| 13 Apr 2024 |
 gibbs_ensamble | 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 command 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. | 15:43:50 |
 kupac | You're right. It's not their responsibility, but maybe there are other reasons to do copy.mode = FALSE? If not, then we can also patch via a PR to nixpkgs. | 17:26:20 |
| 14 Apr 2024 |
| gibbs_ensamble | Originally copy.mode was not even specified, the line was like this
file.copy(srcdir, tmp_name, recursive = TRUE)
which according to the R documentation sets by default copy.mode = TRUE.
So I think that manually setting copy.mode = FALSE should be fine.
Patching via a PR to nixpkgs sounds like a great idea (I didn't know you could do that, I'm new to NixOS).
If you have time maybe you could do it? If not that's ok but it will take me a few days (at least) to go through the docs. | 00:10:53 |
 jbedo | Open an issue and tag us | 01:07:23 |
| jbedo | Btw there’s an r specific matrix room #r:nixos.org if you need help with r | 01:08:36 |
| gibbs_ensamble | In reply to @jb:vk3.wtf
Open an issue and tag us Ok thanks | 09:24:41 |
| 15 Apr 2024 |
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| 17 Apr 2024 |
| kupac | Hello, friends! Does anybody know an easy way to quert sparql from R? I found {SPARQL}, which has been archived on CRAN, and {glitter} looks nice, but it's not on CRAN (yet?) Anything else out there? | 09:22:13 |
| kupac | * Hello, friends! Does anybody know an easy way to query sparql from R? I found {SPARQL}, which has been archived on CRAN, and {glitter} looks nice, but it's not on CRAN (yet?) Anything else out there? | 09:22:29 |
| kupac | I just realise this has nothing to do with nix, i don't know why I posted here :) | 09:23:31 |
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 Daniel Fahey | I've written a derivation for TerminusDB, an open source knowledge graph database. I have an open PR on Nixpkgs and would love if someone could review it! https://github.com/NixOS/nixpkgs/pull/303209 | 19:36:43 |
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