OHW22 R environment changes

[abkfenris]

Please comment with any R packages that are need for OHW22 here. We are looking to get all of these at least a week before the main event starts, so we aren't changing anything for the undergrads!

Please use a checkbox for each package so we can track what has been added, ex:

- [ ] some-awesome-package, link to documentation if the conda package isn't obvious to someone who doesn't use it, or CRAN source

The current R environment is defined in https://github.com/oceanhackweek/jupyter-image/blob/main/r/environment.yml

[btupper]

We think this is complete... (but you you thinking just confuses things.)

CRAN

• sf https://CRAN.R-project.org/package=sf
• stars https://CRAN.R-project.org/package=stars
• plotly https://CRAN.R-project.org/package=plotly
• tidyverse https://CRAN.R-project.org/package=tidyverse
• rlang https://CRAN.R-project.org/package=rlang
• assetthat https://CRAN.R-project.org/package=assertthat
• httr https://CRAN.R-project.org/package=httr
• xml2 https://CRAN.R-project.org/package=xml2
• rvest https://CRAN.R-project.org/package=rvest
• viridis https://CRAN.R-project.org/package=viridis
• scales https://CRAN.R-project.org/package=scales
• ggspatial https://CRAN.R-project.org/package=ggspatial
• leaflet https://CRAN.R-project.org/package=leaflet
• ncdf4 https://CRAN.R-project.org/package=ncdf4
• terra https://CRAN.R-project.org/package=terra
• raster https://CRAN.R-project.org/package=raster
• marmap https://CRAN.R-project.org/package=marmap
• plot.matrix https://CRAN.R-project.org/package=plot.matrix
• xts https://CRAN.R-project.org/package=xts
• tsibble https://CRAN.R-project.org/package=tsibble

GITHUB

• BigelowLab/xyzt https://github.com/BigelowLab/xyzt
• BigelowLab/ghrsst https://github.com/BigelowLab/ghrsst
• BigelowLab/bsw https://github.com/BigelowLab/bsw
• BigelowLab/obpg https://github.com/BigelowLab/obpg
• BigelowLab/ersst https://github.com/BigelowLab/ersst
• BigelowLab/hycom https://github.com/BigelowLab/hycom
• kwstat/pals https://github.com/kwstat/pals

[abkfenris]

• gh cli tool https://github.com/conda-forge/gh-feedstock

[abkfenris]

@btupper those should be deployed.

I was able to install most via Conda, except for the few from CRAN that I left unchecked. When an install from CRAN or Github fails, it doesn't exit correctly to fail the build, so I'd suggest trying the environment to see if everything is working as you expect.

[btupper]

OK! Thank you! @jevanilla and @Cross22 - can you each give it a shakedown?

[ocefpaf]

We start next Monday! It would be awesome if you all can upload your notebooks to our tutorial repo and test them in the hub.

[btupper]

Roger that! We shall be using the RStudio server and Rmarkdown documents for the tutorials.

The first tutorial is being vetted within the lab to catch the most egregious boo-boos. The first kicks off with a short video which is linked in the Rmarkdown tutorial. We are assuming that the presenter can simply play the youtube from that link - happy to be corrected. Hollywood has yet to call me, and I think I know why now... https://youtu.be/2ZWFYWMwq1c

The second tutorial is under construction but should be ready in the next 2 days. It uses the same software as the first tutorial.

We are juggling vacations and a small personnel shuffle this week, but, have no worries, we'll make it. What could possibly go wrong?

P.S. The Rmarkdown files are located in the xytz R package. https://github.com/BigelowLab/xyzt

[jevanilla]

@abkfenris

Can we also get:

• rerddap https://cran.r-project.org/web/packages/rerddap/index.html
• rnoaa https://cran.r-project.org/web/packages/rnoaa/index.html

[abkfenris]

Is there a way to get remotes:install_cran and remotes:install_github to exit non 0?

https://github.com/oceanhackweek/jupyter-image/runs/7813411273?check_suite_focus=true#step:6:2900

It really doesn't want to let me know when something fails and breaks the build.

