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carpentries-incubator / bioc-project

Introduction to the Bioconductor project
https://carpentries-incubator.github.io/bioc-project
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add a section #61

Open jokergoo opened 1 year ago

jokergoo commented 1 year ago

In this PR, I added a new section "The install.packages() function" to introduce how to install Bioconductor packages with the command install.packages(). Feel free to accept it or reject it (if you think it makes the teaching complicated).

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kevinrue commented 7 months ago

Sorry for leaving this repository unattended for so long.

My first instinct was that this may be beyond the scope of the episode. However, I see that I've already included a section "going further" that lists other R functions to install packages, so I would contradict myself there.

Thinking about it more, I think your addition is an important message to users. Given that it relates to installing packages, I would move it from the end of the page where you seem to have place it, to the same level as my "going further block". In fact, I think that the two could be combined and make the whole thing cleaner.

I think this requires a bit attention and care to polish, which I'm sorry to say I don't have right now.

One more note I would add is that I'm not sure I'd highlight setRepositories() if it relies on a pop-up window. I personally prefer to call options(repos = BiocManager::repositories() to achieve the same effect entirely programmatically. It also saves the screenshot, as the code displays much more nicely in the episode format. What do you think?