Using the R package reticulate within a Singularity container - r

Question

reticulate is an R package to call Python code from R, that I find easy to use on my local computer and I sometimes get working within a Singularity container.
In this question I will post a simple reprex about code that worked two months ago,
at https://github.com/richelbilderbeek/reticulate_on_singularity
and I hope you can help to get it to work again.
Here is the part of the Singularity script
(the full script can be found here, so one can confirm I use -for example- a fresh Miniconda install)
that creates the Conda environment in the /opt/ormr folder
(Singularity recommends to use a system folder, hence the opt, ormr is Swedish for snake), which works fine:
%post
# ...
Rscript -e 'reticulate::conda_create(envname = "/opt/ormr")'
Rscript -e 'reticulate::use_condaenv(condaenv = "/opt/ormr")'
Rscript -e 'reticulate::use_python(python = reticulate:::python_binary_path("/opt/ormr"), required = TRUE)'
Rscript -e 'reticulate::conda_install(packages = "scipy", envname = "/opt/ormr")'
Rscript -e 'reticulate:::conda_list_packages(envname = "/opt/ormr")'
However, in the test section of the Singularity script, this goes wrong, probably because the section above (the post section) has full access rights, where test does not have this:
%test
# ...
Rscript -e 'reticulate::use_condaenv(condaenv = "/opt/ormr")'
The -I think- relevant part of the error message is shown below (copied from this GitHub Actions log and full error message is at the bottom of this post):
OSError: [Errno 30] Read-only file system: '/opt/ormr/.tmphx9hr3g2'
`$ /miniconda/bin/conda run --prefix /opt/ormr --no-capture-output python -c import os; print(os.environ['PATH'])`
I would conclude that Conda creates a temporary file in the now-read-only folder /opt/ormr.
How need I fix this problem?
Or, in general, how can use reticulate from within a Singularity container? A working example would be great (I have found none that work)!
Thanks, Richel Bilderbeek
Full error message
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1080, in __call__
return func(*args, **kwargs)
File "/miniconda/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/miniconda/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "/miniconda/lib/python3.9/site-packages/conda/cli/main_run.py", line 25, in execute
script_caller, command_args = wrap_subprocess_call(on_win, context.root_prefix, prefix,
File "/miniconda/lib/python3.9/site-packages/conda/utils.py", line 403, in wrap_subprocess_call
with Utf8NamedTemporaryFile(mode='w', prefix=tmp_prefix, delete=False) as fh:
File "/miniconda/lib/python3.9/site-packages/conda/auxlib/compat.py", line 88, in Utf8NamedTemporaryFile
return NamedTemporaryFile(
File "/miniconda/lib/python3.9/tempfile.py", line 541, in NamedTemporaryFile
(fd, name) = _mkstemp_inner(dir, prefix, suffix, flags, output_type)
File "/miniconda/lib/python3.9/tempfile.py", line 251, in _mkstemp_inner
fd = _os.open(file, flags, 0o600)
OSError: [Errno 30] Read-only file system: '/opt/ormr/.tmphx9hr3g2'
`$ /miniconda/bin/conda run --prefix /opt/ormr --no-capture-output python -c import os; print(os.environ['PATH'])`
environment variables:
CIO_TEST=<not set>
CONDA_ROOT=/miniconda
CURL_CA_BUNDLE=<not set>
GITHUB_EVENT_PATH=/github/workflow/event.json
GITHUB_PATH=/__w/_temp/_runner_file_commands/add_path_10663761-8f12-43e3-b986-5f70
909c4322
GOPATH=/go
LD_LIBRARY_PATH=/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-
java/lib/server:/.singularity.d/libs
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
USER_PATH=/go/bin:/usr/local/go/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/us
r/bin:/sbin:/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/loc
al/sbin
active environment : None
user config file : /root/.condarc
populated config files :
conda version : 4.11.0
conda-build version : not installed
python version : 3.9.5.final.0
virtual packages : __linux=5.11.0=0
__glibc=2.33=0
__unix=0=0
__archspec=1=x86_64
base environment : /miniconda (read only)
conda av data dir : /miniconda/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /miniconda/pkgs
/root/.conda/pkgs
envs directories : /root/.conda/envs
/miniconda/envs
platform : linux-64
user-agent : conda/4.11.0 requests/2.27.1 CPython/3.9.5 Linux/5.11.0-1027-azure debian/ glibc/2.33
UID:GID : 0:0
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Error in Sys.setenv(PATH = new_path) : wrong length for argument
Calls: <Anonymous> ... use_python -> python_config -> python_munge_path -> Sys.setenv
In addition: Warning message:
In system2(conda, c("run", in_env, run_args, shQuote(cmd), args), :
running command ''/miniconda/bin/conda' run --prefix '/opt/ormr' --no-capture-output 'python' -c "import os; print(os.environ['PATH'])"' had status 1
Execution halted