Config/reticulate in package DESCRIPTION file does not install Python dependencies

[mcanigueral]

I'm using my own Python functions wrapped by my R package functions, so I have the Python Pandas dependency in my R Package.
I would like to see all my Python dependencies installed in the project's active Python environment when I install my package from GitHub. Thus, I have been following this article of reticulate.
I have introduced the following to the DESCRIPTION file, whith pip = FALSE since I want to use condaenv:

Config/reticulate:
  list(
    packages = list(
        list(package = "pandas", pip = FALSE)
    )
  )

And I have introduced the following to an R script package_utils.R in package's R/ folder:

pyenv <- new.env()
.onLoad <- function(libname, pkgname) {
    reticulate::configure_environment(pkgname, force = TRUE)
    reticulate::source_python(system.file("python/utils.py", package = pkgname), envir = pyenv)
}

The python script with my Python functions is located in package's inst/python/utils.py folder, and all functions are loaded in a global environment pyenv in order to be accessible from all other R functions.

Then, when I make the CRAN check or install the package i get the following error:

/bin/bash: /home/mcanigueral/Desktop/R packages/evflex/renv/python/condaenvs/renv-python/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Updating evflex documentation
Loading evflex
Error in py_run_file_impl(file, local, convert) : 
  ModuleNotFoundError: No module named 'pandas'

Then, the Config/reticulate in DESCRIPTION is not installing the dependencies automatically. What do I need to configure a part from these files above?

Thanks!

[kevinushey]

Then, when I make the CRAN check or install the package i get the following error:

The biggest problem here is that normally, R packages shouldn't be downloading and installing software onto the CRAN build machines when running tests. I also think it is unlikely to me that you would want to spend time debugging test failures that might only occur on CRAN's machines.

All that said, I have a test package here:

https://github.com/kevinushey/usespandas

and it seems to work as expected:

remotes::install_github("kevinushey/usespandas")

library(reticulate)
library(usespandas)

conda_create("usespandas-test")
use_condaenv("usespandas-test", required = TRUE)

py_config()
py_module_available("pandas")

I see:

> library(reticulate)
> library(usespandas)
> conda_create("usespandas-test")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/kevinushey/Library/r-miniconda/envs/usespandas-test

  added / updated specs:
    - python


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.12.5          |   py39h6e9494a_1         143 KB  conda-forge
    python-3.9.1               |h2502468_5_cpython        12.6 MB  conda-forge
    python_abi-3.9             |           1_cp39           4 KB  conda-forge
    setuptools-49.6.0          |   py39h6e9494a_3         950 KB  conda-forge
    tzdata-2021a               |       he74cb21_0         121 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        13.8 MB

The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2020.12.5-h033912b_0
  certifi            conda-forge/osx-64::certifi-2020.12.5-py39h6e9494a_1
  libcxx             conda-forge/osx-64::libcxx-11.0.1-habf9029_0
  libffi             conda-forge/osx-64::libffi-3.3-h046ec9c_2
  ncurses            conda-forge/osx-64::ncurses-6.2-h2e338ed_4
  openssl            conda-forge/osx-64::openssl-1.1.1i-h35c211d_0
  pip                conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.9.1-h2502468_5_cpython
  python_abi         conda-forge/osx-64::python_abi-3.9-1_cp39
  readline           conda-forge/osx-64::readline-8.0-h0678c8f_2
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py39h6e9494a_3
  sqlite             conda-forge/osx-64::sqlite-3.34.0-h17101e1_0
  tk                 conda-forge/osx-64::tk-8.6.10-h0419947_1
  tzdata             conda-forge/noarch::tzdata-2021a-he74cb21_0
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010



Downloading and Extracting Packages
setuptools-49.6.0    | 950 KB    | ########## | 100% 
tzdata-2021a         | 121 KB    | ########## | 100% 
python_abi-3.9       | 4 KB      | ########## | 100% 
certifi-2020.12.5    | 143 KB    | ########## | 100% 
python-3.9.1         | 12.6 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate usespandas-test
#
# To deactivate an active environment, use
#
#     $ conda deactivate

[1] "/Users/kevinushey/Library/r-miniconda/envs/usespandas-test/bin/python"
> use_condaenv("usespandas-test", required = TRUE)
> py_config()

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/kevinushey/Library/r-miniconda/envs/usespandas-test

  added / updated specs:
    - pandas


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libblas-3.9.0              |       8_openblas          11 KB  conda-forge
    libcblas-3.9.0             |       8_openblas          11 KB  conda-forge
    libgfortran-5.0.0          |9_3_0_h6c81a4c_17          19 KB  conda-forge
    libgfortran5-9.3.0         |      h6c81a4c_17         1.7 MB  conda-forge
    liblapack-3.9.0            |       8_openblas          11 KB  conda-forge
    llvm-openmp-11.0.1         |       h7c73e74_0         268 KB  conda-forge
    numpy-1.20.0               |   py39h3c955ea_0         5.4 MB  conda-forge
    pandas-1.2.1               |   py39h089d6f7_0        10.8 MB  conda-forge
    pytz-2021.1                |     pyhd8ed1ab_0         239 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        18.5 MB

The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-8_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-8_openblas
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_17
  libgfortran5       conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_17
  liblapack          conda-forge/osx-64::liblapack-3.9.0-8_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.12-openmp_h54245bb_1
  llvm-openmp        conda-forge/osx-64::llvm-openmp-11.0.1-h7c73e74_0
  numpy              conda-forge/osx-64::numpy-1.20.0-py39h3c955ea_0
  pandas             conda-forge/osx-64::pandas-1.2.1-py39h089d6f7_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pytz               conda-forge/noarch::pytz-2021.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0



Downloading and Extracting Packages
libcblas-3.9.0       | 11 KB     | ########## | 100% 
numpy-1.20.0         | 5.4 MB    | ########## | 100% 
libgfortran-5.0.0    | 19 KB     | ########## | 100% 
liblapack-3.9.0      | 11 KB     | ########## | 100% 
libblas-3.9.0        | 11 KB     | ########## | 100% 
llvm-openmp-11.0.1   | 268 KB    | ########## | 100% 
libgfortran5-9.3.0   | 1.7 MB    | ########## | 100% 
pytz-2021.1          | 239 KB    | ########## | 100% 
pandas-1.2.1         | 10.8 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Done!
python:         /Users/kevinushey/Library/r-miniconda/envs/usespandas-test/bin/python
libpython:      /Users/kevinushey/Library/r-miniconda/envs/usespandas-test/lib/libpython3.9.dylib
pythonhome:     /Users/kevinushey/Library/r-miniconda/envs/usespandas-test:/Users/kevinushey/Library/r-miniconda/envs/usespandas-test
version:        3.9.1 | packaged by conda-forge | (default, Jan 26 2021, 01:32:59)  [Clang 11.0.1 ]
numpy:           [NOT FOUND]

NOTE: Python version was forced by use_python function
> py_module_available("pandas")
[1] TRUE

[mcanigueral]

Thanks for your answer!
I see now that the installation of Python dependencies specified in Config/reticulate is done when running py_config(). I missed this part.
I'm closing this. Thanks again.

[kevinushey]

In particular, it's done as soon as Python is initialized -- so packages can be loaded, users can configure the version of Python to be used, and then once a version of Python is selected the requisite Python modules can be installed.