I'll take another swing with the dependencies it wants.

[abkfenris]

Ok, within 6 hours 2i2c will get a PR with the updated image, then we need to wait for one of their engineers to merge it.

[jevanilla]

We start next Monday! It would be awesome if you all can upload your notebooks to our tutorial repo and test them in the hub.

@ocefpaf I sent a PR with my notebooks to oceanhackweek/ohw-tutorials

oceanhackweek/ohw-tutorials#87

[abkfenris]

Those changes should be live on the hub: 2i2c-org/infrastructure#1622

[abkfenris]

It looks great, thanks!! As I mentioned over email, it looks like we don't yet have a couple of the libraries in our R image. But we'll manage. For reference, the libraries seem to be:

• emo
• markdown (though we do have rmarkdown)
• metR
• udunits2
• xaringan

Gracias!

Updated: Note to self (I'll move these notes elsewhere, soon): All these packages except emo are in conda-forge.

Originally posted by @emiliom in oceanhackweek/ohw-tutorials#91 (comment)

[abkfenris]

emo can't be installed: #55

[emiliom]

emo can't be installed: #55

Based on @paocorrales's R code and some Googling, I'm pretty sure it's this emoji library:
https://github.com/hadley/emo

And apparently it's installed from github. In R speak:

# install.packages("devtools")
devtools::install_github("hadley/emo")

Thanks for adding the R packages from conda-forge!

[abkfenris]

Ok, that looks like it did the trick.

[emiliom]

Thank you, @abkfenris & @ocefpaf !!

ref PR #55 and PR oceanhackweek/ohw-tutorials#91

[emiliom]

This is not a final request yet, but I wanted to draft it here. It's for a tutorial on Wednesday.

• r-tmap, https://anaconda.org/conda-forge/r-tmap
• r-tmaptools, https://anaconda.org/conda-forge/r-tmaptools.

The instructor said tmap is used (plus other packages already in the R image), and I've asked her to check and let us know if tmaptools is also needed, so we can add both in one PR.

That rounds out the packages needed for the 4 tutorials in the Espanol satellite, R & Python.

[abkfenris]

Tmap and friend is in #58

[emiliom]

Darn you're too fast! I was about to add one LAST one (I swear):

• mapproj. It's on conda-forge.

[abkfenris]

Looks like something else already brought mapproj in.

jupyter-image/r/conda-linux-64.lock

Line 411 in d20444f

https://conda.anaconda.org/conda-forge/linux-64/r-mapproj-1.2.8-r41hcfec24a_0.tar.bz2#452f9179c0b907ec358cc6b33ef0d2b5

[emiliom]

Awesome! I forgot to check the conda lock file.

[loreabad6]

Hello, not sure if it will be needed in the end but can you please add "sfnetworks", "tidygraph" and "igraph"

[loreabad6]

Hello, not sure if it will be needed in the end but can you please add "sfnetworks", "tidygraph" and "igraph"

Hi again, can you let me know if the packages could be installed.
If still on time can you add "mapview" as well?

As a backup I will add the demo to my local binder. Thanks!

[abkfenris]

Hello, not sure if it will be needed in the end but can you please add "sfnetworks", "tidygraph" and "igraph"

Hi again, can you let me know if the packages could be installed. If still on time can you add "mapview" as well?

As a backup I will add the demo to my local binder. Thanks!

I'm working on adding those now. The image is currently building https://github.com/oceanhackweek/jupyter-image/actions/runs/2876389472
Then I'll submit the new image to 2i2c to get them to approve it.

[abkfenris]

2i2c has approved it, now we are waiting on one of their workflows to finish, then the packages will be usable once you shut down and restart your server. https://github.com/2i2c-org/infrastructure/runs/7882280892?check_suite_focus=true

[emiliom]

Wow, thank you @abkfenris !