Git repo failing when hashing via http://git2nixsha.dev #209
Comments
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This is probably related: #159 I don’t know what’s going on exactly, there seems to be an issue with certain repos. In my tests (for that other issue), I ran the api locally and was able to get the results. So I don’t really know what’s going on yet... We are working on making this work without using the remote server if Nix is available. So this would be done locally and should work more consistently. |
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Let's also investigate while implementing linked whishlist for 0.8.0: #143 |
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Hey @b-rodrigues and @eliocamp This should be solved when hashing locally (the new feature added: ). library(rix)
metR <- list(package_name = "metR",
repo_url = "https://github.com/eliocamp/metR",
branch_name = "master",
commit = "1dd5d391d5da6a80fde03301671aea5582643914")
rix(r_ver = "4.3.2",
git_pkgs = metR,
ide = "rstudio",
project_path = "_test",
overwrite = TRUE,
print = FALSE)This generates the following expression in # This file was generated by the {rix} R package v0.8.0 on 2024-07-04
# with following call:
# >rix(r_ver = "219f896bdf192721446db4fedc338eebf732057d",
# > git_pkgs = metR,
# > ide = "rstudio",
# > project_path = ".",
# > overwrite = TRUE)
# It uses nixpkgs' revision 219f896bdf192721446db4fedc338eebf732057d for reproducibility purposes
# which will install R version 4.3.2.
# Report any issues to https://github.com/b-rodrigues/rix
let
pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/219f896bdf192721446db4fedc338eebf732057d.tar.gz") {};
git_archive_pkgs = [
(pkgs.rPackages.buildRPackage {
name = "metR";
src = pkgs.fetchgit {
url = "https://github.com/eliocamp/metR";
branchName = "master";
rev = "1dd5d391d5da6a80fde03301671aea5582643914";
sha256 = "sha256-CLTX347KwwsNyuX84hw2/n/9HwQHBYQrGDu7jFctGO4=";
};
propagatedBuildInputs = builtins.attrValues {
inherit (pkgs.rPackages)
checkmate
data_table
digest
Formula
formula_tools
ggplot2
gtable
memoise
plyr
scales
sf
stringr
purrr
isoband
lubridate;
};
})
];
system_packages = builtins.attrValues {
inherit (pkgs)
R
glibcLocales
nix;
};
in
pkgs.mkShell {
LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then "${pkgs.glibcLocales}/lib/locale/locale-archive" else "";
LANG = "en_US.UTF-8";
LC_ALL = "en_US.UTF-8";
LC_TIME = "en_US.UTF-8";
LC_MONETARY = "en_US.UTF-8";
LC_PAPER = "en_US.UTF-8";
LC_MEASUREMENT = "en_US.UTF-8";
buildInputs = [ git_archive_pkgs system_packages ];
}
nix_build(project_path = "_test")
# ...takes a while to build since we cannot get it from the official nix cachix cache ;-)
[100%] Generating gdal.jar, build/maven/gdal-3.8.4.jar, build/maven/gdal-3.8.4-sources.jar, build/maven/gdal-3.8.4.pom, build/maven/gdal-3.8.4-javadoc.jar
Buildfile: /tmp/nix-build-gdal-3.8.4.drv-0/source/swig/java/build.xml
init:
[echo] version = 3.8.4
compile:
[mkdir] Created dir: /tmp/nix-build-gdal-3.8.4.drv-0/source/build/swig/java/build/classes
[javac] Compiling 88 source files to /tmp/nix-build-gdal-3.8.4.drv-0/source/build/swig/java/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 7
[javac] error: Source option 7 is no longer supported. Use 8 or later.
[javac] error: Target option 7 is no longer supported. Use 8 or later.
BUILD FAILED
/tmp/nix-build-gdal-3.8.4.drv-0/source/swig/java/build.xml:25: Compile failed; see the compiler error output for details.
Total time: 0 seconds
make[2]: *** [swig/java/CMakeFiles/java_binding.dir/build.make:107: swig/java/gdal.jar] Error 1
make[1]: *** [CMakeFiles/Makefile2:9841: swig/java/CMakeFiles/java_binding.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
error: builder for '/nix/store/ilcpzhq2jpva5pkwvk5r5fwd9gnx7zcj-gdal-3.8.4.drv' failed with exit code 2;
last 10 log lines:
> [javac] error: Source option 7 is no longer supported. Use 8 or later.
