Error when converting Seurat to SingleCellExperiment
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@lirongrossmann-23954
Last seen 5 months ago

Enter the body of text here

Hi, I am trying to convert a Seurat object to SingleCellExperiment and getting the error below. Anyone had similar issues?

Code should be placed in three backticks as shown below

sce.object<- as.SingleCellExperiment(seurat.object)

Error in h(simpleError(msg, call)) : error in evaluating the argument 'flesh' in selecting a method for function 'relist': lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/GenomeInfoDb/R/GenomeInfoDb.rdb' is corrupt In addition: Warning messages: 1: In new_GRanges("GRanges", seqnames = seqnames, ranges = ranges, : restarting interrupted promise evaluation 2: In new_GRanges("GRanges", seqnames = seqnames, ranges = ranges, : internal error -3 in R_decompress1

include your problematic code here with any corresponding output

please also include the results of running the following in an R session

sessionInfo( ) ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value
version R version 4.0.3 (2020-10-10) os macOS Catalina 10.15.7
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-12-08
```

Seurat SingleCellExperiment • 227 views
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Aaron Lun ★ 27k
@alun
Last seen 17 hours ago
The city by the bay

This just looks like someone tried to update or reinstall GenomeInfoDb while your R session was running. Try restarting R.

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Thanks so much! It worked!

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