qmd file not recognizing conda environment in libPaths

[jjhuang4]

Description

I recently got started with using Quarto to make my personal blog, and I'm currently using miniforge/mamba to manage my environment. Specifically, I have an environment datasci-env where I have Python and R libraries installed from the conda-forge channel.

I'm running into an issue where my index.qmd file doesn't seem to recognize my conda environment, despite it being activated in my VSCode IDE. Running "quarto check knitr" in the terminal gives me the following output:

Quarto 1.6.39
[>] Checking R installation...........OK
Version: 4.1.3
Path: C:/Users/jrh25/miniforge3/envs/datasci-env/lib/R
LibPaths:
- C:/Users/jrh25/miniforge3/envs/datasci-env/Lib/R/library
knitr: 1.43
rmarkdown: 2.22

[>] Checking Knitr engine render......OK

Which I interpret as Quarto recognizing my conda environment, but I see the following output when I try to load the "reticulate" library in index.qmd, and when I display libPaths():

As you can see, reticulate isn't being recognized due to it not being found in libPaths, and my conda environment isn't displayed among the paths shown by libPaths().

I also run into a similar issue in my GitHub actions workflow in the render and publish step, specifically when I include "engine: knitr" in the YAML of my index.qmd file, where it again doesn't include my conda environment in libPaths:

[4/6] posts/1-07-2025/index.qmd
Error in loadNamespace(x) : there is no package called ‘rmarkdown’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
R installation:
Version: 4.4.2
Path: /usr/lib/R
LibPaths:
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
knitr: (None)
rmarkdown: (None)

The knitr package is not available in this R installation.
Install with install.packages("knitr")

The rmarkdown package is not available in this R installation.
Install with install.packages("rmarkdown")

This is confusing, because it conflicts with what I saw from Quarto when I ran "quarto check knitr" in the terminal, where my conda environment is the sole libPath. What could be the issue here and how do I address it? Is it an issue with VSCode, the Quarto extension, or how I configured my qmd file? I've tried scouring the documentation but haven't found anything relating to this issue.

Thanks in advance!

[mcanouil]

Could you share a small self-contained "working" (reproducible) example to work with, i.e., a complete Quarto document or a Git repository? The goal is to make it as easy as possible for us to recreate your problem so that we can fix it: please help us help you! Thanks.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code blocks (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[jjhuang4]

Hi, thank you for getting back to me.

Here are the results of quarto check:

Quarto 1.6.39
[>] Checking environment information...
      Quarto cache location: C:\Users\jrh25\AppData\Local\quarto
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.6.39
      Path: C:\Users\jrh25\AppData\Local\Programs\Quarto\bin
      CodePage: 1252

[>] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[>] Checking LaTeX....................OK
      Using: TinyTex
      Path: C:\Users\jrh25\AppData\Roaming\TinyTeX\bin\windows\
      Version: 2023

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....OK
      Version: 3.12.8 (Conda)
      Path: C:/Users/jrh25/miniforge3/envs/datasci-env/python.exe
      Jupyter: 5.7.2
      Kernels: ir, python3

[>] Checking Jupyter engine render....OK

[>] Checking R installation...........OK
      Version: 4.1.3
      Path: C:/Users/jrh25/miniforge3/envs/datasci-env/lib/R
      LibPaths:
        - C:/Users/jrh25/miniforge3/envs/datasci-env/Lib/R/library
      knitr: 1.43
      rmarkdown: 2.22

[>] Checking Knitr engine render......OK

I also did some further digging and found a workable solution to one of my issues. I added a .Rprofile file to my working directory.

.Rprofile:

.libPaths(c("C:/Users/jrh25/miniforge3/envs/datasci-env/Lib/R/library"))
library(reticulate)
use_condaenv(condaenv="datasci-env", conda="C:/Users/jrh25/miniforge3/condabin/conda.bat", required=TRUE)

This should add the path to my conda environment's R libraries to R library paths, and also point reticulate to my conda python installation.

I've tested this setup with the following qmd:

---
title: "Testing with knitr engine"
date: "2025-01-08"
categories: [news, code, analysis]
engine: knitr
---

```{r}
.libPaths()
```

```{r}
library(reticulate)
py_config()
getwd()
```

```{python}
import pandas as pd
import numpy as np

arr = np.array([1, 2, 3, 4, 5])
arr
```

```{r}
arr <- py$arr
print(arr)
```

```{python}
r['arr']
r.arr
```

Checking .libPaths() gives me:

> .libPaths()
[1] "C:/Users/jrh25/miniforge3/envs/datasci-env/Lib/R/library"
[2] "C:/Program Files/R/R-4.4.2/library"

Checking py_config() for reticulate gives me:

> py_config()
python:         C:/Users/jrh25/miniforge3/envs/datasci-env/python.exe
libpython:      C:/Users/jrh25/miniforge3/envs/datasci-env/python312.dll
pythonhome:     C:/Users/jrh25/miniforge3/envs/datasci-env
version:        3.12.8 | packaged by conda-forge | (main, Dec  5 2024, 14:06:27) [MSC v.1942 64 bit (AMD64)]
Architecture:   64bit
numpy:          C:/Users/jrh25/miniforge3/envs/datasci-env/Lib/site-packages/numpy      
numpy_version:  1.26.4
sys:            [builtin module]

NOTE: Python version was forced by use_python() function

So far everything appears to run seamlessly locally, although I'm still having issues with the Quarto render / publish step in my GitHub actions workflow, where I'm getting the following error:

[4/7] posts/1-08-2025/index.qmd
Error in library(reticulate) : there is no package called ‘reticulate’
Execution halted
Error in library(reticulate) : there is no package called ‘reticulate’
Execution halted
Problem with running R found at /usr/bin/Rscript to check environment configurations.
Please check your installation of R.

[cderv]

Can you activate more verbose tracing for quarto check please ?
See https://quarto.org/docs/troubleshooting/#verbose-mode

It seems quarto check knitr does find the R version associated with your conda environment as we see

[>] Checking R installation...........OK
      Version: 4.1.3
      Path: C:/Users/jrh25/miniforge3/envs/datasci-env/lib/R
      LibPaths:
        - C:/Users/jrh25/miniforge3/envs/datasci-env/Lib/R/library
      knitr: 1.43
      rmarkdown: 2.22

But then when running quarto render it seems another libPaths is used.

Could you also run a quarto render with a cell containing

```{r}
R.home()
.libPaths()
```

to see which is used during rendering.

I don't have easy testing environment for this as I don't use CONDA but I am wondering if our detection is not working for some reason.

QUARTO_R can be set to the R version of your conda env to tell quarto which R to use by the way. Also I guess you activated your environment before running quarto render.

Anyhow, I would expect quarto check to return same version used during quarto render so we'll see. Thank you !

[jjhuang4]

The render/fpublish error just appears to be an issue with environment setup in the Github actions workflow itself, so an easier workaround right now seems to be just running

quarto render
quarto publish gh-pages

In my terminal, which successfully builds and deploys my website. I'll get rid of the workflow for now; I'm satisfied with just being able to run R and Python cells in my code.

[cderv]

Just so you know quarto publish will render your project by default. No need to call quarto render first.
If you need to for some reason, you may want quarto publish gh-pages --no-render

[jjhuang4]

I tried adding verbose trace and running both R.home() and libPaths() in the same cell.

Here is some relevant output I found:

-- Searching for R binary --
Looking for 'Rscript' in QUARTO_R: undefined
Looking for 'Rscript' in R_HOME: undefined
Looking for 'Rscript' in PATH.
[execProcess] which Rscript
[execProcess] Success: false, code: 1
Quarto did no found Rscript and will try to use it directly.

And quarto only seems to render .libPaths().

On a side note, it looks like my GitHub workflow is passing all steps now... I don't know the exact reason why but I'll keep my fingers crossed until it breaks again, and I'll try some more troubleshooting when that happens.

[cderv]

That is really odd that R is not found.

If you share your repo, I can have a look in the workflow if you want, in case I see something.

Something related to current news on github action: ubuntu-latest switched to Ubuntu 24, and I think R is no more installed by default. It must be installed separately. Just sharing in case your workflow was relying on Ubuntu and R on system.

[jjhuang4]

Sorry, I didn't see your reply previously. Here's my github repo. My current workflow file runs on ubuntu-latest, so that might be the issue as you've described. I'll check the documentation to see how to set up R manually.

https://github.com/jjhuang4/jjhuang4.github.io/blob/main/.github/workflows/publish.yml

[cderv]

I see you've installed R now (jjhuang4/jjhuang4.github.io@083c956)

Does it work as expected ?

[jjhuang4]

I think so:

-- Searching for R binary --
Looking for 'Rscript' in QUARTO_R: undefined
Looking for 'Rscript' in R_HOME: undefined
Looking for 'Rscript' in PATH.
[execProcess] which Rscript
[execProcess] Success: true, code: 0
Found in PATH at /usr/local/bin/Rscript

[cderv]

All good then ! Cool !