Seg fault with reticulate

[csgillespie]

I'm trying to render a simple Rmd.

• I can render test.Rmd locally (Ubuntu)
• But using the Dockerfile below, I get a seg fault

Steps:

1. Build image below: docker build . --tag="segfault-reprex"
2. Try knit the Rmd in the container: docker run segfault-reprex Rscript -e "rmarkdown::render('/root/test.Rmd')"

---

The file test.Rmd (note I've add two ' to render the knitr backticks):

---
output: pdf_document
---

```{r setup}
reticulate::virtualenv_create(
  envname = "./venv",
  packages = c("matplotlib")
)

venv_path = file.path(getwd(), "venv")
reticulate::use_virtualenv(venv_path, required = TRUE)
'```

```{python}
import matplotlib.pyplot as plt
plt.plot([1, 2, 3], [4, 5, 6])
'```

---

Dockerfile

FROM rocker/r-ver:latest
RUN apt update && apt install -y python3.8-venv python3-dev pandoc
RUN Rscript -e 'install.packages(c("reticulate", "rmarkdown"))'
COPY test.Rmd /root/