flint, ntl: Fix pkgsStatic builds, clean-up derivations (#445050)

pkgs/by-name/fl/flint/checkPhase.patch

···
+https://github.com/flintlib/flint/pull/2411
+
+From 9957b17e6b08bd57790f7da1344b4d92eefc0b38 Mon Sep 17 00:00:00 2001
+From: Ross Smyth <[e-mail]>
+Date: Sun, 21 Sep 2025 15:58:57 -0400
+Subject: [PATCH] Fix duplicate symbols linker error
+
+When I run `make check` I get linker errors without
+this patch
+---
+ src/double_interval.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/double_interval.h b/src/double_interval.h
+index a423257db2..5f685c283f 100644
+--- a/src/double_interval.h
++++ b/src/double_interval.h
+@@ -13,7 +13,7 @@
+ #define DOUBLE_INTERVAL_H
+ 
+ #ifdef DOUBLE_INTERVAL_INLINES_C
+-#define DOUBLE_INTERVAL_INLINE
++#define DOUBLE_INTERVAL_INLINE static
+ #else
+ #define DOUBLE_INTERVAL_INLINE static inline
+ #endif

pkgs/by-name/ms/msolve/package.nix

···
   stdenv,
   fetchFromGitHub,
   autoreconfHook,
-  flint3,
+  flint,
   gmp,
   mpfr,
   llvmPackages,
···
   ];
 
   buildInputs = [
-    flint3
+    flint
     gmp
     mpfr
   ]

pkgs/by-name/no/normaliz/package.nix

···
   fetchFromGitHub,
   autoreconfHook,
   gmpxx,
-  flint3,
+  flint,
   nauty,
 }:
 
···
 
   buildInputs = [
     gmpxx
-    flint3
+    flint
     nauty
   ];
 

pkgs/by-name/nt/ntl/package.nix

···
 
 assert withGf2x -> gf2x != null;
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "ntl";
   version = "11.5.1";
 
   src = fetchurl {
-    url = "http://www.shoup.net/ntl/ntl-${version}.tar.gz";
-    sha256 = "sha256-IQ0GwxMGy8bq9oFEU8Vsd22djo3zbXTrMG9qUj0caoo=";
+    url = "http://www.shoup.net/ntl/ntl-${finalAttrs.version}.tar.gz";
+    hash = "sha256-IQ0GwxMGy8bq9oFEU8Vsd22djo3zbXTrMG9qUj0caoo=";
   };
 
+  strictDeps = true;
+  depsBuildBuild = [
+    perl # needed for ./configure
+  ];
   buildInputs = [
     gmp
   ];
 
-  nativeBuildInputs = [
-    perl # needed for ./configure
-  ];
-
-  sourceRoot = "${pname}-${version}/src";
+  sourceRoot = "ntl-${finalAttrs.version}/src";
 
   enableParallelBuilding = true;
 
···
   configurePlatforms = [ ];
 
   # reference: http://shoup.net/ntl/doc/tour-unix.html
+  dontAddStaticConfigureFlags = true; # perl config doesn't understand it.
   configureFlags = [
     "DEF_PREFIX=$(out)"
-    "SHARED=on" # genereate a shared library (as well as static)
     "NATIVE=off" # don't target code to current hardware (reproducibility, portability)
     "TUNE=${
       if tune then
···
         "generic" # "chooses options that should be OK for most platforms"
     }"
     "CXX=${stdenv.cc.targetPrefix}c++"
+    "AR=${stdenv.cc.targetPrefix}ar"
+  ]
+  ++ lib.optionals (!stdenv.hostPlatform.isStatic) [
+    "SHARED=on" # genereate a shared library
   ]
   ++ lib.optionals withGf2x [
     "NTL_GF2X_LIB=on"
     "GF2X_PREFIX=${gf2x}"
   ];
 
