Package build depending on openMP failing on MacOS, certainly due to not using Apple's clang

[code-instable]

Hello,

I am trying to install a R package from a github repository using rix, and it seems like I'm having troubles compiling it because of the openMP lib, which is a common issue on macOS, but whose solution does not seem ot work when combined with nix. That is why I come here to find some help after trying some stuff that did not work out:

I have the following rix generated config

rix::rix(
    system_pkgs = NULL,
    r_ver = paste0(R.version$major, ".", R.version$minor),
    r_pkgs = NULL,
    git_pkgs = list(
        list(package_name = "adaptiveFTS", repo_url = "https://github.com/hmaissoro/adaptiveFTS", commit = "af5a9859165a7f95046a7c57683e7094e3f4de9f")
    ),
    tex_pkgs = NULL,
    ide = "none",
    project_path = ".",
    overwrite = TRUE,
    print = FALSE,
    message_type = "verbose"
)

giving

# This file was generated by the {rix} R package v0.15.5 on 2025-03-12
# with following call:
# >rix(r_ver = "4.4.2",
#  > r_pkgs = NULL,
#  > system_pkgs = NULL,
#  > git_pkgs = list(list(package_name = "adaptiveFTS",
#  > repo_url = "https://github.com/hmaissoro/adaptiveFTS",
#  > commit = "af5a9859165a7f95046a7c57683e7094e3f4de9f")),
#  > tex_pkgs = NULL,
#  > ide = "none",
#  > project_path = ".",
#  > overwrite = TRUE,
#  > print = FALSE,
#  > message_type = "verbose")
# 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/2025-02-24.tar.gz") {};
  
    adaptiveFTS = (pkgs.rPackages.buildRPackage {
      name = "adaptiveFTS";
      src = pkgs.fetchgit {
        url = "https://github.com/hmaissoro/adaptiveFTS";
        rev = "af5a9859165a7f95046a7c57683e7094e3f4de9f";
        sha256 = "sha256-cWjDmKBy2bxukl4lsDPHyLreRyPnCz/mcBfFUagGjAo=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          caret
          data_table
          fastmatrix
          MASS
          Rcpp
          Rdpack
          RcppArmadillo;
      };
    });
    
  system_packages = builtins.attrValues {
    inherit (pkgs) 
      glibcLocales
      nix
      R;
  };
  
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 = [ adaptiveFTS   system_packages ];
  
}

which led to the following error once entering nix-shell

nix-shell

giving the following error :

> /nix/store/0jd4fjnnrfz0dfxbc5lgfyxjfay73i77-clang-wrapper-19.1.7/bin/c++ -std=gnu++11 -I"/nix/store/p6p2ckx4mysfkkzw1z9849gy8ll5vfmv-R-4.4.2/lib/R/include" -DNDEBUG  -I'/nix/store/c8v12zmy5z76aw6lkazvcw4skfwfdjxv-r-Rcpp-1.0.14/library/Rcpp/include' -I'/nix/store/hwnahz939f559rj12zj6yaxkkrk3g1x0-r-RcppArmadillo-14.2.3-1/library/RcppArmadillo/include' -isystem /nix/store/j3dhkx4m14m38drh3f40bccrwrgzlsg5-libcxx-19.1.7-dev/include/c++/v1    -fPIC  -g -O2   -c RcppExports.cpp -o RcppExports.o
       > 04_estimate_mean_cpp.cpp:2:10: fatal error: 'omp.h' file not found
       >     2 | #include <omp.h>
       >       |          ^~~~~~~

---

here is why I tried :

• adding pkgs.llvmPackages.openmp to the buildInputs did not change anything

# default.nix
buildInputs = [ adaptiveFTS   system_packages pkgs.llvmPackages.openmp ];

same when adding pkgs.apple-sdk, trying to get the required openMP library

• nor adding suggested flags to the Makevars file via a postPatch

adaptiveFTS = (pkgs.rPackages.buildRPackage {
      name = "adaptiveFTS";
      src = pkgs.fetchgit {
        url = "https://github.com/hmaissoro/adaptiveFTS";
        rev = "af5a9859165a7f95046a7c57683e7094e3f4de9f";
        sha256 = "sha256-cWjDmKBy2bxukl4lsDPHyLreRyPnCz/mcBfFUagGjAo=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          caret
          data_table
          fastmatrix
          MASS
          Rcpp
          Rdpack
          RcppArmadillo;
      };
      postPatch = ''
      echo "CPPFLAGS += -Xclang -fopenmp" >> src/Makevars
      echo "LDFLAGS += -lomp" >> src/Makevars
      '';
    });

I really don't know how to solve it, any idea ?

thanks!

[b-rodrigues]

pkgs.llvmPackages.openmp is a dependency of adaptiveFTS, but you added it as a dependency of the shell. You need to change the expression like so:

    adaptiveFTS = (pkgs.rPackages.buildRPackage {
      name = "adaptiveFTS";
      src = pkgs.fetchgit {
        url = "https://github.com/hmaissoro/adaptiveFTS";
        rev = "af5a9859165a7f95046a7c57683e7094e3f4de9f";
        sha256 = "sha256-cWjDmKBy2bxukl4lsDPHyLreRyPnCz/mcBfFUagGjAo=";
      };
      propagatedBuildInputs = builtins.attrValues {
        inherit (pkgs.rPackages) 
          caret
          data_table
          fastmatrix
          MASS
          Rcpp
          Rdpack
          RcppArmadillo;
      } ++ [ pkgs.llvmPackages.openmp ]; <------- right here!
    });
    

and can leave the rest as-is. This type of fix is exactly what we (by "we" I mean the R packagers for Nix) do for packages released on CRAN and Bioconductor, so users don’t have to deal with it. But unfortunately, we can’t do that for every package released on Github...
Also, I highly recommend you don’t write the script to generate the expression like this:

rix::rix(
    system_pkgs = NULL,
    r_ver = paste0(R.version$major, ".", R.version$minor),
    r_pkgs = NULL,

as this would generate a different expression if executed on a different version of R. Instead, I recommend you hardcode the version of R, or even better, set a date with date = "2025-03-10" for example.

[code-instable]

thanks for the answer in record time !
I am going to try it out 😉

also about the part of adding hidden dependencies, I am totally fine with having to do it myself, I am pretty new to nix (have been using nix as primary package manager for 3 months now) and the learning curve is quite steep. I do appreciate your time for helping me on this :)

I'm sure this discussion can allow also other people to be able to solve some of their own problems when using Rix. Even though these questions are more about nix itself than Rix, the R community is probably not familiar with nix.

I've just come across your article that should have helped me solve the issue by myself. sorry for that "read the f manual" moment 🫠

[code-instable]

I can also confirm that your suggested modification works ✅ (did not even need the postPatch, as you mentioned)

Thanks once again for taking time helping a newbie like me! I hope this was not too inconvenient 😬

[b-rodrigues]

Thanks once again for taking time helping a newbie like me! I hope this was not too inconvenient 😬

if I didn’t want to help people (and newbies are people too) I wouldn’t do open source in my spare time and play video games instead (sifu keeps waiting) 😆