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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Issue using SingleR within another R package #103

Closed bbimber closed 3 years ago

bbimber commented 5 years ago

We are trying to use SingleR within my lab's R package, which essentially builds pipeline's from other scRNAseq tools. I found something interesting when I called CreateSinglerObject(). This ends up failing with the error 'hpca not found'. I determined that if I do something like this from within our package code:

assign hpca to global environment

hpca <<- SingleR::hpca CreateSinglerObject(....)

then it will work. I dont quite understand why this is happening, but I thought I would report it.

dviraran commented 5 years ago

Thanks for the info. I guess this is related to the way your package loads SingleR.

You might want to take a look at the new version we will soon submit to bioconductor - https://github.com/LTLA/SingleR, that would probably be a better fit for a pipeline package.