> [javac] error: Target option 7 is no longer supported. Use 8 or later.
>
> BUILD FAILED
> /tmp/nix-build-gdal-3.8.4.drv-0/source/swig/java/build.xml:25: Compile failed; see the compiler error output for details.
>
> Total time: 0 seconds
> make[2]: *** [swig/java/CMakeFiles/java_binding.dir/build.make:107: swig/java/gdal.jar] Error 1
> make[1]: *** [CMakeFiles/Makefile2:9841: swig/java/CMakeFiles/java_binding.dir/all] Error 2
> make: *** [Makefile:146: all] Error 2
For full logs, run 'nix log /nix/store/ilcpzhq2jpva5pkwvk5r5fwd9gnx7zcj-gdal-3.8.4.drv'.
error: 1 dependencies of derivation '/nix/store/58s1d8wqnl901qma286clvwyxk8m0fri-r-sf-1.0-15.drv' failed to build
error: 1 dependencies of derivation '/nix/store/c35djnxrbn1apdndmv6jf7bmy1bary88-r-metR.drv' failed to build
error: 1 dependencies of derivation '/nix/store/37bgkq0akrcppybv8cgi7wl2gmwpg9d2-nix-shell.drv' failed to build@b-rodrigues The question I have is why are online hashing vs. local hashing not the same? Can you experimentally change the newly locally implemented To sum up, the Git repo is not failing now anymore with the newest version (see changelog), however the issue with building seems to be a darwin-aarch64 related Nix issue (currently tested on Mac); guess linux does work. @eliocamp can you briefly confirm? Thanks a lot for reporting and generally your detailed feedback on Nix :-) |
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We get an internal server error when doing it online; my gut feeling tells me it takes quite long to download (what we do locally) and process the hashing in this case. Maybe quite a bit of (reverse) deps involved. So it maybe something with response timing? > req <- curl::curl_fetch_memory(url = 'http://git2nixsha.dev:1506/hash?repo_url=https://github.com/eliocamp/metR&branchName=master&commit=1dd5d391d5da6a80fde03301671aea5582643914')
> jsonlite::fromJSON(rawToChar(req$content))
$error
[1] "500 - Internal server error" |
philipp-baumann
changed the title
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I'm getting |
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That’s very surprising, could you do |
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@philipp-baumann I’ll work on it this weekend; also I think I’ll get completely rid of the branchName argument, as per our Matrix discussion. After some thinking, I think that what you propose makes the most sense: since the commit correctly identifies the code at a point in time, no need for it, and we might as well get rid of it before submitting to CRAN.
@eliocamp Are you trying to build the same expression as Philipp, above? From an R session running from your system, or a Nix R session that contains rix? I wonder if perhaps (but I don’t know why/how) you local library of packages might interfere? |
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@eliocamp could you try with latest master? You can now remove the 'branchName': |
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Can confirm that library(rix)
metR <- list(package_name = "metR",
repo_url = "https://github.com/eliocamp/metR",
commit = "1dd5d391d5da6a80fde03301671aea5582643914")
rix(r_ver = "4.3.2",
git_pkgs = metR,
ide = "rstudio",
project_path = ".",
overwrite = FALSE,
print = TRUE)creates the default.nix file correctly. nix-build fails with Not sure if a nix/rix bug or just that that particular commit doesn't work. It seems to be a compilation error and metR doesn't have any source code that needs compiling, though. |
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it's sf that fails, in particular gdal apparently, what happens with a more recent commit ? |
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Not even rix::rix(r_ver = "4.3.2",
r_pkgs = "metR",
ide = "rstudio",
project_path = ".",
overwrite = TRUE,
print = TRUE)works. 😱 I don't know if something changed with my system or with rix, but before environments would build in a few seconds and now it's taking ages. |
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Hello, still trying to use NIX, and I had the same error message. I used the code from your tutorial : rix(
r_ver = "latest",
r_pkgs = c("dplyr", "janitor"),
git_pkgs = list(
list(
package_name = "housing",
repo_url = "https://github.com/rap4all/housing/",
commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
),
list(
package_name = "fusen",
repo_url = "https://github.com/ThinkR-open/fusen",
commit = "d617172447d2947efb20ad6a4463742b8a5d79dc"
)
),
ide = "code",
project_path = path_default_nix,
overwrite = TRUE
)And get I'm afraid that for an applied statistician quite non devops savvy, the use of NIX / RIX ; the learning curve is too steep. |
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that's weird, are you the latest version of rix? |
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I installed it like this : utils::remove.packages("rix")
install.packages("rix", repos = c(
"https://b-rodrigues.r-universe.dev",
"https://cloud.r-project.org"
))
require(rix)Then ran this : path_default_nix <- tempdir()
rix(
r_ver = "latest",
r_pkgs = c("dplyr", "janitor"),
git_pkgs = list(
list(
package_name = "housing",
repo_url = "https://github.com/rap4all/housing/",
