NUMPY NOT FOUND BUT ACTUALLY INSTALLED

[ericpeny]

I have conda installed on the server, created an environment, installed all packages needed.
I checked conda, python, library as following.

(trialbot) bash-4.2$ which conda
~/miniconda3/bin/conda
(trialbot) bash-4.2$ which python
~/miniconda3/envs/trialbot/bin/python
(trialbot) bash-4.2$ python
Python 3.10.14 (main, Mar 21 2024, 16:24:04) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.__version__
'1.26.4'

In Rstudio, I setup env variable in .Renviron as

RETICULATE_PYTHON=~/miniconda3/envs/trialbot/bin/python3.10
I set python interpreter using ~/miniconda3/envs/trialbot/bin/python
I set all the configure as many as possible
Sys.setenv(RETICULATE_PYTHON = "~/miniconda3/envs/trialbot/bin/python")
use_python("~/miniconda3/envs/trialbot/bin/python")

But NUMPY NOT FOUND!

py_config()
python: /home/e0564278/miniconda3/envs/trialbot/bin/python
libpython: /home/e0564278/miniconda3/envs/trialbot/lib/libpython3.10.so
pythonhome: /home/e0564278/miniconda3/envs/trialbot:/home/e0564278/miniconda3/envs/trialbot
version: 3.10.14 (main, Mar 21 2024, 16:24:04) [GCC 11.2.0]
numpy: [NOT FOUND]

NOTE: Python version was forced by RETICULATE_PYTHON

And I even forced it to install, but no help.
reticulate::py_install(envname = "~/miniconda3/envs/trialbot", python_version = '3.10.14',
packages = "numpy", pip = TRUE, pip_ignore_installed = TRUE)

What can I do?

[t-kalinowski]

My best guess is that this is a different manifestation of a binary incompatibility between the R build and the Conda built NumPy.

Do you see the same error if you use a virtualenv?

[ericpeny]

My best guess is that this is a different manifestation of a binary incompatibility between the R build and the Conda built NumPy.

Do you see the same error if you use a virtualenv?

Thank you for your quick reply! I tried to create a virtualenv, and use it in RSTUDIO, and still get numpy not found. If the incompatibility exisits, how can I solve it?

[t-kalinowski]

What is the output from running this?

library(reticulate)
install_python("3.10:latest")
virtualenv_create(force = TRUE, version = "3.10")
.rs.restartR() # restart R manually if outside RStudio

reticulate::py_config()

[ericpeny]

What is the output from running this?

library(reticulate)
install_python("3.10:latest")
virtualenv_create(force = TRUE, version = "3.10")
.rs.restartR() # restart R manually if outside RStudio

reticulate::py_config()

I always have this system python path numpy loaded.

[t-kalinowski]

Do you know how the other Numpy is getting placed on sys.path?

Is PYTHONPATH defined?

Sys.getenv("PYTHONPATH")

Perhaps some other mechanism?

[t-kalinowski]

It might make sense for us to invoke pip with the -I flag: https://docs.python.org/3/using/cmdline.html#cmdoption-I

[ericpeny]

Do you know how the other Numpy is getting placed on sys.path?

Is PYTHONPATH defined?

Sys.getenv("PYTHONPATH")

Perhaps some other mechanism?

Thank you! I reset my PYTHONPATH, removed the system python library, then it works!