error: PCH file uses a newer PCH format that cannot be read

[idontgetoutmuch]

Describe the bug

I am trying to run the example here: https://avehtari.github.io/casestudies/Motorcycle/motorcycle_gpcourse.html#

> model_gpcovf <- cmdstan_model(stan_file = file_gpcovf)
Compiling Stan program...
error: PCH file uses a newer PCH format that cannot be read

1 error generated.

make: *** [make/program:55: /tmp/Rtmp67aYAA/model-17d992624d5b1] Error 1

Error: An error occured during compilation! See the message above for more information.
In addition: Warning message:
CmdStan's precompiled header (PCH) files may need to be rebuilt.
If your model failed to compile please run rebuild_cmdstan().
If the issue persists please open a bug report. 
> rebuild_cmdstan()
rm -f -r test
rm -f 
rm -f 
rm -f 
rm -f 
  removing dependency files
rm -f src/cmdstan/main.d   stan//src/stan/model/model_header.d
rm -f   
rm -f   
  cleaning sundials targets
rm -f stan/lib/stan_math/lib/sundials_5.7.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.7.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.7.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_5.7.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_5.7.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_5.7.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_5.7.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_5.7.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_5.7.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_5.7.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_5.7.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_5.7.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_5.7.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_memory.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.7.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.7.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.7.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.7.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.7.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.7.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o stan/lib/stan_math/lib/sundials_5.7.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o
  cleaning Intel TBB targets
rm -f -rf stan/lib/stan_math/lib/tbb
rm -f bin/stanc bin/stansummary bin/print bin/diagnose
rm -f -r src/cmdstan/main*.o bin/cmdstan
rm -f stan/src/stan/model/model_header.hpp.gch
rm -f examples/bernoulli/bernoulli examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.d examples/bernoulli/bernoulli.hpp
rm -f -r 
arch: posix_spawnp: make: Bad CPU type in executable

To Reproduce

Install nix sh <(curl -L https://nixos.org/nix/install) and then nix-shell with a shell.nix:

let

rOverlay = rself: rsuper: {
  rPackages = rsuper.rPackages.override {
    overrides = {

      smcsamplers = (rself.rPackages.buildRPackage {
        name = "smcsamplers";
        src = rself.fetchFromGitHub {
          owner = "pierrejacob";
          repo = "smcsamplers";
          rev = "097192f7d5df520d9b026d442dfec493a3051374";
          sha256 = "00facn1ylcbai4sbcidpp991899csz2ppmmkv0khvqxfncddr0f2";
        };
        propagatedBuildInputs = [ rsuper.rPackages.coda rsuper.rPackages.MASS rsuper.rPackages.mvtnorm rsuper.rPackages.loo rsuper.rPackages.shape rsuper.rPackages.rstan rsuper.rPackages.tidyverse rsuper.rPackages.doParallel rsuper.rPackages.igraph rsuper.rPackages.ggraph rsuper.rPackages.doRNG rsuper.rPackages.reshape2 ];
      });

      cmdstanr = (rself.rPackages.buildRPackage {
        name = "cmdstanr";
        src = rself.fetchFromGitHub {
          owner = "stan-dev";
          repo = "cmdstanr";
          rev = "2e24ec873c5513b41fba90ee59e0dffcd27a479c";
          sha256 = "sha256:0nrqlidsrykszasdypsldsbhv4dcbrj9awyyzq7rb6kc5y8fnhvi";
        };
        propagatedBuildInputs = [ rsuper.rPackages.coda rsuper.rPackages.MASS rsuper.rPackages.mvtnorm rsuper.rPackages.loo rsuper.rPackages.shape rsuper.rPackages.rstan rsuper.rPackages.tidyverse rsuper.rPackages.doParallel rsuper.rPackages.igraph rsuper.rPackages.ggraph rsuper.rPackages.doRNG rsuper.rPackages.reshape2 rsuper.rPackages.data_table rsuper.rPackages.posterior ];
      });

    };
  };
};

in

{ nixpkgs ? import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/21.11.tar.gz") {
  config.allowBroken = true;
  overlays = [ rOverlay ];
  system = "x86_64-darwin";
}
}:

let
  R-with-my-packages = nixpkgs.rWrapper.override{
    packages = with nixpkgs.rPackages; [
      tidyverse
      plotly
      jqr
      matrixStats
      aws_s3
      DBI
      RPostgres
      gapminder
      gg_gap
      DT
      TTR
      patchwork
      shiny
      shinyjs
      reshape2
      openmetrics
      dplyr
      ggplot2
      readxl
      purrr
      openxlsx

      smcsamplers
      cmdstanr
      tidybayes
      bayesplot
    ]; };

  pkgs = nixpkgs;

in

pkgs.stdenv.mkDerivation {
  name = "xxx";

  buildInputs = with pkgs.rPackages; [
    pkgs.libintlOrEmpty
    R-with-my-packages
    pkgs.darwin.apple_sdk.frameworks.Cocoa
  ];
}

Expected behavior
I would expect the example to run as shown on the website.

Operating system
Apple M1 Max macOS 12.2.1

CmdStanR version number

> packageVersion("cmdstanr")
[1] ‘0.5.0’

Additional context

[idontgetoutmuch]

This fixes the problem: NixOS/nixpkgs#165765 and then I don't need system = "x86_64-darwin";.

[rok-cesnovar]

Thanks!