commit = "1c860959310b80e67c41f7bbdc3e84cef00df18e"
),
list(
package_name = "fusen",
repo_url = "https://github.com/ThinkR-open/fusen",
commit = "d617172447d2947efb20ad6a4463742b8a5d79dc"
)
),
ide = "code",
project_path = path_default_nix,
overwrite = TRUE
)And got this error message : For information : I use r installed with rig, so if some lib paths are hardcoded it could be a problem. |
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instead of |
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I got the same result with a "normal" directory. The error only occurs when I set some remote installations with git_pkgs. |
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can you then successfully build the generated expression using nix-build? |
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Could you try |
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I did, and the error message is : I checked that a normal |
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yes there are two ways to compute the hash and both are failing for you. What operating system are you using? does your installation of Nix work? can you run |
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So I typed nix-shell --expr --show-trace "$(curl -sl https://raw.githubusercontent.com/b-rodrigues/rix/master/inst/extdata/default.nix)"(I added --show-trace to have a better error message since the expression alone give few informations). I get the following error The |
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there's something wrong with your Nix installation, you don't need root to use Nix. How did you install Nix? did you use the determinate systems installer? |
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@philipp-baumann this convo makes me think we need a |
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My current version is The determinate systems installer never worked, I didn't save all the error messages, but it did not install seamlessly. I had to : nix-channel --add https://nixos.org/channels/nixpkgs-unstable
sudo nix-channel --updateand then an |
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The result of was the following error message building '/nix/store/hi03px6v99iri5invmkqmi47caz82bdb-r-curl-5.0.1.drv'...
unpacking sources
unpacking source archive /nix/store/wxldyqldqvs02jafv6pgp31z7qy2a9v2-curl_5.0.1.tar.gz
source root is curl
setting SOURCE_DATE_EPOCH to timestamp 1686179412 of file curl/MD5
patching sources
updateAutotoolsGnuConfigScriptsPhase
configuring
patching script interpreter paths in configure
configure: interpreter directive changed from "#!/bin/sh" to "/nix/store/ir0j7zqlw9dc49grmwplppc7gh0s40yf-bash-5.2-p15/bin/sh"
building
running tests
installing
During startup - Warning messages:
1: package 'utils' in options("defaultPackages") was not found
2: package 'stats' in options("defaultPackages") was not found
Error: .onLoad failed in loadNamespace() for 'utils', details:
call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
error: cannot popen '/nix/store/m1kcpc0n70sam6c1x8fdx6c5vwxjacia-which-2.21/bin/which 'uname' 2>/dev/null', probable reason 'Cannot allocate memory'
* removing '/nix/store/8yq377d5hgg0hjk93w5na89fnfbq4wdg-r-curl-5.0.1/library/curl'
error: builder for '/nix/store/hi03px6v99iri5invmkqmi47caz82bdb-r-curl-5.0.1.drv' failed with exit code 1
error: 1 dependencies of derivation '/nix/store/v0b2663c9s4kwz0hibqshq94x6z9dwch-r-rix.drv' failed to buildIs this message useful in anyway ? |
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yeah I think that something is not quite right with your installation. It's possible to install Nix using the determinate systems installer but also the official Nix installer but it requires more work. I don't think using the ubuntu repos to install Nix will work, because it'll be missing configuration steps that other installers perform. The best approach really is to the determinate systems installer and ideally not have a system wide install of R either |
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My installation of R is through rig, and it should not be a problem. |
that's a good sign, happy to hear :-) |
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It seems it worked ? Here is the end of the message : Now, what would be the safest next steps to try and buil a rix environment using VSCode (or RStudio if you feel it's more stable). Do you think I have to kill my rig R installation and go for a new R installation with the default directory I don't like so much ? Or can I try and launch VSCode with the R plugin and specify the R interpreter I want and launch rix from there ? |
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you should generate an expression where ide="code" and then build it using nix-build . Then drop into the shell using nix-shell and run code from that shell . Code will see this R
Sent from Proton Mail Android
…-------- Original Message --------
On 9/9/24 17:54, Matthieu Gousseff wrote:
It seems it worked ? Here is the end of the message :
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/929fx96hhwpbqwcr75c4jwn73kgam79f-r-rix
checking for references to /build/ in /nix/store/929fx96hhwpbqwcr75c4jwn73kgam79f-r-rix...
