Rstudio on Mac Failure

[jgeller112]

I just tried to open a rstudio session within the nix shell and am getting the below error

node:46306) electron: Failed to load URL: http://127.0.0.1:14333/ with error: ERR_CONNECTION_REFUSED
(Use `RStudio --trace-warnings ...` to show where the warning was created)
(electron) 'webContents.clearHistory' is deprecated and will be removed. Please use 'webContents.navigationHistory.clear' instead.

When a session is open I get something like this:

[b-rodrigues]

You can ignore the warnings from the console, the issue here is what’s shown inside the RStudio session. It seems you also have homebrew on this machine, and that homebrew installed some version of ssl, which in turn is causing issues because RStudio (which was installed by Nix) tries to load it. This can unfortunately happen because at runtime, nix shells are not completely isolated from the rest of your machine. So there’s only two, quite radical options:

• get rid of homebrew altogether and take the nix pill 100%
• use another IDE that doesn’t need to load ssl at runtime

I’ll also ask in the R for nix matrix channel and see if we can improve the packaging of RStudio to perhaps ignore this kind of things. Maybe that would work

[b-rodrigues]

btw, can you also share your default.nix here? so I can try to reproduce on my mac (which doesn’t have homebrew)

[b-rodrigues]

We might be able to patch rstudio to ignore this kind of thing: to help us debug, could you run:

find / -name rsession 2>/dev/null

in a terminal? you should get something like:

/nix/store/kxjr50in6aaqwyv4jjdbch3361chp4r9-RStudio-2024.04.2+764/Applications/RStudio.app/Contents/Resources/app/bin/rsession

then run:

otool -L /nix/store/kxjr50in6aaqwyv4jjdbch3361chp4r9-RStudio-2024.04.2+764/Applications/RStudio.app/Contents/Resources/app/bin/rsession

and copy and paste the output here

[jgeller112]

We might be able to patch rstudio to ignore this kind of thing: to help us debug, could you run:

find / -name rsession 2>/dev/null

in a terminal? you should get something like:

/nix/store/kxjr50in6aaqwyv4jjdbch3361chp4r9-RStudio-2024.04.2+764/Applications/RStudio.app/Contents/Resources/app/bin/rsession

then run:

otool -L /nix/store/kxjr50in6aaqwyv4jjdbch3361chp4r9-RStudio-2024.04.2+764/Applications/RStudio.app/Contents/Resources/app/bin/rsession

and copy and paste the output here

dyld[56365]: Library not loaded: /opt/homebrew/opt/openssl@3/lib/libssl.3.dylib
Referenced from: <0E2A913E-7B96-3B62-A7BE-18A4CFAABB7E> /nix/store/1w7281cixl7vi8wyp6gmc1grmj1shw8d-RStudio-2024.04.2+764/Applications/RStudio.app/Contents/Resources/app/bin/rsession
Reason: tried: '/opt/homebrew/opt/openssl@3/lib/libssl.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/openssl@3/lib/libssl.3.dylib' (no such file), '/opt/homebrew/opt/openssl@3/lib/libssl.3.dylib' (no such file), '/usr/local/lib/libssl.3.dylib' (no such file), '/usr/lib/libssl.3.dylib' (no such file, not in dyld cache)
zsh: abort
(base) jasongeller@Jasons-Mac-mini ~ %

[jgeller112]

I have been using Positron on mac but would like this to work for rstudio.

[TomaSajt]

Could you tell us what nixpkgs revision you are using?
Also, how are you running the program?
(Are you using flakes? Are you using nix-darwin?)
Any kind of extra information would be appreciated.

It doesn't seem like the rstudio package came from the cache: did you have to build it yourself?

If yes, my main hypothesis is the following: you were trying to download rstudio when it wasn't cached yet (unrelated to rstudio), so it rebuilt it on your system. However, since the sandbox is not completely enabled on darwin, your local openssl installation might have leaked in into the build process.