+  enableParallelChecking = true;
   doCheck = true; # takes some time
 
-  meta = with lib; {
+  meta = {
     description = "Library for doing Number Theory";
     longDescription = ''
       NTL is a high-performance, portable C++ library providing data
···
     homepage = "http://www.shoup.net/ntl/";
     # also locally at "${src}/doc/tour-changes.html";
     changelog = "https://www.shoup.net/ntl/doc/tour-changes.html";
-    teams = [ teams.sage ];
-    license = licenses.gpl2Plus;
-    platforms = platforms.all;
+    teams = [ lib.teams.sage ];
+    license = lib.licenses.gpl2Plus;
+    platforms = lib.platforms.all;
     # Does not cross compile
     # https://github.com/libntl/ntl/issues/8
     broken = !(stdenv.buildPlatform.canExecute stdenv.hostPlatform);
   };
-}
+})

pkgs/by-name/pp/pplite/package.nix

···
   lib,
   fetchurl,
   fetchpatch,
-  flint3,
+  flint,
   gmp,
 }:
 
···
   };
 
   buildInputs = [
-    flint3
+    flint
     gmp
   ];
 

pkgs/by-name/s7/s7/package.nix

···
   fetchFromGitLab,
   stdenv,
 
-  flint3,
+  flint,
   gmp,
   libmpc,
   mpfr,
···
   };
 
   buildInputs =
-    lib.optional withArb flint3
+    lib.optional withArb flint
     ++ lib.optionals withGMP [
       gmp
       mpfr

pkgs/by-name/sa/sage/package.nix

···
       self: super: {
         # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
         sagelib = self.callPackage ./sagelib.nix {
-          inherit flint3;
+          inherit flint;
           inherit sage-src env-locations singular;
           inherit (maxima) lisp-compiler;
           linbox = pkgs.linbox;
···
       python3
       singular
       palp
-      flint3
+      flint
       pythonEnv
       maxima
       ;
···
       extraLibs = pythonRuntimeDeps;
     }; # make the libs accessible
 
-  singular = pkgs.singular.override { inherit flint3; };
+  singular = pkgs.singular.override { inherit flint; };
 
   maxima = pkgs.maxima-ecl.override {
     lisp-compiler = pkgs.ecl.override {
···
   # openblas instead of openblasCompat. Apparently other packages somehow use flints
   # blas when it is available. Alternative would be to override flint to use
   # openblasCompat.
-  flint3 = pkgs.flint3.override { withBlas = false; };
+  flint = pkgs.flint.override { withBlas = false; };
 
   # Multiple palp dimensions need to be available and sage expects them all to be
   # in the same folder.

pkgs/by-name/sa/sage/sage-env.nix

···
   rubiks,
   blas,
   lapack,
-  flint3,
+  flint,
   gmp,
   mpfr,
   zlib,
···
         export LDFLAGS='${
           lib.concatStringsSep " " (
             map (pkg: "-L${pkg}/lib") [
-              flint3
+              flint
               gap
               glpk
               gmp
···
               singular
               gmp.dev
               glpk
-              flint3
+              flint
               gap
               mpfr.dev
             ]

pkgs/by-name/sa/sage/sagelib.nix

···
   eclib,
   ecm,
   fflas-ffpack,
-  flint3,
+  flint,
   gap,
   giac,
   givaro,
···
     eclib
     ecm
     fflas-ffpack
-    flint3
+    flint
     gap
     giac
     givaro

pkgs/by-name/si/singular/package.nix

···
   sharutils,
   file,
   getconf,
-  flint3,
+  flint,
   ntl,
   mpfr,
   cddlib,
···
   configureFlags = [
     "--enable-gfanlib"
     "--with-ntl=${ntl}"
-    "--with-flint=${flint3}"
+    "--with-flint=${flint}"
   ]
   ++ lib.optionals enableDocs [
     "--enable-doc-build"
···
   buildInputs = [
     # necessary
     gmp
-    flint3
+    flint
     # by upstream recommended but optional
     ncurses
     readline

pkgs/by-name/sy/symengine/package.nix

···
   fetchFromGitHub,
   cmake,
   gmp,
-  flint3,
+  flint,
   mpfr,
   libmpc,
   withShared ? true,
···
 
   buildInputs = [
     gmp
-    flint3
+    flint
     mpfr
     libmpc
   ];

pkgs/development/libraries/flint/3.nix pkgs/by-name/fl/flint/package.nix

···
   lib,
   stdenv,
   fetchurl,
-  gmp,
-  mpfr,
-  ntl,
+  fetchpatch,
   windows,
   autoconf,
   automake,
   gettext,
   libtool,
-  openblas ? null,
+  gmp,
+  mpfr,
+  ntl,
   blas,
   lapack,
+  boehmgc,
+  openblas ? null,
   withBlas ? true,
   withNtl ? !ntl.meta.broken,
+  withGc ? false,
 }:
 
 assert
   withBlas
   -> openblas != null && blas.implementation == "openblas" && lapack.implementation == "openblas";
 