patching script interpreter paths in /nix/store/929fx96hhwpbqwcr75c4jwn73kgam79f-r-rix
rewriting symlink /nix/store/929fx96hhwpbqwcr75c4jwn73kgam79f-r-rix/nix-support/propagated-user-env-packages to be relative to /nix/store/929fx96hhwpbqwcr75c4jwn73kgam79f-r-rix
Now, what would be the safest next steps to try and buil a rix environment using VSCode (or RStudio if you feel it's more stable). Do you think I have to kill my rig R installation and go for a new R installation with the default directory I don't like so much ? Or can I try and launch VSCode with the R plugin and specify the R interpreter I want and launch rix from there ?
—
Reply to this email directly, [view it on GitHub](#209 (comment)), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/AAW4EMV4ULDHKATZM74DOU3ZVXAEPAVCNFSM6AAAAABJZOVRJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZYGQ4DSMRSG4).
You are receiving this because you were mentioned.Message ID: ***@***.***>
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Well, I think I reached my limit for today :
The rix() returned the same error when I tried to install github packages : Could it be that nix uses a port that my system administrators do not allow ? If so, how could I check this ? In order to still try to have a small victory, I tried to generate a nix environment with only cran packages and to launch vscode from there. So I ran So for now I'd say :
I'd be grateful if one of you could tell me how to check if the problem comes from my network permissions. I'll stop for today, my brain is "stack overflowed" for today, thank you for your patience and will to help. |
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Here's the morning update. I worked from home today to test : it seems the problem with github packages comes from the way my university network is configured. From home, the packages seem to install. So I have to ask my sysadmins if they would allow the proper ports. Do you know why ports are different when downloading from CRAN and from github ? Is there a way to specify this in the rix function ? At least, I can create the nix environments from home and use them at work. One thing not resolved, though, is that I have to add path to nix manually after each reboot. I guess there is a way to include a way to add it in some kind of profile, but I admit there are lots of ".bashrc", ".profile" and such things and I don't know where to specify it. And last but not least, even though I created the nix.default with the PS : the bold font is just to help separate issues, not a way to show any impatience, as I'm on the contrary grateful for the help. |
Thanks for the update. I think those diagnostics help to strengthen debugging, although not all is directly related to {rix} but rather general nix tooling. It is however stuff that other users could experience. If we can make debugging smoother, e.g. also how @b-rodrigues has suggested add some diagnostics functions that summarize what we already adjust in {rix} to make it work in different contexts. Especially in mixed computer systems where users have R tooling and libraries and linked system dependences at host system and software cleanly managed at nix level in the Nix store. Ideally you would achieve to adjust your setup at work so that you can also achieve to hash the github sources of R packages locally. I *think you should have
There is an easy way to do it. You can use your # add these lines in your $HOME/.bashrc or $HOME/.profile substituting your actual username
export PATH=$PATH:/home/<your-username>/.nix-profile/bin:/nix/var/nix/profiles/default/bin
If you use the R extension which i would recommend, then you need to enable bracketed paste. https://francojc.github.io/posts/r-in-vscode/ There is a section with the lines to add here. I think its a matter of preference, but i usually open vscode/vscodium first on my host and then just use
No offence taken. |
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Thank you. I added the path in my .profile ut added a line to check if it was already in and this didn't seem to work. I will go back to my workplace and see what the error message is concerning git packages and see what blocks non cran packages and see if I can get a proxy set. I still encounter small problems using VSCode. I'm not sure if it is just standard use of VSCode with R or a Rix problem, as it only appears after using rix(), and this would be a different issue. Cannot open the connectionwarning messages from top-level task callback 'vsc.workspace' |
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I think you might be having the same issue than here #281 I will be changing the port serving the api after I'm back from holidays it should work then |
That is unusual. Have you also tried with source $HOME/.bashrcThen check the updated path that should include the bin folder of the nix profile. echo $PATH
That is how the function should behave, i.e. create this custom .Rprofile as a side-effect, to make sure the user library is excluded in the library path (what
The problem is that you are loading workspace.json from the /tmp subfolder. Why are you using a tmp folder and not a home subdir to host your vscode project?
