Problems knitting a .Rmd file with reticulate using python from a conda env

bv2 commented 3 years ago

Hi,

I am not able to knit an Rmd file that uses reticulate when using a Python version from a conda environment.

For example: The following .Rmd file stops during the knitting process without any error in the first chunk. It only occurs when knitting the file, I can run the code of each chunk without any problems. Also I am able to knit the file if I comment the first line (reticulate::use_python("/opt/anaconda3/envs/mofa/bin/python")).

---
title: "Example"
---
```{r}
reticulate::use_python("/opt/anaconda3/envs/my_env/bin/python")
reticulate::py_config()

sessionInfo()


Do you have any suggestions what could be the problem?
This is my sessionInfo:

R version 4.1.0 (2021-05-18)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Big Sur 10.16

Matrix products: default

BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):

[1] Rcpp_1.0.7 lattice_0.20-44 png_0.1-7 digest_0.6.27

[5] grid_4.1.0 R6_2.5.0 jsonlite_1.7.2 magrittr_2.0.1

[9] evaluate_0.14 rlang_0.4.11 stringi_1.7.3 jquerylib_0.1.4

[13] Matrix_1.3-4 bslib_0.2.5.1 reticulate_1.20 rmarkdown_2.9

[17] tools_4.1.0 stringr_1.4.0 xfun_0.24 yaml_2.2.1

[21] compiler_4.1.0 htmltools_0.5.1.1 knitr_1.33 sass_0.4.0

kevinushey commented 3 years ago

Some questions that will help narrow down the issue:

Do you see this issue with other Python installations (e.g. not using Anaconda)?
Do you see this issue with other Conda environments, or only this one?
If you recently updated Rcpp, you may also need to reinstall other packages depending on Rcpp. Does reinstalling reticulate and its dependencies help?
How are you rendering the document -- e.g. within RStudio via the Knit button, or in the R console via rmarkdown::render()? Does the behavior differ depending on how the document is rendered?

bv2 commented 3 years ago

Hi @kevinushey , thanks for taking a look at this problem. Here some more details:

I see this issue only with Anaconda, e.g. with the base python installation it works fine ("/usr/bin/python")
this happens for all Conda environments
re-installing reticulate did not help
it happens when rendering the file via the Knit button. Using rmarkdown::render() works fine, while devtools::build() to build html vignettes inside a package also does not work.

kevinushey commented 3 years ago

it happens when rendering the file via the Knit button. Using rmarkdown::render() works fine, while devtools::build() to build html vignettes inside a package also does not work.

Do you see this issue if you run devtools::build() from the command line; e.g. in a plain R session outside of RStudio? Any chance you can share the package sources in case I'm able to reproduce in that context?

bv2 commented 3 years ago

The package built issue also appears from the command line but I am mostly wondering about the problem with a simple example as above when using the Knit button.

Prior to my last update of R (to R4.1) this always worked fine. Could this be specific to the combination of being on a Mac (10.16), using R 4.1 and having reticulate configured to use a conda environment? Or is this related to something in my personal setup I would have to change?

rstudio / reticulate