[b-rodrigues]

it's this nixpkgs revision https://github.com/rstats-on-nix/nixpkgs/tree/2025-03-03

it's basically a fork of master at that day, looking at the commit history you'll find the nixos/nixpkgs revision it's based on. It's not flakes but a shell generated by rix.

How do you know rstudio wasn't downloaded from the cache.nixos.org ?

However, since the sandbox is not completely enabled on darwin

I wasn't aware of this, interesting

[jgeller112]

Here is my default.nix file

# This file was generated by the {rix} R package v0.15.6 on 2025-03-12
# with following call:
# >rix(date = "2025-03-03",
#  > r_pkgs = required_packages,
#  > system_pkgs = c("quarto",
#  > "git",
#  > "pandoc",
#  > "cmdstan",
#  > "nix"),
#  > git_pkgs = list(list(package_name = "cmdstanr",
#  > repo_url = "https://github.com/stan-dev/cmdstanr",
#  > commit = "12211d4b35605d416d6e22078db81cfe9e5a64f5")),
#  > tex_pkgs = c("amsmath",
#  > "ninecolors",
#  > "apa7",
#  > "scalerel",
#  > "threeparttable",
#  > "threeparttablex",
#  > "endfloat",
#  > "environ",
#  > "multirow",
#  > "tcolorbox",
#  > "pdfcol",
#  > "tikzfill",
#  > "fontawesome5",
#  > "framed",
#  > "newtx",
#  > "fontaxes",
#  > "xstring",
#  > "wrapfig",
#  >      "tabularray",
#  > "siunitx",
#  > "fvextra",
#  > "geometry",
#  > "setspace",
#  > "fancyvrb",
#  > "anyfontsize"),
#  > ide = "rstudio",
#  > project_path = ".",
#  > overwrite = TRUE,
#  > r_ver = "4.4.3")
# It uses the `rstats-on-nix` fork of `nixpkgs` which provides improved
# compatibility with older R versions and R packages for Linux/WSL and
# Apple Silicon computers.
# Report any issues to https://github.com/ropensci/rix
let
 pkgs = import (fetchTarball "https://github.com/rstats-on-nix/nixpkgs/archive/2025-03-03.tar.gz") {};
 
  rpkgs = builtins.attrValues {
    inherit (pkgs.rPackages) 
      brms
      colorspace
      cowplot
      data_table
      easystats
      emmeans
      flextable
      ggdist
      ggeffects
      ggokabeito
      ggrepel
      ggtext
      here
      hypr
      knitr
      MetBrewer
      modelbased
      patchwork
      posterior
      ragg
      tidybayes
      tidylog
      tidyverse
      tinytable;
  };
 
    cmdstanr = (pkgs.rPackages.buildRPackage {
      name = "cmdstanr";
      src = pkgs.fetchgit {
        url = "https://github.com/stan-dev/cmdstanr";
        rev = "12211d4b35605d416d6e22078db81cfe9e5a64f5";
        sha256 = "sha256-/9YftAbbJCkDoV7M0nctRKpr5Y7ir63aJdCiDzG3KpI=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          checkmate
          data_table
          jsonlite
          posterior
          processx
          R6
          withr
          rlang;
      };
    });
  
  tex = (pkgs.texlive.combine {
    inherit (pkgs.texlive) 
      scheme-small
      amsmath
      anyfontsize
      apa7
      endfloat
      environ
      fancyvrb
      fontawesome5
      fontaxes
      framed
      fvextra
      geometry
      multirow
      newtx
      ninecolors
      pdfcol
      scalerel
      setspace
      siunitx
      tabularray
      tcolorbox
      threeparttable
      threeparttablex
      tikzfill
      wrapfig
      xstring;
  });
  
  system_packages = builtins.attrValues {
    inherit (pkgs) 
      cmdstan
      git
      glibcLocales
      nix
      pandoc
      quarto
      R;
  };
 
  wrapped_pkgs = pkgs.rstudioWrapper.override {
    packages = [ cmdstanr rpkgs  ];
  };
 
  shell = 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 = [ cmdstanr rpkgs tex system_packages  wrapped_pkgs ];
    
  }; 
in
  {
    inherit pkgs shell;
  }

[TomaSajt]

I looked at the git history, and yes, this snapshot was taken between two electron changes. This way Hydra (the cache CI) never built it.
Unfortunate timing.

