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<PurpleSym>Ah no, we cannot use esbuild, because it does not bundle css into the same JavaScript file, which RStudio depends on.
<rekado>so then the upgrade is ready to merge?
<PurpleSym>I want to make sure the desktop version works as well.
<PurpleSym>And then I guess then we can merge the change to node-build-system (CI looks good) and the new RStudio.
<PurpleSym>Strange that it rebuilt ungoogled-chromium 🤨
<rekado>when you upgraded all the node packages, did you use some kind of automation?
<rekado>or was that literally just the result of running the npm importer a few times and tweaking its output?
<PurpleSym>I just ran the importer on every dependency in package.json.
<PurpleSym>Sorry, no magic ☹️
<PurpleSym>The desktop version is showing an annoying update prompt.
<rekado>we can patch that out
<PurpleSym>Yeah, looking into that.
<rekado>I only just noticed this huge pull request:
<PurpleSym>I’ve seen it, but it doesn’t look complete. There’s lots of todo’s in there.
<PurpleSym>Alright, I finally pushed the RStudio update.
<PurpleSym>Thanks rekado !
<rekado>thank you!
<rekado>sometimes I’m thinking about starting a fork of RStudio that doesn’t use but talks to an independent R REPL like ESS does.
<rekado>reusing all of that Java stuff for the UI
<rekado>but replacing all the weird session handling
<rekado>and then add a feature to launch a new R session within a Guix container.
<civodul>is there a preprint of somewhere?
<zimoun>civodul: no. Or I am not aware, that’s not the spirit of this medical field, sadly.
<zimoun>I do not remember which paper corresponds to which Git repo. Well, for instance:
<rekado>nothing on biorxiv
<civodul>so i guess we won't add it to the "Examples" section of
<civodul>(i believe Inserm, CNRS, etc. all require that papers be first posted on a preprint server)
<zimoun>Is it not available for you?
<zimoun>(My colleagues tell me that it’s not a requirement but only a strong recommandation.)
<civodul>ah yes, this one works, thanks!
<civodul>it only has excerpts though, IIUC
<civodul>i was looking for an "availability" or "reproducibility" section, which i cannot see here
<zimoun>ahah! you are so naive about “medical paper” :-)
<zimoun>it’s the complete paper.
<zimoun>And what you are looking for is the “supplemental Methods” which is not part of the paper.
<zimoun>if you download the compressed archive containing this “supplemental Methods”, you have a section “Data and code Sharing”
<zimoun>And this section points to
<zimoun>which are the description of “availability” and “reproducibility”, somehow.
<civodul>hmm ok!
<civodul>not what i expected :-)
<zimoun>yeah, how make stuff complicted when they could be simpler. :-)
<civodul>i'm looking for an example of a paper with a long list of package name/version pairs
<civodul>anyone has something like that at hand?
<civodul>rekado, zimoun maybe?
<zimoun>no, I do not have at hand. And often, people do not publish that. That just publish a couple of name/version pairs; letting the rest as an excercise for the reader. :-)
<rekado>civodul: here’s one with a table containing just the names:
<rekado>I don’t think this is terribly common
<civodul>you mean it's less common than providing nothing?
<rekado>in bioinfo papers they often just point to a git repo, mention the programming language, and the dependencies are not explicitly mentioned
<rekado>this one has a long list of dependencies (names, versions, method of installation) in the supplementary files:
<rekado>method of installation is “Conda”, “Manual Download”, or “Manual Registration and Download” :)
<rekado>this one has a terrifying “Installation” section with LD_LIBRARY_PATH and conditionals:
<rekado>e.g. “If after installation of pyopenms, an error message comes up informing that a library cannot be loaded, ‘openssl’ library needs to be installed as well.”
<rekado>it’s wild out there.
<rekado>most often I encounter just a link to a repo on github, without commit. The claim is that the repo describes all installation instructions and dependencies in sufficient detail.
<civodul>looks fun :-)
<rekado>in reality these instructions are often absent or relegated to “pip install”
<civodul>starting to look good: