minc_tools: migrate to by-name (#512527)

pkgs/by-name/mi/minc_tools/package.nix

@@ -6,14 +6,17 @@
   makeWrapper,
   flex,
   bison,
-  perl,
-  TextFormat,
+  perlPackages,
   libminc,
   libjpeg,
   nifticlib,
   zlib,
 }:
 
+let
+  inherit (perlPackages) perl TextFormat;
+in
+
 stdenv.mkDerivation {
   pname = "minc-tools";
   version = "2.3.06-unstable-2024-11-28";
@@ -30,6 +33,16 @@ stdenv.mkDerivation {
   # Upstream issue: https://github.com/BIC-MNI/minc-tools/issues/123
   postPatch = ''
     substituteInPlace CMakeLists.txt --replace-fail "SET CMP0026 OLD" "SET CMP0026 NEW"
+
+    # FIX: Rename the colliding NAN token to MINC_NAN in the flex/bison parser files
+    sed -i 's/\bNAN\b/MINC_NAN/g' progs/minccalc/gram.y progs/minccalc/lex.l
+
+    # FIX: Rename the colliding fdiv function to avoid glibc 2.42 <math.h> conflicts
+    sed -i 's/\bfdiv\b/minc_fdiv/g' progs/mincblob/mincblob.c
+
+    # FIX: Remove legacy unprototyped C declarations that break under GCC 15 strictness
+    sed -i 's/, \*mat_create()//g' conversion/minctoecat/ecat_write.c
+    sed -i 's/\*fopen(), //g' conversion/minctoecat/ecat_write.c
   '';
 
   nativeBuildInputs = [

pkgs/top-level/all-packages.nix

@@ -10181,10 +10181,6 @@ with pkgs;
     useRx3d = true;
   };
 
-  minc_tools = callPackage ../applications/science/biology/minc-tools {
-    inherit (perlPackages) perl TextFormat;
-  };
-
   raxml-mpi = raxml.override { useMpi = true; };
 
   ### SCIENCE/MACHINE LEARNING