Should be solved by using a later revision, where rstudio is cached.

[TomaSajt]

AFAICT NixOS/nixpkgs#384339 will fix the issue permanently.

It was only fixed accidentally by upstream: they renamed CMakeGlobals.txt to cmake/globals.cmake.
This fixes it because nixpkgs's cmake tooling goes through all .cmake files and makes sure that no path beginning with /opt remains.

[b-rodrigues]

@TomaSajt many thanks for your help !

@jgeller112 could you try with the 2025-03-10?

[jgeller112]

Fixed! Thanks for your help!

[jgeller112]

You can ignore the warnings from the console, the issue here is what’s shown inside the RStudio session. It seems you also have homebrew on this machine, and that homebrew installed some version of ssl, which in turn is causing issues because RStudio (which was installed by Nix) tries to load it. This can unfortunately happen because at runtime, nix shells are not completely isolated from the rest of your machine. So there’s only two, quite radical options:

• get rid of homebrew altogether and take the nix pill 100%
• use another IDE that doesn’t need to load ssl at runtime

I’ll also ask in the R for nix matrix channel and see if we can improve the packaging of RStudio to perhaps ignore this kind of things. Maybe that would work

I have removed homebrew but still getting the above errors. I am not sure what is going on. I was able to get rstudio running on another mac, but not my home macs.

[jgeller112]

You can ignore the warnings from the console, the issue here is what’s shown inside the RStudio session. It seems you also have homebrew on this machine, and that homebrew installed some version of ssl, which in turn is causing issues because RStudio (which was installed by Nix) tries to load it. This can unfortunately happen because at runtime, nix shells are not completely isolated from the rest of your machine. So there’s only two, quite radical options:

• get rid of homebrew altogether and take the nix pill 100%
• use another IDE that doesn’t need to load ssl at runtime

I’ll also ask in the R for nix matrix channel and see if we can improve the packaging of RStudio to perhaps ignore this kind of things. Maybe that would work

I have removed homebrew but still getting the above errors. I am not sure what is going on. I was able to get rstudio running on another mac, but not my home macs.

I have reinstalled everything.

[b-rodrigues]

did that other mac have hombrew ? did you use the latest available date (2025-03-10)? maybe remove the result file in the folder of your project, run nix-store --gc and build the environment with the latest date again

[TomaSajt]

My first guess would be that your rstudio build (which referenced the old location for openssl) is still locally cached by the nix store.

If you don't care about having to download some packages again, try garbage-collecting your store. Maybe that fixes it.

In any case, NixOS/nixpkgs#384339 is close to being merged. That should fix your problem in theory.

Would you be willing to try that branch out?

[jgeller112]

did that other mac have hombrew ? did you use the latest available date (2025-03-10)? maybe remove the result file in the folder of your project, run nix-store --gc and build the environment with the latest date again

It did have homebrew. I try building it again.

[b-rodrigues]

Would you be willing to try that branch out?

to try the branch, replace rstats-on-nix in your default.nix with TomaSajt and the date in the same url with rstudio, and you should be able to try out this fixed rstudio version! then, once it's merged you could go back to rstats-on-nix on nix with a date posterior to the merge

[jgeller112]

Would you be willing to try that branch out?

to try the branch, replace rstats-on-nix in your default.nix with TomaSajt and the date in the same url with rstudio, and you should be able to try out this fixed rstudio version! then, once it's merged you could go back to rstats-on-nix on nix with a date posterior to the merge

@TomaSajt and @b-rodrigues that worked!

[b-rodrigues]

That's great news!

[jgeller112]

I'll hold off on sharing with collaborators until the merge is complete

[TomaSajt]

The PR is merged so I assume the latest snapshots will work now.