

[mihem]

Hi Mike, well Bioconductor R 4.3 and Bioc 3.17 are pretty new (End of April), so for projects that have been started a few weeks or months ago and are under renv control, I would prefer to keep these older version.

But thanks for fixing, I will update soon for future projects and report if I still experience this issue.