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drisso / SingleCellExperiment

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.
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Mistake Locks R Terminal #75

Open DarioS opened 6 months ago

DarioS commented 6 months ago

I notice a few times that if I make a mistake, the error message will be printed immediately but I won't be able to use the terminal for a few minutes and the process can't be interrupted. R has to be forcefully terminated.

> assay(fibroSCE, "merged") <- altExps(fibroSCE) # Intended to write altExp(fibroSCE, "merged")
Error in `assays<-`(`*tmp*`, withDimnames = withDimnames, ..., value = `*vtmp*`) : 
  please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,

It is doing something, but not clear what.

    PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND   
2605798 dario     20   0   99.7g  83.7g 153432 R 100.0  11.1 160:09.35 rsession

In case it helps, I was trying to move something from main experiment to assay section, to make it useful for plotting.

reducedDimNames(2): PCA UMAP
mainExpName: merged
altExpNames(2): RNA SCT
LTLA commented 6 months ago

I have no idea. SCE's not doing any extra error handling for assay<-, AFAIK.