From ec81fe00d90995f7b14fe8823c894fe133015e2f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A1szl=C3=B3=20Kupcsik?= <koopac@gmail.com>
Date: Wed, 3 Apr 2024 23:32:48 +0200
Subject: [PATCH] rPackages.Rhisat2: fix build
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fixed for aarch-linux by @b-rodrigues

Co-authored-by: Justin Bedő <cu@cua0.org>
---
 pkgs/development/r-modules/default.nix | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index ecc3d2d66b42..4714543de68a 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -408,6 +408,7 @@ let
     RcppZiggurat = [ pkgs.gsl ];
     reprex = [ pkgs.which ];
     rgdal = with pkgs; [ proj.dev gdal ];
+    Rhisat2 = [ pkgs.which pkgs.hostname ];
     gdalcubes = [ pkgs.pkg-config ];
     rgeos = [ pkgs.geos ];
     Rglpk = [ pkgs.glpk ];
@@ -1218,6 +1219,17 @@ let
       '';
     });
 
+    # backported patch from 1.9
+    Rhisat2= old.Rhisat2.overrideAttrs (attrs: {
+      patches = [ (pkgs.fetchpatch {
+        url = "https://github.com/fmicompbio/Rhisat2/commit/a0f27b018831b39f080f99e6db8a4b876fd56fc3.patch";
+        sha256 = "sha256-FbYkP/WFmbfQmxArkHgushgVgY0XSypbK8Z5ivQK8k4=";
+      }) ];
+      env = (attrs.env or { }) // {
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -w";
+      };
+    });
+
     s2 = old.s2.overrideAttrs (attrs: {
       PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
       PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto";