From acab8c7bedaa1773d2f7bf7b5705dfae9ff5a602 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A1szl=C3=B3=20Kupcsik?= <koopac@gmail.com>
Date: Thu, 24 Oct 2024 20:59:37 +0200
Subject: [PATCH] rPackages.ChemmineOB: fix compile error

- Don't override openbabel
- fix pointer name in ChemmineOB src instead
---
 pkgs/development/r-modules/default.nix | 22 ++++++----------------
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index d17cf9941491a..cec9098ae3662 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -801,7 +801,7 @@ let
     sphereTessellation = with pkgs; [ gmp.dev mpfr.dev ];
     vapour = with pkgs; [ proj.dev gdal ];
     MedianaDesigner = [ pkgs.zlib.dev ];
-    ChemmineOB = [ pkgs.eigen ];
+    ChemmineOB = with pkgs; [ eigen openbabel ];
     DGP4LCF = [ pkgs.lapack pkgs.blas ];
   };
 
@@ -1582,29 +1582,19 @@ let
       PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
     });
 
-    ChemmineOB = let
-      # R package doesn't compile with the latest (unstable) version.
-      # Override from nixpkgs-23.11
-      openbabel3 = pkgs.openbabel.overrideAttrs (attrs: {
-        version = "3.1.1";
-        src = pkgs.fetchFromGitHub {
-          owner = "openbabel";
-          repo = "openbabel";
-          rev = "openbabel-${lib.replaceStrings ["."] ["-"] attrs.version}";
-          sha256 = "sha256-wQpgdfCyBAoh4pmj9j7wPTlMtraJ62w/EShxi/olVMY=";
-        };
-      });
-    in
-    old.ChemmineOB.overrideAttrs (attrs: {
+    ChemmineOB = old.ChemmineOB.overrideAttrs (attrs: {
       # pkg-config knows openbabel-3 without the .0
       # Eigen3 is also looked for in the wrong location
+      # pointer was changed in newer version of openbabel:
+      #   https://github.com/openbabel/openbabel/commit/305a6fd3183540e4a8ae1d79d10bf1860e6aa373
       postPatch = ''
         substituteInPlace configure \
           --replace-fail openbabel-3.0 openbabel-3
         substituteInPlace src/Makevars.in \
           --replace-fail "-I/usr/include/eigen3" "-I${pkgs.eigen}/include/eigen3"
+        substituteInPlace src/ChemmineOB.cpp \
+          --replace-fail "obsharedptr<" "std::shared_ptr<"
       '';
-      buildInputs = attrs.buildInputs ++ [openbabel3];
     });
 
     ps = old.ps.overrideAttrs (attrs: {