'Jupyter get stuck in docker container
I have created a jupyter_lab docker and usually it works quite fine but sometimes it get stuck. Usually i could never reproduce this problem but now, apparently he totally doesn't like this file (https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/genes/refGene.gtf.gz). Using R, once I
gtf=read.table("refGene.gtf",header=TRUE,sep="\t")
it looks like everything is loaded fine but if in another cell I call for
print(gtf)
it just get stuck there. And the weird thing is that it get stuck even if instead of printing the gtf variable I ask him to print any other thing. Also if I put together in the same cell
gtf=read.table("refGene.gtf",header=TRUE,sep="\t") print(gtf)
It works properly but then i cannot use anymore the other cells. If i exec a /bin/bash into the same opened docker that has the stuck jupyterlab and I open R with the terminal and perform the same tasks I dont have any problem, so looks like is a cell jupyter lab problem.
Solution 1:[1]
I have found the problem. @lckr/jupyterlab_variableinspector slow everything down with big data. Just remove this and everything will work again.
Sources
This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.
Source: Stack Overflow
| Solution | Source |
|---|---|
| Solution 1 | LucaStormreig |