-stdenv.mkDerivation rec {
-  pname = "flint3";
+stdenv.mkDerivation (finalAttrs: {
+  pname = "flint";
   version = "3.3.1";
 
   src = fetchurl {
-    url = "https://flintlib.org/download/flint-${version}.tar.gz";
+    url = "https://flintlib.org/download/flint-${finalAttrs.version}.tar.gz";
     hash = "sha256-ZNcOUTB2z6lx4EELWMHaXTURKRPppWtE4saBtFnT6vs=";
   };
 
+  patches = [
+    # Remove once/if https://github.com/flintlib/flint/pull/2411 is merged
+    # Required or else during the check phase the build fails while
+    # linking a test due to duplicate symbol errors
+    ./checkPhase.patch
+  ];
+
+  strictDeps = true;
   nativeBuildInputs = [
     autoconf
     automake
···
   ++ lib.optionals withNtl [
     ntl
   ]
+  ++ lib.optionals withGc [
+    boehmgc
+  ]
   ++ lib.optionals stdenv.hostPlatform.isMinGW [
     windows.pthreads
   ];
···
   ]
   ++ lib.optionals withNtl [
     "--with-ntl=${ntl}"
+  ]
+  ++ lib.optionals withGc [
+    "--with-gc=${boehmgc}"
   ];
 
   enableParallelBuilding = true;
-
+  enableParallelChecking = true;
   doCheck = true;
 
-  meta = with lib; {
+  meta = {
     description = "Fast Library for Number Theory";
-    license = licenses.lgpl3Plus;
-    maintainers = with maintainers; [ smasher164 ];
-    teams = [ teams.sage ];
-    platforms = platforms.all;
+    license = lib.licenses.lgpl3Plus;
+    maintainers = [ lib.maintainers.smasher164 ];
+    teams = [ lib.teams.sage ];
+    platforms = lib.platforms.all;
     homepage = "https://www.flintlib.org/";
     downloadPage = "https://www.flintlib.org/downloads.html";
   };
-}
+})

pkgs/development/ocaml-modules/apron/default.nix

···
   findlib,
   camlidl,
   mlgmpidl,
-  flint3,
+  flint,
   pplite,
 }:
 
···
     mpfr
     ppl
     camlidl
-    flint3
+    flint
     pplite
   ];
   propagatedBuildInputs = [ mlgmpidl ];

pkgs/development/ocaml-modules/mopsa/default.nix

···
   clang,
   libclang,
   libllvm,
-  flint3,
+  flint,
   mpfr,
   pplite,
   ocaml,
···
   buildInputs = [
     arg-complete
     camlidl
-    flint3
+    flint
     libclang
     mpfr
     pplite

pkgs/development/r-modules/default.nix

···
       pkg-config
       gmp.dev
       mpfr.dev
-      flint3
+      flint
     ];
     fingerPro = [ pkgs.gsl ];
     Formula = [ pkgs.gmp ];

pkgs/top-level/aliases.nix

···
   flashrom-stable = flashprog; # Added 2024-03-01
   flatbuffers_2_0 = flatbuffers; # Added 2022-05-12
   flatcam = throw "flatcam has been removed because it is unmaintained since 2022 and doesn't support Python > 3.10"; # Added 2025-01-25
+  flint3 = flint; # Added 2025-09-21
   floorp = throw "floorp has been replaced with floorp-bin, as building from upstream sources has become unfeasible starting with version 12.x"; # Added 2025-09-06
   floorp-unwrapped = throw "floorp-unwrapped has been replaced with floorp-bin-unwrapped, as building from upstream sources has become unfeasible starting with version 12.x"; # Added 2025-09-06
   flow-editor = flow-control; # Added 2025-03-05

pkgs/top-level/all-packages.nix

···
   };
   fftwMpi = fftw.override { enableMpi = true; };
 
-  flint = flint3;
-
-  flint3 = callPackage ../development/libraries/flint/3.nix { };
-
   fltk13 = callPackage ../development/libraries/fltk { };
   fltk14 = callPackage ../development/libraries/fltk/1.4.nix { };
   fltk13-minimal = fltk13.override {