When jupyterlab uses the R kernel, runing a cell keeps showing * and no output. What could cause this and how to solve it ?

[li1311139481]

Description

When you run two cells in quick succession in the R kernel, you will get * and will not get output again unless you restart the kernel

Reproduce

this is my file
expdf.csv
use it to run the first cell
search()
library(data.table)
library(openxlsx)
library(plyr)
rawdata = read.csv("/cluster/facility/hlhuang/zifeng001/ZF004_GuoAo_HHpaper_RNAseq/expdf.csv", sep = ',', header = T)
head(rawdata)

WT_mean <- data.frame(WT_mean=rowMeans(rawdata[,c("WT1","WT2","WT3","WT4","WT5")]))
KO_mean <- data.frame(KO_mean=rowMeans(rawdata[,c("KO1","KO2","KO3","KO4","KO5")]))
data <- cbind(rawdata,WT_mean,KO_mean)
head(data)
if you run the second cell when the status is busy, you will get * and don't get a output. the only choose is restart kernel.

However , if you wait a moment ,and the status become Idle (not busy) , you can get output normally.

• Operating System and version:
  centos 7
• Browser and version:
  Microsoft Edge 106.0.1370.52
• JupyterLab version:
  

Troubleshoot Output

Paste the output from running `jupyter troubleshoot` from the command line here.
You may want to sanitize the paths in the output.

Command Line Output

What could cause this and how to solve it ?

Paste the output from your command line running `jupyter lab` here, use `--debug` if possible.

Browser Output

Paste the output from your browser Javascript console here, if applicable.

[welcome]

Thank you for opening your first issue in this project! Engagement like this is essential for open source projects! 🤗

If you haven't done so already, check out Jupyter's Code of Conduct. Also, please try to follow the issue template as it helps other other community members to contribute more effectively.

You can meet the other Jovyans by joining our Discourse forum. There is also an intro thread there where you can stop by and say Hi! 👋

Welcome to the Jupyter community! 🎉

[li1311139481]

by the way, I will get output immediately，but the status still show busy. What could cause this and how to solve it ?
My jupyterlab was installed on centos7 and opened by local browser enter IP address. the verions of jupyter is

the R kernel version is 1.3. Someone else can help me ? thanks

[sherry1000001]

I met the same problem. It occurs only when I try to plot. The kernel state is always busy even when running the simplest "plot(1)", but the log file doesn't show any errors or warnings. Could anyone help to figure it out?

[kklot]

same here, running everything is fine but cannot plot.

[seqyuan]

same here,
I meet the problem when i load a seurat rds object
library(Seurat)
rds <- readRDS("data.rds")

when the cell finished read the rds, the cell is always busy, can not run other cells, even a print(1).

[Elysia0528]

I meet the same problem when i use Seurat , Could anyone tell me how to solve this . Thanks!

[seqyuan]

I meet the same problem when i use Seurat , Could anyone tell me how to solve this . Thanks!

I notice the latest version of anaconda will meet this issue. when I reinstall the old anaconda version ,the probleme
solved: https://repo.anaconda.com/archive/Anaconda3-2023.03-1-Linux-x86_64.sh

[li1311139481]

Hello everyone.
A lot of people run into this problem, but it doesn't seem to get much attention from developers.
I have not encountered this problem recently. If you do, please update your jupyterlab if possible