diff --git a/pkgs/development/compilers/cmdstan/default.nix b/pkgs/development/compilers/cmdstan/default.nix
index 8d3e738aa1b4..ad84e13d369e 100644
--- a/pkgs/development/compilers/cmdstan/default.nix
+++ b/pkgs/development/compilers/cmdstan/default.nix
@@ -1,4 +1,13 @@
-{ lib, stdenv, fetchFromGitHub, stanc, python3, buildPackages, runtimeShell }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, python3
+, stanc
+, buildPackages
+, runtimeShell
+, runCommandCC
+, cmdstan
+}:
 
 stdenv.mkDerivation rec {
   pname = "cmdstan";
@@ -12,39 +21,43 @@ stdenv.mkDerivation rec {
     hash = "sha256-c+L/6PjW7YgmXHuKhKjiRofBRAhKYCzFCZ6BOX5AmC4=";
   };
 
-  nativeBuildInputs = [ stanc ];
-
-  buildFlags = [ "build" ];
-  enableParallelBuilding = true;
-
-  doCheck = true;
-  nativeCheckInputs = [ python3 ];
-
-  CXXFLAGS = lib.optionalString stdenv.isDarwin "-D_BOOST_LGAMMA";
-
   postPatch = ''
     substituteInPlace stan/lib/stan_math/make/libraries \
       --replace "/usr/bin/env bash" "bash"
-    patchShebangs .
-  '' + lib.optionalString stdenv.isAarch64 ''
-    sed -z -i "s/TEST(CommandStansummary, check_console_output).*TEST(CommandStansummary, check_csv_output)/TEST(CommandStansummary, check_csv_output)/" \
-      src/test/interface/stansummary_test.cpp
   '';
 
+  nativeBuildInputs = [
+    python3
+    stanc
+  ];
+
   preConfigure = ''
+    patchShebangs test-all.sh runCmdStanTests.py stan/
+  ''
+  # Fix inclusion of hardcoded paths in PCH files, by building in the store.
+  + ''
+    mkdir -p $out/opt
+    cp -R . $out/opt/cmdstan
+    cd $out/opt/cmdstan
     mkdir -p bin
     ln -s ${buildPackages.stanc}/bin/stanc bin/stanc
   '';
 
-  makeFlags = lib.optional stdenv.isDarwin "arch=${stdenv.hostPlatform.darwinArch}";
+  makeFlags = [
+    "build"
+  ] ++ lib.optionals stdenv.isDarwin [
+    "arch=${stdenv.hostPlatform.darwinArch}"
+  ];
 
-  checkPhase = ''
-    ./runCmdStanTests.py -j$NIX_BUILD_CORES src/test/interface
-  '';
+  # Disable inclusion of timestamps in PCH files when using Clang.
+  env.CXXFLAGS = lib.optionalString stdenv.cc.isClang "-Xclang -fno-pch-timestamp";
+
+  enableParallelBuilding = true;
 
   installPhase = ''
-    mkdir -p $out/opt $out/bin
-    cp -r . $out/opt/cmdstan
+    runHook preInstall
+
+    mkdir -p $out/bin
     ln -s $out/opt/cmdstan/bin/stanc $out/bin/stanc
     ln -s $out/opt/cmdstan/bin/stansummary $out/bin/stansummary
     cat > $out/bin/stan <<EOF
@@ -52,10 +65,19 @@ stdenv.mkDerivation rec {
     make -C $out/opt/cmdstan "\$(realpath "\$1")"
     EOF
     chmod a+x $out/bin/stan
+
+    runHook postInstall
   '';
 
-  # Hack to ensure that patchelf --shrink-rpath get rids of a $TMPDIR reference.
-  preFixup = "rm -rf stan";
+  passthru.tests = {
+    test = runCommandCC "cmdstan-test" { } ''
+      cp -R ${cmdstan}/opt/cmdstan cmdstan
+      chmod -R +w cmdstan
+      cd cmdstan
+      ./runCmdStanTests.py -j$NIX_BUILD_CORES src/test/interface
+      touch $out
+    '';
+  };
 
   meta = with lib; {
     description = "Command-line interface to Stan";