[BUG] Sometimes, downloading packages from Bioconductor fails.

[MrHedmad]

Describe the bug
Sometimes, the download of packages from Bioconductor (e.g. in the prep modules) fails, and the container crashes.

To Reproduce
Steps to reproduce the behavior:

1. Install biotea
2. Run the analysis presented in the paper
3. When downloading pd.hugene.1.0.st.v1, sometimes the download cannot be run, an the resulting timeout causes a crash.

Expected behavior
Expected to download the package as normal.

Desktop:

• OS: Arch Linux
• BioTEA Version (Run biotea info biotea): 1.0.0
• Docker engine version (Run docker --version): 20.10.17, build 100c70180f
• BioTEA container version (if applicable): latest (1.0.1)

[MrHedmad]

It is unclear why, or how, the package download fails. Is it just an issue of bioconductor? Of our office internet? Of something else entirely?

Someone, please triage this!

[MrHedmad]

I've taken another look at the packages involved and, in short, there is not much we can do. We read package data from (e.g.) read.celfiles and it automatically fetches the data that it needs to parse that specific model of array. If bioconductor dies, we cannot really change the internal function call.

If and when this becomes a really bad issue, we might think of something (download all data packages locally?), but not right now. Closing as wontfix.