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Package list for a robust Base R workspace for geoscience applications on MAAP #742
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Other notes:
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Rocker is often a good starting point of comparison https://github.com/rocker-org/geospatial/blob/master/Dockerfile |
I checked and VEDA does in fact use Rocker. The full list to match that would be:
Along with various Binary libraries required.
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I have a image building successfully for this, but had a couple questions @wildintellect
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Also, I cannot find the binary library |
@grallewellyn I'll look into these. Generally in |
I see Fgmutils, nlraa, and sfarrow on CRAN, but I don't see leaflet_proxy and tools |
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Have a look at how Rocker does it, this is our reference, as it's what VEDA deploys and very similar to our target goal. https://github.com/rocker-org/rocker-versioned2/blob/master/dockerfiles/geospatial_4.3.1.Dockerfile |
From CRAN:
Maybe from Conda:
A note about @grallewellyn don't wait on a response from @pahbs, just go ahead with everything else for this release, and we'll work to clear this up for next release.
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@wildintellect Where is the API for I am not sure what you mean by copying the way this link https://github.com/rocker-org/rocker-versioned2/blob/master/dockerfiles/geospatial_4.3.1.Dockerfile does it. Why would we want a dockerfile for every version? Regarding, The image can build fine without all the binary libraries, are you saying remove all of them? Or is it fine to just remove I don't see leafletproxy on CRAN, conda or pip- are you referring to a GitHub repo? |
Oh, leafletproxy is a command in the What I mean is look at how that dockerfile works, it calls https://github.com/rocker-org/rocker-versioned2/blob/master/scripts/install_geospatial.sh which then uses https://github.com/rocker-org/rocker-versioned2/blob/master/scripts/bin/install2.r to actually do the install. We can drop |
@wildintellect So something like
And https://github.com/rocker-org/rocker-versioned2/blob/master/scripts/bin/install2.r is the same then we call |
@grallewellyn that's the basic idea, you can probably drop the |
I have this working, but I am not able to install Fgmutils via the r script and I am still looking into this |
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@grallewellyn for
So add those to the environment yaml for conda, and then the install.packages for Fgmutils should work. |
But I was struggling to figure out why the dependencies weren't installing Thanks for the |
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Is your feature request related to a problem? Please describe.
MAAP scientists need a robust Base R workspace that will limit the need for repeatedly installing many basic add-ons upon each workspace re-start. While we recognize the need to do this for a variety of special-case packages that are not commonly used, we should not do this for packages that are routinely used across almost all R notebooks.
Routine packages would include those that support, for example:
We can keep and update a list of package requests here:
https://docs.google.com/spreadsheets/d/1mrQ3gdcxZHZNTksUmLz6qqqNSNxhAoonB9znLU0c0pk/edit?usp=sharing
Describe the solution you'd like
We would like:
Describe alternatives you've considered
Alternatives include always adding these packages manually, by each user, every time they need to re-start a workspace running R
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