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<civodul>interesting slide deck on R & reproducibility: https://umr-astre.pages.mia.inra.fr/presentations/reproducible-research-in-r/

<civodul>rekado, zimoun: ↑

<civodul>it does mention Guix, just to say it's "overkill for reproducible research" :-)

<civodul>like, "it must be useful, but only for reproducibility professionals"?

<zimoun>civodul: considering only R packages, indeed Guix helps for more reproducibility but it is not a game changer because the R community is already doing a huge work of curation and maintainance.

<zimoun>although it is hard to re-set the same R environment as in 2020; when it is trivial with guix time-machine. ;-)

<zimoun>Have a nice week-end

<civodul>but i guess R doesn't have a tool that takes a list of package/versions as input and reinstantiates it?

<drakonis>require, maybe?

<drakonis>there's no straightforward way to do versioning

<drakonis>using devtools is the closest way to achieving it

<rekado>civodul: heh, that’s cute.

<rekado>civodul: the R people that I know use packrat: https://rstudio.github.io/packrat/

<rekado>or at least they point to it when asked about how they would reproduce their R environment.

<civodul>oh so you can give it some sort of a manifest?

<rekado>(pointing to something is much more common than actual use, no matter what aspect of reproducibility)

<rekado> https://rstudio.github.io/packrat/commands.html

<rekado>you can take a snapshot of your R environment, bundle it up for sharing, and then later unbundle it again.

<civodul>sounds pretty cool

<rekado>but this fails when you use things that aren’t 100% R

<civodul>how frequent is that, though?

<civodul>R seems to be well isolated from the rest of the world

<rekado>there are lots of packages near the root of the graph that are bindings to C libraries

<rekado>I maintain a little VM-on-demand thing that lets you create a Guix environment, spawn an AWS EC2 VM with RStudio, where the environment can be used.

<rekado>I need to allow users to use install.packages or devtools

<rekado>so the environment needs to have all sorts of “common” libraries and toolchains

<rekado>things like cairo, curl, gcc-toolchain, etc

<rekado>or else you just can’t build any of the popular R packages

<rekado>gzip, cairo, libxt, openssl, curl, zlib, etc

<rekado>that said, packrat can be “good enough”

<rekado>certainly better than just sessionInfo()

<civodul>i see

<civodul>yeah folks take those libraries for granted

<civodul>as if it were hardware

<civodul>maybe that's often "good enough"

<civodul>well, gcc-toolchain is more of a problem than say zlib

IRC channel logs

2022-06-24.log