various problems with linux deployment

[vjcitn]

Not sure if anyone is trying this out on linux. I am trying example(use_sdio) on the current checkout. On a 22.04 machine in NSF cloud I hit

On AnVIL in a custom container,

Error in py_module_import(module, convert = convert) : 
  ImportError: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: version `OPENSSL_3.4.0' not found (required by /home/rstudio/.cache/R/basilisk/1.18.0/SpatialData/0.99.16/anndata_env/lib/python3.10/site-packages/pyarrow/../../.././././libs2n.so.1)
Run `reticulate::py_last_error()` for details.

I will try to smoke these out. Some detailed pinning for basilisk, and maybe some OS checks/runtime specs will be needed.

[vjcitn]

I am concerned that we will start diverging from the python group if we have to pin a number of components to versions that are obsolete in their view. We really need working CI and close synchronization to the user code base endorsed by Luca et al. Should we start using a specific conda channel in our basilisk environment? Could that accomplish the desired synchronization?

[vjcitn]

update:

.env <- BasiliskEnvironment(
    pkgname="SpatialData", envname="anndata_env",
    pip = c("spatialdata==0.2.5", "spatialdata-io==0.1.5"),
    packages=c("anndata==0.9.1", "zarr==2.14.2"))

seems to permit solution for use_sdio on both linux and mac, testing and will PR soon.

[vjcitn]

So R CMD check fails for various reasons, seemingly unrelated to changes above. the table.Rmd in vignettes causes an error in check. I will introduce the change above as a very limited PR.

[HelenaLC]

Thanks Vince. Anything not python-related (eg vignette) I can look into.