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I'm maintaining most of the R packages in Guix and helping hundreds of users at a research institute with their R stuff. I haven't seen any problems like that.

by rekado 4y ago

I'm maintaining most of the R packages in Guix and helping hundreds of users at a research institute with their R stuff. I haven't seen any problems like that. The order of installation does not (and cannot) matter. The most common problem I've seen is that people mix packages from Guix with those built with install.packages that have been linked with incompatible system libraries, which cannot possibly work. This problem is easily avoided --- either by using a container shell (guix shell -C) with a separate toolchain (not the system's toolchain) or by not using `install.packages` (e.g. use `guix.install` instead).

goosedragons 4y ago
Are any of your R users TMB users? Because I ran into that in multiple setups (Guix SD and Guix on foreign distros) where only a specific ordering worked even when using guix shell --pure. This was back in the R 4.1.2 days. In theory it should be impossible and yet I ran into it. No I was not mixing packages installed via. install.packages. Right now with the latest version of Guix and R 4.2.1 TMB is not usable. Try running: "guix shell --container r r-tmb make gcc-toolchain gfortran-toolchain" then try running the linreg.R (with the corresponding cpp file, or any of the examples) example from https://github.com/kaskr/adcomp/tree/master/tmb_examples https://github.com/kaskr/adcomp/tree/master/tmb_examples and you'll run into "did you mean 'bad_array_new_length'? This is on a Guix SD system too... And you have to specify make,gcc-toolchain and gfortran-toolchain for it to work normally. If you leave out gfortran-toolchain it compiles but you can't load it and it doesn't work without make. Previously I had it working with those 5 packages in a specific order. Perhaps this is a TMB only problem but it's a giant PITA when it works fine on non-Guix setups.
- rekado 4y ago
  Thanks for the details. I noticed that gcc-toolchain and gfortran-toolchain are mismatched: the former is at version 12 while the latter is at version 10. (Someone must have forgotten to update gfortran when they updated gcc-toolchain.) I get no errors when using this environment: guix shell --container r-minimal r-tmb coreutils make gcc-toolchain@10 gfortran-toolchain@10 (Feel free to send future problem reports to bug-guix@gnu.org.)

by rekado 4y ago

goosedragons 4y ago

Are any of your R users TMB users? Because I ran into that in multiple setups (Guix SD and Guix on foreign distros) where only a specific ordering worked even when using guix shell --pure. This was back in the R 4.1.2 days. In theory it should be impossible and yet I ran into it. No I was not mixing packages installed via. install.packages. Right now with the latest version of Guix and R 4.2.1 TMB is not usable. Try running: "guix shell --container r r-tmb make gcc-toolchain gfortran-toolchain" then try running the linreg.R (with the corresponding cpp file, or any of the examples) example from https://github.com/kaskr/adcomp/tree/master/tmb_examples https://github.com/kaskr/adcomp/tree/master/tmb_examples and you'll run into "did you mean 'bad_array_new_length'? This is on a Guix SD system too... And you have to specify make,gcc-toolchain and gfortran-toolchain for it to work normally. If you leave out gfortran-toolchain it compiles but you can't load it and it doesn't work without make. Previously I had it working with those 5 packages in a specific order. Perhaps this is a TMB only problem but it's a giant PITA when it works fine on non-Guix setups.

rekado 4y ago
Thanks for the details. I noticed that gcc-toolchain and gfortran-toolchain are mismatched: the former is at version 12 while the latter is at version 10. (Someone must have forgotten to update gfortran when they updated gcc-toolchain.) I get no errors when using this environment: guix shell --container r-minimal r-tmb coreutils make gcc-toolchain@10 gfortran-toolchain@10 (Feel free to send future problem reports to bug-guix@gnu.org.)