| 27 Mar 2024 |
|  @javier.fuentes:matrix.org joined the room. | 18:37:52 |
| @javier.fuentes:matrix.org | Hi there, I'm trying to add new kernels to jupyterhub server with no luck, the example in man configuration.nix is:
services.jupyterhub.kernels = {
python3 = let
env = (pkgs.python3.withPackages (p: with p; [
ipykernel ...
Can anybody tell me how to get a working env = for R?. (pkgs.R.withPackages ( is not an option apparently.
| 20:01:30 |
| @javier.fuentes:matrix.org | * Hi there, I'm trying to add new kernels to jupyterhub server with no luck, the example in man configuration.nix is:
services.jupyterhub.kernels = {
python3 = let
env = (pkgs.python3.withPackages (p: with p; [
ipykernel
...
Can anybody tell me how to get a working env = for R?. (pkgs.R.withPackages ( doesn't work.
| 20:02:43 |
 jbedo | In reply to @javier.fuentes:matrix.org
Hi there, I'm trying to add new kernels to jupyterhub server with no luck, the example in man configuration.nix is:
services.jupyterhub.kernels = {
python3 = let
env = (pkgs.python3.withPackages (p: with p; [
ipykernel
...
Can anybody tell me how to get a working env = for R?. (pkgs.R.withPackages ( doesn't work.
the R ecosystem uses a different (older) interface, it'll be pkgs.rWrapper.override ..., check the manual for details: https://nixos.org/manual/nixpkgs/stable/#r | 21:55:15 |
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| 13 Apr 2024 |
| @gibbs_ensamble:matrix.org | Hello! The last few days I have been trying to install IRkernel on NixOS using a simple flake.nix that create a shell with R and some packages. However, IRkernel requires running the comand IRkernel::installspec() inside of the R repl.
This commands returns a permission denied error in NixOS.
After digging through the source code of installspec, I found the issue:
1) when IRkernel is installed, a file called kernel.json is stored in some /nix/store subfolder
2) this file is then copied to a temporary directory
3) the file is then overwritten to change some of its entries.
Point 3 causes the error, since it's a read-only file due to the immutable nature of NixOS.
To fix this, it's sufficient to specify copy.mode = FALSE when the file is copied in step 2 i.e.
file.copy(srcdir, tmp_name, recursive = TRUE, copy.mode = FALSE)
My question is: do you think it makes sense to do a pull request to the IRkernel repository?
One could argue that installing the package through install.packages("IRkernel") is still possible on NixOS and in fact R will ask the user if it's ok to install it in a local directory because it detects a read-only directory by default.
This is not the Nix way of doing things but it's not the responsibility of the original author to do things the Nix way. | 13:55:00 |
| @gibbs_ensamble:matrix.org | * Hello! For the last few days I have been trying to install
IRkernel on NixOS using a simple flake.nix that creates a shell with R and some packages. However, IRkernel requires running the command IRkernel::installspec() inside of the R repl.
This commands returns a permission denied error in NixOS.
After digging through the source code of installspec, I found the issue:
1) when IRkernel is installed, a file called kernel.json is stored in some /nix/store subfolder
2) this file is then copied to a temporary directory
3) the file is then overwritten to change some of its entries.
Point 3 causes the error, since it's a read-only file due to the immutable nature of NixOS.
To fix this, it's sufficient to specify copy.mode = FALSE when the file is copied in step 2 i.e.
file.copy(srcdir, tmp_name, recursive = TRUE, copy.mode = FALSE)
My question is: do you think it makes sense to do a pull request to the IRkernel repository?
One could argue that installing the package through install.packages("IRkernel") is still possible on NixOS and in fact R will ask the user if it's ok to install it in a local directory because it detects a read-only directory by default.
This is not the Nix way of doing things but it's not the responsibility of the original author to do things the Nix way. | 14:01:57 |
