Installation Issue: '/usr/bin' exists but is not a virtual environment

Start with the keras::install_keras() entry point and the reticulate::install_miniconda() setup described in the report, then inspect how virtualenv_install() handles /usr/bin. Reproduce on the reported Pop!_OS or Ubuntu environment using the supplied commands and diagnostic output. Done means installation no longer treats /usr/bin as a virtual environment and TensorFlow can be imported.

I followed these instructions:

# install the development version of packages, in case the
# issue is already fixed but not on CRAN yet.
install.packages("remotes")
remotes::install_github(sprintf("rstudio/%s", c("reticulate", "tensorflow", "keras")))
reticulate::miniconda_uninstall() # start with a blank slate
options(timeout=300) # Missing from your instructions, 
                                   # but necessary given my ISP
reticulate::install_miniconda()
keras::install_keras()

And got the following error mesages:

* Miniconda has been successfully installed at "~/.local/share/r-miniconda".
[1] "/home/ralmond/.local/share/r-miniconda"
> keras::install_keras()
Error in virtualenv_install(envname = envname, packages = packages, ignore_installed = pip_ignore_installed,  : 
  '/usr/bin' exists but is not a virtual environment

This is just running under Pop_OS (Ubuntu derivative) 20.10. the miniconda installation worked fine under Mac_OS.

Diagnostic info:

> py_config()
python:         /usr/bin/python3.9
libpython:      /usr/lib/python3.9/config-3.9-x86_64-linux-gnu/libpython3.9.so
pythonhome:     //usr://usr
version:        3.9.7 (default, Sep 10 2021, 14:59:43)  [GCC 11.2.0]
numpy:          /usr/lib/python3/dist-packages/numpy
numpy_version:  1.19.5
tensorflow:     [NOT FOUND]

NOTE: Python version was forced by RETICULATE_PYTHON
> tensorflow::tf_config()
Valid installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
 /usr/bin/python3.9

Python exception encountered:
 ModuleNotFoundError: No module named 'tensorflow'

You can install TensorFlow using the install_tensorflow() function.
 
> reticulate::import("tensorflow")
Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'tensorflow'
> reticulate::py_last_error()
$type
[1] "ModuleNotFoundError"

$value
[1] "No module named 'tensorflow'"

$traceback
[1] "  File \"/home/ralmond/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py\", line 39, in _import_hook\n    module = _import(\n"

$message
[1] "ModuleNotFoundError: No module named 'tensorflow'"

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 21.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] reticulate_1.24

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8       lattice_0.20-45  png_0.1-7       
 [4] zeallot_0.1.0    rappdirs_0.3.3   grid_4.1.2      
 [7] R6_2.5.1         jsonlite_1.7.3   magrittr_2.0.2  
[10] tfruns_1.5.0     cli_3.2.0        rlang_1.0.1     
[13] whisker_0.4      Matrix_1.4-0     generics_0.1.2  
[16] keras_2.8.0      tools_4.1.2      xfun_0.29       
[19] compiler_4.1.2   base64enc_0.1-3  tensorflow_2.8.0
[22] knitr_1.37   
>