Python - `plotnine` plots throw: "Error rendering plot to 'Auto' size: RPC timed out..."

[milesalanmoore]

System details:

Positron and OS details:

Positron Version: 2025.02.0 (Universal) build 137
Code - OSS Version: 1.96.0
Commit: f4b7966
Date: 2025-01-30T15:14:42.529Z
Electron: 32.2.6
Chromium: 128.0.6613.186
Node.js: 20.18.1
V8: 12.8.374.38-electron.0
OS: Darwin arm64 23.1.0
M1 Macbook Pro 2020 Sonoma 14.1.1

Interpreter details:

Python 3.12.2

Describe the issue:

plotnine plots, specifically, cause the "Error rendering plot to 'Auto' size: RPC timed out after 30 seconds ... " error (see below for full message) after 30 seconds. Where as matplotlib do not.

Steps to reproduce the issue:

import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from plotnine import *

# Generate linear data
np.random.seed(42)
x = np.linspace(0, 10, 100)
y = 2 * x + 1 + np.random.normal(0, 1, 100) 

df = pd.DataFrame({'x': x, 'y': y})

# --- Plotting with Matplotlib ---
# NOTE: This one produces no error

plt.figure(figsize=(8, 6))
plt.scatter(x, y, label="Data Points", color='blue')
plt.plot(x, 2*x + 1, label="y = 2x + 1", color='red', linestyle='--')
plt.title("Linear Data with Matplotlib")
plt.legend()
plt.grid(True)
plt.show()

# --- Plotting with Plotnine --- 
# ERROR: Wait for this plot to throw the error (30 seconds)

(
    ggplot(df, aes(x='x', y='y')) +
    geom_point(color='blue') +
    geom_smooth(method='lm', color='red', se=False) +
    ggtitle("Linear Data with Plotnine") +
    theme_classic()
)

Were there any error messages in the UI, Output panel, or Developer Tools console?

Error rendering plot to 'Auto' size: RPC timed out after 30 seconds: {"jsonrpc":"2.0","method":"get_intrinsic_size"} (-32603)

[jonvanausdeln]

@milesalanmoore , thank you for the report! Is this happening every time you run this file?

I'm also assuming you don't see the plot at all?

I just tried with the latest release 2025.02.0-171 and don't see the issue.

[milesalanmoore]

Hi! Thanks for the response. Indeed, anytime I make a plot with plotnine actually actually. I don't think ggplot2 in R or base R plotting produces this error, nor seaborn in Python. However, consistently, plotnine plots do. I've been using plotnine in positron for several days and have notice this across datasets / projects.

Maybe I modified a setting somewhere, I will try a fresh install of positron and follow up!

[milesalanmoore]

Howdy @jonvanausdeln,

Following up: I followed the instructions here to reset positron and reinstall the latest version:

Positron Version: 2025.02.0 (Universal) build 171
Code - OSS Version: 1.96.0
Commit: 55f7331
Date: 2025-02-10T16:03:19.797Z
Electron: 32.2.6
Chromium: 128.0.6613.186
Node.js: 20.18.1
V8: 12.8.374.38-electron.0
OS: Darwin arm64 23.1.0

Unfortunately, the plotting error persists -- still only with plotnine code. Indeed rerunning the same plotnine.ggplot block triggers the error each time and it seems to occur irrespective of any of the settings in the plotting window (i.e. Fit, 50%, etc.).

I should also add, the plots do render, they just also throw the above error.

[juliasilge]

On my machine, it takes ~20 sec to generate that example plot, and then afterwards I do in fact see an additional RPC timeout error after the plot appears:

Error rendering plot to 'Auto' size: RPC timed out after 30 seconds: {"jsonrpc":"2.0","method":"get_intrinsic_size"} (-32603)

[milesalanmoore]

I noticed this also occurring today (rather unreliably) even on matplotlib plots on a work machine running windows and

Positron Version: 2025.02.0 (user setup) build 171
Code - OSS Version: 1.96.0
Commit: 55f73310e900d46f5f472b4b7e2baa552aa2f157
Date: 2025-02-10T16:01:46.203Z
Electron: 32.2.6
Chromium: 128.0.6613.186
Node.js: 20.18.1
V8: 12.8.374.38-electron.0
OS: Windows_NT x64 10.0.26100

if I am able to pin down a REPL for the matplotlib plots triggering this as well I will post it here!

[juliasilge]

With this version of Positron:

Positron Version: 2025.03.0 (Universal) build 83
Code - OSS Version: 1.96.0
Commit: aa00c75
Date: 2025-02-24T02:42:51.848Z
Electron: 32.2.6
Chromium: 128.0.6613.186
Node.js: 20.18.1
V8: 12.8.374.38-electron.0
OS: Darwin arm64 24.3.0

I no longer see the plot taking 20 sec to generate (now it is very fast), but something weird is still going on. After I first execute the plotnine code, I see the plot being executed but then sort of a ghost plot trying to render:

After 30 sec, I see the timeout error:

This is with the exact same venv that I was using before and saw the ~20 seconds for rendering.

If I run the same code in a Jupyter notebook in Positron, there are no errors so I'd guess this is something about the interaction of our Plots pane and plotnine.