bio-gappa: fix build with gcc15

pkgs/by-name/bi/bio-gappa/fix-cstdint.patch

@@ -0,0 +1,12 @@
+diff --git a/libs/CLI11/include/CLI/Validators.hpp b/libs/CLI11/include/CLI/Validators.hpp
+index 536f8a6..3371905 100644
+--- a/libs/CLI11/include/CLI/Validators.hpp
++++ b/libs/CLI11/include/CLI/Validators.hpp
+@@ -18,6 +18,7 @@
+ // Could be swapped for filesystem in C++17
+ #include <sys/stat.h>
+ #include <sys/types.h>
++#include <cstdint>
+ 
+ namespace CLI {
+ 

pkgs/by-name/bi/bio-gappa/package.nix

@@ -8,6 +8,7 @@
   libz,
   bzip2,
   xz,
+  versionCheckHook,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -34,8 +35,10 @@ stdenv.mkDerivation (finalAttrs: {
     xz
   ];
 
-  # CMake 2.8.7 is deprecated and is no longer supported by CMake > 4
-  # https://github.com/NixOS/nixpkgs/issues/445447
+  patches = [
+    ./fix-cstdint.patch
+  ];
+
   postPatch = ''
     substituteInPlace CMakeLists.txt --replace-fail \
       "cmake_minimum_required (VERSION 2.8.7 FATAL_ERROR)" \
@@ -52,6 +55,9 @@ stdenv.mkDerivation (finalAttrs: {
     runHook postInstall
   '';
 
+  nativeInstallCheckInputs = [ versionCheckHook ];
+  doInstallCheck = !stdenv.hostPlatform.isDarwin; # skip on Darwin - missing /libz.1.dylib in sandbox
+
   meta = {
     homepage = "https://github.com/lczech/gappa";
     description = "Toolkit for analyzing and visualizing phylogenetic (placement) data";