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I am not sure, but it is possible that R want to be its own package manager which interferes with Guix? A similar problem seems to appear in Python, where there

by jnxx 4y ago

I am not sure, but it is possible that R want to be its own package manager which interferes with Guix? A similar problem seems to appear in Python, where there on Distributions like Debian there is kind of a struggle which package manager - the system-defined packages, or the user-defined ones like pip - have the last word. I have used Guix a bit with Common Lisp libraries, and that works like a charm. I also found it useful to be able to use new Emacs packages like the newest version of Magit, without having to install or supersede the OS installation.

goosedragons 4y ago
R does have it's own package manager but I was explicitly not using it because I read there could be issues, instead only installing packages through Guix. It was mainly a problem compiling things within R as if the order of how gcc-toolchain and the R package were setup it straight up wouldn't work. With later versions it just broke entirely and I never managed to fix it.
- wdkrnls 4y ago
  Despite R being the most commonly packaged software on Guix and it being a GNU project and a "common lisp for dummies" lispy language which is used by millions of students, researchers and data scientists, the developers seem to have a noticeable animosity towards it (although not as much as the "snake people"). This makes me sad, as R users would be the first to sign up for what Guix offers if it worked well and the RcppGuile R package could be used as a template for bridging the gap between the spartan scheme infrastructure and the extremely rich and beginner friendly R infrastructure. I feel like this could also help motivate the Guix developers to improve the documentation and guile porcelain interfaces so they could be used directly instead of the copious bash code they all seem to relish writing.
  - rekado 4y ago
    I don't follow. Are you saying that Guix developers have animosity towards R or the other way around? In any case I haven't seen animosity on either side. FWIW I also wrote guix.install, which lets you install R packages through Guix (whether or not they are available in Guix) from within a running R session. I'm maintaining R packages in Guix and woudl like to see more adoption of Guix among R users, so if you have any recommendations on what pain points there are and how to overcome them I'd be happy to hear them.
- wdkrnls 4y ago
  I have not experienced that for what it's worth... atleast not after I rebuilt the whole profile.
- JHonaker 4y ago
  This… shouldn’t happen. The whole point of Nix and Guix is that you can have multiple versions of the same thing in different dependency chains. It’s designed to avoid precisely this issue. If a package relies on something it should be built before hand, and if and only if it’s identical (well content addressable vs inputs is a whole other thing) it will share the dependency. Would you mind sharing exactly what the R packages you were having problems with were? I wonder if you were relying on globally installed versions of things instead of an R installation that had the packages wrapped into its environment. I’m more familiar with Nix, but you’ll typically see people do something like add this to a local project build input or development shell: r-lang.withPackages with rPackages; [ r-ggplot2 r-data-table ]; Rather than nix-env -iA r-4.2 r-ggplot2 r-data-table Or the Guix equivalent guix install r … Globally installing things can lead to situations where you think it should work but if you really think about how the store dependencies work, they don’t.
  - goosedragons 4y ago
    Yeah and that's part of what made it so confusing. Even in a pure Guix shell it only worked in a specific order. Packages were R, TMB (an R package), gcc-toolchain, gfortran-toolchain and make. You need to be able to compile C++. If was R specified before the toolchains then nothing could be compiled with TMB. I forget the exact error. I did not have those packages globally installed and I saw the same problems with Guix SD and a foreign distros. But with R 4.2 I ran into a different problem and never fixed, that anything using the RcppEigen header would not compile. And I don't believe Guix has the same wrapping packages into R style as Nix.
    - JHonaker 4y ago
      I was too frustrated by the insistence on libre purity by the main Guix channels, even if I think it is superior software, so I switched to Nix (and actually went fully NixOS after a month or so). I had R package compilation issues on 4.2 as well, but I also had them on my Windows work machine. I'll try to test things out and see if I can figure out if it's still an issue.
    - yencabulator 4y ago

by jnxx 4y ago

goosedragons 4y ago

R does have it's own package manager but I was explicitly not using it because I read there could be issues, instead only installing packages through Guix. It was mainly a problem compiling things within R as if the order of how gcc-toolchain and the R package were setup it straight up wouldn't work. With later versions it just broke entirely and I never managed to fix it.

wdkrnls 4y ago
Despite R being the most commonly packaged software on Guix and it being a GNU project and a "common lisp for dummies" lispy language which is used by millions of students, researchers and data scientists, the developers seem to have a noticeable animosity towards it (although not as much as the "snake people"). This makes me sad, as R users would be the first to sign up for what Guix offers if it worked well and the RcppGuile R package could be used as a template for bridging the gap between the spartan scheme infrastructure and the extremely rich and beginner friendly R infrastructure. I feel like this could also help motivate the Guix developers to improve the documentation and guile porcelain interfaces so they could be used directly instead of the copious bash code they all seem to relish writing.
- rekado 4y ago
  I don't follow. Are you saying that Guix developers have animosity towards R or the other way around? In any case I haven't seen animosity on either side. FWIW I also wrote guix.install, which lets you install R packages through Guix (whether or not they are available in Guix) from within a running R session. I'm maintaining R packages in Guix and woudl like to see more adoption of Guix among R users, so if you have any recommendations on what pain points there are and how to overcome them I'd be happy to hear them.
wdkrnls 4y ago
I have not experienced that for what it's worth... atleast not after I rebuilt the whole profile.
JHonaker 4y ago
This… shouldn’t happen. The whole point of Nix and Guix is that you can have multiple versions of the same thing in different dependency chains. It’s designed to avoid precisely this issue. If a package relies on something it should be built before hand, and if and only if it’s identical (well content addressable vs inputs is a whole other thing) it will share the dependency. Would you mind sharing exactly what the R packages you were having problems with were? I wonder if you were relying on globally installed versions of things instead of an R installation that had the packages wrapped into its environment. I’m more familiar with Nix, but you’ll typically see people do something like add this to a local project build input or development shell: r-lang.withPackages with rPackages; [ r-ggplot2 r-data-table ]; Rather than nix-env -iA r-4.2 r-ggplot2 r-data-table Or the Guix equivalent guix install r … Globally installing things can lead to situations where you think it should work but if you really think about how the store dependencies work, they don’t.
- goosedragons 4y ago
  Yeah and that's part of what made it so confusing. Even in a pure Guix shell it only worked in a specific order. Packages were R, TMB (an R package), gcc-toolchain, gfortran-toolchain and make. You need to be able to compile C++. If was R specified before the toolchains then nothing could be compiled with TMB. I forget the exact error. I did not have those packages globally installed and I saw the same problems with Guix SD and a foreign distros. But with R 4.2 I ran into a different problem and never fixed, that anything using the RcppEigen header would not compile. And I don't believe Guix has the same wrapping packages into R style as Nix.
  - JHonaker 4y ago
    I was too frustrated by the insistence on libre purity by the main Guix channels, even if I think it is superior software, so I switched to Nix (and actually went fully NixOS after a month or so). I had R package compilation issues on 4.2 as well, but I also had them on my Windows work machine. I'll try to test things out and see if I can figure out if it's still an issue.
  - yencabulator 4y ago