Error in GitHub Action Virtualenv_create with R-devel and Reticulate

[pbulsink]

Hello, we have a recurrent error with reticulate for rdevel on ubuntu in our github action:

https://github.com/SCasanova/f1dataR/actions/runs/8149812048/job/22275075253

In particular, trying to create a virtualenv causes the following error:

Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : 
  invalid non-character version specification 'x' (type: double)
Calls: virtualenv_create ... as.numeric_version -> numeric_version -> .make_numeric_version

Other versions of R on the same platform (release and oldrel) and with specified (3.11) or generic (3.x) versions of python pass.
R-Devel on other platforms (windows-latest/macos-latest) with specified (3.11) or generic (3.x) versions of python fail.

Code suffering the error:

      - name: setup r-reticulate venv
        shell: Rscript {0}
        run: |
          python_packages <- c("numpy", "fastf1")
          library(reticulate)
          virtualenv_create("r-reticulate", Sys.which("python"))
          virtualenv_install("r-reticulate", python_packages)
          path_to_python <- virtualenv_python("r-reticulate")
          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
                     Sys.getenv("GITHUB_ENV"))

[t-kalinowski]

Thanks for reporting.

I beleive the development version of reticulate already has a fix for the latest r-devel. Do you still see the error if you install reticulate from main branch?

We'll have a new CRAN release in a few weeks time.

[pbulsink]

Thanks for that advice. I re-ran on GHA with reticulate from github and everything ran correctly.

For others who may experience the same issue and want to use reticulate from github instead of CRAN, I added the following lines before my setup-reticulate step (after r-lib/actions/setup-r-dependencies@v2):

      - name: Install remotes
        run: |
          Rscript -e "install.packages('remotes')"

      - name: Install dev reticulate from Github
        run: |
          Rscript -e "remotes::install_github('rstudio/reticulate')"

[eddelbuettel]

I am seeing the same error (in an Ubuntu 24.04 container) with version 1.39.0 which should have the fix.

Any idea? I installed packages python3-dev python3-pip python3-venv python-is-python3 from Ubuntu 24.04.

> library(reticulate)
> virtualenv_create()
Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : 
  invalid non-character version specification 'x' (type: double)
>
>
> traceback()
8: stop(msg, domain = NA)
7: .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
6: numeric_version(x)
5: as.numeric_version(e2)
4: Ops.numeric_version(py_version, 3)
3: virtualenv_module(python)
2: module %||% virtualenv_module(python)
1: virtualenv_create()
>
> packageVersion("reticulate")
[1] ‘1.39.0’
> 

[t-kalinowski]

Thanks for reporting. It looks like there are two stray py_version > 3 comparisons that I didn't update with the initial fix:

reticulate/R/virtualenv.R

Line 453 in 74627cd

package <- if (py_version < 3) "python-pip" else "python3-pip"

However, those lines of code are only evaluated when we're already composing a nicer error message because pip or venv is missing. Since you've already installed python3-venv, something else is also going wrong, which we'll need to investigate.

[eddelbuettel]

So I was trying to get a minimal environment going when batch package building. The displayed sudo apt install python3-venv is clearly not enough. Adding python3-pip python3-dev python-is-python3 appears to work once, but not when I restarted the container (huh?).

Could it be that we are running into subtle 'focal vs jammy' differences?

[eddelbuettel]

Getting closer, thanks to your fine and focussed commit I was able to poke. I think the first test passes

root@78709e774099:/# Rscript -e 'reticulate:::python_has_module("/usr/bin/python3", "pip")'
[1] TRUE
root@78709e774099:/# 

but the second was not testing for venv present so my R 4.4.1 nagged over the comp with 3 instead of "3".

(This was after

apt update -qq; apt install r-cran-reticulate python3-pip python3-dev python3-venv python-is-python3

in a rocker/r2u:noble container.)

[t-kalinowski]

The only other thing I could think of is that this dpkg check failed because the output of dpkg changed subtly:

reticulate/R/virtualenv.R

Line 436 in 74627cd

if (!any(grepl("\\bpython[0-9.]*-venv\\b", system("dpkg -l", intern = TRUE))))

However, I tried in docker containers derived from both rocker/r2u:noble and ubuntu:24.04 and was unable to reproduce the error. dpkg -l still gave the expected output, and reticulate::virtualenv_create() succeeded without issue after apt install -y python3-venv had run.

[eddelbuettel]

Yes that works here too. (Same 22.04 container I still had open)

root@78709e774099:/# Rscript -e 'any(grepl("\\bpython[0-9.]*-venv\\b", system("dpkg -l", intern = TRUE)))'
[1] TRUE
root@78709e774099:/# 

[t-kalinowski]

If you can share a Dockerfile where reticulate::virtualenv_create() errors, I'll be happy to take a look.

[eddelbuettel]

Hm, that command works (after apt update -qq; apt install r-cran-reticulate python3-pip python3-dev python3-venv python-is-python3). So maybe my (much more feeble?) bug report is that the echo'ed line on sudo apt install python3-venv is to short?

[eddelbuettel]

And the same command I ran a few comments and hours earlier, ie from inside R, now also works. I must have been missing python3-dev I guess?

[t-kalinowski]

Thanks. I just pushed an update to improve the error message and mention python3-dev.

[eddelbuettel]

I presume I could iterate and try to find the minimal set that let's us build the required venv.

(One thing, by the way, I was thinking but have been able to check with your code. Would having an env that auto-creates the default venv if missing be helpful?)

[t-kalinowski]

Would having an env that auto-creates the default venv if missing be helpful?

Do you mean something like this?

reticulate:::.onLoad <- function(...) {
  ...
  if (!virtualenv_exists("r-reticulate") && 
      !is.null(virtualenv_starter())
    virtualenv_create()
}

[eddelbuettel]

Yep, pretty much. Because right now what happens is

• package 'ABC' depends on reticulate
• reticulate gets installed
• reticalete dies on loading because no venv is there

Obviously, I can jump in and create it for the builds that need it (now that I know the missing ingredients) but it would be simpler if the needed step was executed auto'magic'ally.