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I have been working with both vscode (packaged in nixpkgs and "natively" via package manager or binary install) and rstudio, Ubuntu, on WSL2 Ubuntu, macOS, it has all been running very smoothly. @MGousseff there is no duplicate space created by the custom .Rprofile. If you call ### File generated by `rix::rix_init()` ###
# 1. Currently, system RStudio does not inherit environmental variables
# defined in `$HOME/.zshrc`, `$HOME/.bashrc` and alike. This is workaround to
# make the path of the nix store and hence basic nix commands available
# in an RStudio session
# 2. For nix-R session, remove `R_LIBS_USER`, system's R user library.`.
# This guarantees no user libraries from the system are loaded and only
# R packages in the Nix store are used. This makes Nix-R behave in pure manner
# at run-time.
{
is_rstudio <- Sys.getenv("RSTUDIO") == "1"
is_nix_r <- nzchar(Sys.getenv("NIX_STORE"))
if (isFALSE(is_nix_r) && isTRUE(is_rstudio)) {
cat("{rix} detected RStudio R session")
old_path <- Sys.getenv("PATH")
nix_path <- "/nix/var/nix/profiles/default/bin"
has_nix_path <- any(grepl(nix_path, old_path))
if (isFALSE(has_nix_path)) {
Sys.setenv(PATH = paste(old_path, nix_path, sep = ":"))
}
rm(old_path, nix_path)
}
if (isTRUE(is_nix_r)) {
current_paths <- .libPaths()
userlib_paths <- Sys.getenv("R_LIBS_USER")
user_dir <- grep(paste(userlib_paths, collapse = "|"), current_paths, fixed = TRUE)
new_paths <- current_paths[-user_dir]
.libPaths(new_paths)
rm(current_paths, userlib_paths, user_dir, new_paths)
}
rm(is_rstudio, is_nix_r)
}
options(dplyr.width = Inf)
So it does all what is explained in Once cause of failure, because of your setup, that you do not have proper nix environment variables that are inherited from the shell set up, is that currently we only have adjustments in rstudio, that this is added according to the PATH in the custom .Rprofile. /nix/var/nix/profiles/default/binSo when not using rstudio, i see a hidden behavior that i have missed when programming the tweaks. https://github.com/b-rodrigues/rix/blob/5a95641f03bb9fc4941e7d420adcdcde754adfc2/R/rix_init.R#L275-L295 |
Thank you very much. I'm sorry you had all these notifications while on vacations. I'll wait for you to modify this before I reach to my sys admins, as it is not always very straightforward to add a proxy or modify port opening here (I don't blame them, attacks are very frequent). |
I think I'm going to have a stroke :-) Seriously, thank you for explaining me all this. I am not very aware of how profils work. |
I have exactly the same situation. only /nix/var/nix/profiles/per-user/root$ ll
total 16
drwxr-xr-x 2 root root 4096 Jun 10 10:47 ./
drwxr-xr-x 3 root root 4096 Jun 10 10:47 ../
lrwxrwxrwx 1 root root 14 Jun 10 10:47 profile -> profile-2-link/
lrwxrwxrwx 1 root root 60 Jun 10 10:47 profile-1-link -> /nix/store/9s6w0vyxcbvvw52bgc97vk2bl082xmhi-user-environment/
lrwxrwxrwx 1 root root 60 Jun 10 10:47 profile-2-link -> /nix/store/xr51aqblxflgkh84kvasbmzi1cfi6ih8-user-environment/This seems a similar issue, and apparently newer nix versions link profiles in # on ubuntu it's also some `.../.local/...` folder
➜ ls -l $HOME/.nix-profile
lrwxr-xr-x 1 philipp staff 48 Dec 16 2023 /Users/philipp/.nix-profile -> /Users/philipp/.local/state/nix/profiles/profileThis explains a bit more about profiles: https://nixos.wiki/wiki/User_Environment ls -l /nix/var/nix/profiles/
total 4
lrwxrwxrwx 1 root root 43 Jun 10 10:47 default -> /nix/var/nix/profiles/per-user/root/profile
drwxr-xr-x 3 root root 4096 Jun 10 10:47 per-userI'd also be interested to resolve which i consider your main problem, respectively, what might be improved to signal in {rix}. Error in sys::exec_internal(cmd = cmd, args = args) :
Executing 'nix-hash' failed with status 1Did the # in bash terminal
echo $PATHSomehow should include in the ":"-separated list: the same in the host rig R session Sys.getenv("PATH")Then there is a second hint i'd like to know: It would be great if you can report the output of these commands in your work ubuntu rig R session Sys.getenv("LD_LIBRARY_PATH")
Sys.getenv("NIX_STORE")You seem to have anaconda installed, don't wanna draw premature conclusions but it can fuck envvars up as well. To get the actual error message of This is what internal hashing (not via nixsha ...server API) should do with a local nix install you have. What rig does is actually another thing. Stuff like this doesn't convince me that it leaves important standard R mechanisms unchanged: r-lib/rig#203 |
