createConfig error for SCE object

[carissaynchen]

Hello, I think this is a really great package! but I'm having issue with the createConfig(sce) command. I've followed the tutorial steps as below:

seu <- readRDS("readySeu_rset.rds")
sce <- as.SingleCellExperiment(seu)
scConf = createConfig(sce)

and this error appears Error in createConfig(sce) : no slot of name "reducedDims" for this object of class "SingleCellExperiment"

despite there are five objects: PCA TSNE UMAP DIFFMAP FDL in the example data. How should I solve this error?

[jfouyang]

Hi! Thanks for using the package!

It seems that you are getting the errors because the internals of the SingleCellExperiment object has changed in the past few months. I have just updated a "patch" onto the github repository which should access the SCE object properly now. Can you reinstall ShinyCell and check if the error disappears?

If everything is ok, you can drop a reply here and I can then close the issue. :)

John

[carissaynchen]

I have reinstalled ShinyCell and run the code as above but when I reach createConfig this error appears:

internal error -3 in R_decompress1Error: lazy-load database '/Users/carissaynchen/Library/R/4.0/library/ShinyCell/R/ShinyCell.rdb' is corrupt

[jfouyang]

This "lazy-load database corrupt" error seems pretty common when you try to reinstall packages.
An example I found is in lme4/lme4#407

1. It seems that restarting your R completely can solve that problem.

2. If that fails, please restart R again and uninstall the package by running remove.packages("ShinyCell") and then install ShinyCell again.

Hope this helps.

[carissaynchen]

Yes, everything works fine now! thank you