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romanhaa / Cerebro

Visualization of scRNA-seq data.
MIT License
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unable to find required package ‘Seurat’ on data load with docker #19

Open moxgreen opened 4 years ago

moxgreen commented 4 years ago

I tried both docker run -p 8080:8080 -v ~/Desktop:/plots romanhaa/cerebro:latest and docker run -p 8080:8080 -v ~/Desktop:/plots romanhaa/cerebro:v1.1.1

when I load the .rds using the browser I get the error unable to find required package ‘Seurat’

romanhaa commented 4 years ago

Hi! That's very strange. I just tested it on my machine and there it worked fine. Could you please try one thing:

docker run -it --rm romanhaa/cerebro:v1.1.1 R
.libPaths()

This should tell us where the R installation inside the container is looking for libraries.

Also, what kind of .rds file are you trying to load?

SebastienNin commented 3 years ago

Hi, I got the same error using the docker image. Here is my "docker image" line for cerebro romanhaa/cerebro latest 96507732c772 5 months ago 2.48GB

When I run it in interactive mod, I got R version 4.0.3 and the .libPaths() command gives me the following: [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" [3] "/usr/lib/R/library"

Also, directly typing library(Seurat) give me Error in library(Seurat) : there is no package called ‘Seurat’

taiwaness commented 3 years ago

Hi, I got a similar error using the docker image.

docker run -p 8080:8080 -v ~/Desktop:/plots romanhaa/cerebro:latest

Loading required package: SeuratObject
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called �SeuratObject�
Warning: Error in .requirePackage: unable to find required package �SeuratObject