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Hello, But I tried to follow the workaround of the issue you pointed to : DeterminateSystems/nix-installer#477... And now my nix install is broken again. I try to reinstall things. I am afraid that so many tedious installation problems will not help the adoption of rix (and to make it clear, I get that it is a nix problem and not a rix problem). About the nix-hash, it worked from my home network, so I think it's more a proxy thing. |
Thanks for your patience. I assume you have on my macOS laptop at home i have just updated from NixCpp to Lix, was really smooth. sudo --preserve-env=PATH nix run \
--experimental-features "nix-command flakes" \
--extra-substituters https://cache.lix.systems --extra-trusted-public-keys "cache.lix.systems:aBnZUw8zA7H35Cz2RyKFVs3H4PlGTLawyY5KRbvJR8o=" \
'git+https://git.lix.systems/lix-project/lix?ref=refs/tags/2.91.0' -- \
upgrade-nix \
--extra-substituters https://cache.lix.systems --extra-trusted-public-keys "cache.lix.systems:aBnZUw8zA7H35Cz2RyKFVs3H4PlGTLawyY5KRbvJR8o="Have you tried uninstalling the determinate system installer via (see https://zero-to-nix.com/start/uninstall ) /nix/nix-installer uninstall? On top, you might also try uninstalling stuff like described in the docs. Probably, the determinate systems nix uninstaller does the same, but it might be worth doing below manually. Also, have you managed to remove your nix installed via apt completely. https://nix.dev/manual/nix/2.18/installation/uninstall # remove nix daemon service
sudo systemctl stop nix-daemon.service
sudo systemctl disable nix-daemon.socket nix-daemon.service
sudo systemctl daemon-reload
# remove files created by nix
sudo rm -rf /etc/nix /etc/profile.d/nix.sh /etc/tmpfiles.d/nix-daemon.conf /nix ~root/.nix-channels ~root/.nix-defexpr ~root/.nix-profile
# remove build users and their groups
for i in $(seq 1 32); do
sudo userdel nixbld$i
done
sudo groupdel nixbld
```
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I uninstalled NIX, and reinstalled it with lix. I'm testing it right now. |
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I uninstalled lix, reinstalled lix, and also ran the recommended instruction (although I did not understand what this was for) Then open R in VS code, st the Rterm at the local install so to run the rix() function. It builds the nix. I thought: well, I add complexity from using rix and using vscode, I'll try to build with ide="rstudio". And when I try to launch rstudio from the nix shell, I get : Rstudio is installed on my computer and works ok aoutside of nix shell. I reached my limit for now. I am convinced building reproducible environments to build and distribute packages with R is important, I am sure the nix/rix solution is useful for those for whom ti works, but I just can't spend more time trying to set it up as I am getting behind on my work. I will for a while just code with the up to date CRAN versions hoping my code will be OK, and I'l come back to all this later. I think NIX should provide a .deb package to make it easy to install and uninstall in the ubuntu/debian community, I think a step-by-step tutorial could be useful (that is first in my general session I do this, then I quit, enter my nix-shell session and launch this and this and then I can run my R scripts into the nix R environment). @philipp-baumann I hope I'll find some time later to try again. Sorry for the time we lost both without having the release to make it all work, it also must be frustrating for you. |
i get it no prob. I think it's really something peculiar in your setup. I have managed to get it working on Ubuntu on two systems, so i'm still positive. @b-rodrigues has also tested it on a latest Ubuntu container and all works smoothly there, too, i think. I would generally advise for diagnostics to start simple. Use a plain R session (not rig R, just the one in apt) in a bash terminal, then install newest rix and see if it works. The other hints are envvars, which depending on the shell environment and IDE might not optimally be loaded for a smooth nix environment. My feeling is we have already done a lot there, there is small things to improve and a diagnostics helper is one of it. Issues like yours are not getting in the way, but are there to learn something. So in that spirit feel free to reiterate over this issue once you have time. We all sometimes want to make it work as simply as possibles and there are trade-offs with deliverables. Cheers! |
