Merge pull request #302192 from Kupac/fix_Rhisat2

rPackages.Rhisat2: fix build

1 files changed, 12 insertions, 0 deletions

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index f2c398c0f4526..f2af3039b6b51 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -413,6 +413,7 @@ 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 ];
@@ -1271,6 +1272,17 @@ 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";