Problem with python submodule when knitting

R Markdown
#1

This is my first attempt to mix R and Python, and I'm running into problems when I try to knit the .Rmd with the following chunks:

library(reticulate)
reticulate::use_python("/home/XXXXX/.pyenv/shims/python", required=TRUE)
py_discover_config()

architect <- import_from_path("src", path=here(), delay_load = FALSE)

print("ok")

res <- architect$utils$camera_utils$get_camera_param()

get_camera_param imports a bunch of other modules from throughout src.utils which is why I did the import at the src level. If I run the chunks manually in Rstudio, it works fine. But when I try to knit the file I get the following error:

Quitting from lines 51-52 (plot_camera.Rmd)
Error in py_get_attr_impl(x, name, silent) :
AttributeError: module 'src.utils' has no attribute 'camera_utils'
Calls: ... py_get_attr_or_item -> py_get_attr -> py_get_attr_impl
Execution halted

Any ideas/suggestions?

#2

Is this possible to share the underlying code so I can reproduce ?

Does the code works in the Python REPL or at the R console ?

The issue is only with R Markdown ?

Having a reproducible example would help investigate. Thanks !

#3

Yes, I only get the error when I try to knit the .Rmd file. It works if I execute in the R console or if I run the chunk manually.

Unfortunately, I can't share the underlying python code. I'll try to mockup some python modules that mimic the import structure that I can share.

#4

Thank you that will help a lot !

#5

@melissawong Also can you try with the development version reticulate ?

remotes::install_github("rstudio/reticulate")

Thank you.

#6

@cderv , I was able to mock up a minimalist example that recreates the problem. In fact, the mock example now fails with the same error whether I try to run the chunk manually or knit it. What's the best way to get the files to you? I've got a *.tgz file with the entire folder structure, but it doesn't look like I can upload *.tgz or *.tar files here.

#7

Can you share the source files on Github ?

You can use a fileshare service and send me the link in DM otherwise.

Also please try the dev version of reticulate thanks.

#8

In case anyone else runs into this problem, using the here package and setting knitr::opts_knit$set(root.dir=here()) fixed my problem with knitting.