Bioc3.19 small bug fixes

maddygriz commented 6 months ago

quick bug fixes:

version numbers are more stringent with classes in R 4.4 (5 != 5.0.0). This affected both Seurat package version in coercion switch and PKC version checking
SpatialExperiment plotting in coercion vignette was not equal to the Seurat plotting. Updated the vignette rather than update the coercion. The coordinates were equal between the two objects, just the plotting was different. I think the Seurat plotting function might have been updated so we needed to update to match.

Version issue is a package building blocker on bioc since one test fails and the coercion vignette can't knit.

R CMD check passed with 5 expected warnings.

R 4.4 install I don't think this update is necessary but it might be.

mgrout81 commented 6 months ago

Test as.Seurat() workes as expected: pass.

mgrout81 commented 6 months ago

Test plots (e.g., A2M) are identical: pass

Very slight difference of outline on points on left-hand plot not consequential.

Nanostring-Biostats / GeomxTools