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for a project now i for example use library("rix")
rix_init()
r_pkgs <- c(
"targets", "tarchetypes", "dplyr", "data.table", "dm", "DiagrammeR", "quarto",
"R.utils", "here", "yaml", "readxl", "reactable", "writexl",
# logging framework
"lgr",
# development tools
"devtools", "styler", "lintr"
)
git_pkgs <- list(
list(
package_name = "rix",
repo_url = "https://github.com/b-rodrigues/rix",
commit = "c64ccaa34eb48ae4dcd78148ace211f72eebcb16"
),
list(
package_name = "fnmate",
repo_url = "https://github.com/MilesMcBain/fnmate/",
commit = "18a4c00536e0deafeb6b3f91e48b53b641f47e6a"
),
list(
package_name = "rscodeio",
repo_url = "https://github.com/anthonynorth/rscodeio",
commit = "88a1a373d64f0bd81b6730eb6fa005fd0baa9078"
)
)
# Define expressions with software environment
rix::rix(
r_ver = "9355fa86e6f27422963132c2c9aeedb0fb963d93", # "3c0be6ff38ccf079cb7976a571c5c865a19230a6",
r_pkgs = r_pkgs,
system_pkgs = c("git", "quarto"),
git_pkgs = git_pkgs,
ide = "rstudio",
project_path = ".",
overwrite = TRUE,
shell_hook = "export QT_XCB_GL_INTEGRATION=none"
)
|
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@MGousseff for rstudio you need to add
in your rix call, as documented (scenario 1). Too bad it's not working well for you, as @philipp-baumann mentioned I was able to get everything running on an Ubuntu vm and on my rpi5 running ubuntu as well. Really wonder what went wrong for you |
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My guess is that rig and nix don't go along too well, with symbolic links from rig messing with things ? |
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I'll test this setup in a vm, thanks! to be honest, the best way is to not have a system wide R version, and rely solely on project specific versions of R managed by Nix. But I know this is not really how most people like to work |
Yeah have to admit me sometimes, too 😅 no reason for it. I think the critical phase is adoption. The transition needs to be frictionless, and i think we are good on track. |
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What ? But you need a system wide R version to create your nix environment with rix. Or you are in a infinite loop : you need nix to launch R to create the rix file which allows you to create the nix environment to launch R to... etc. I'll try to uninstall rig and my versions of R, install the latest Rbase, install RIX and create a setup. But I need to find a couple of hours, and I'm behind on my job. By the way, have you tried rix with positron ? The future replacement of Rstudio, or at least the new IDE provided by posit (Rstudio mother company) is in beta public version. It deals with R and python in a fork of VScode. I'm trying it (after the weird messages I get with rix in vscode). It feels not bad, even if debugging capabilites are still behind what I had with intellij (which I loved so much until the plugin broke and we realized only one man was on it and didn't answer anymore). |
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as described in the Readme, you can simply run a temporary shell to generate a default.nix by running as for Positron: I've been trying to package it for NixOS 😁 |
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So here is what I did
What doesn't work:
What works:
What SURPRISINGLY WORKS:
What I'd love: Thank you both @b-rodrigues @philipp-baumann. I hope you don't feel this was a waste of time. I'd like to write a quick summary of this and how to install and use nix/lix and rix, but I don't have any "blogging platform anymore". Maybe some people will find this issue helpful. |
Yes, this was my experience as well. FYI, this seems to be the case with many other editors, such as emacs and neovim. In any case, glad it works for you now! |
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I think that we can now close this. @MGousseff should you have another problem, don't hesitate to open an issue! |
I'm getting a 500 error for a github package.
The information of repo, branch and commit sha is correct as far as I can tell: eliocamp/metR@1dd5d39
Other similar remotes seem to work correctly.
This seems to be an issue on the git2nisha thing, though. For some reason it fails with the first repo.
Any commit seems to fail, too.
Am I missing something in the specification of the remote?
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