Merge pull request #298957 from Feyorsh/sage-dep

sage: fix dependencies on Darwin/Clang16

pkgs/applications/science/math/gfan/default.nix

···
 
   postPatch = lib.optionalString stdenv.cc.isClang ''
     substituteInPlace Makefile --replace "-fno-guess-branch-probability" ""
+
+    for f in $(find -name "*.h" -or -name "*.cpp"); do
+        substituteInPlace "$f" --replace-quiet "log2" "_log2"
+    done
   '';
 
   buildFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "CXX=${stdenv.cc.targetPrefix}c++" ];

pkgs/applications/science/math/sage/sage-env.nix

···
 , ecm
 , lcalc
 , rubiks
-, flintqs
 , blas
 , lapack
 , flint3
···
     ecm
     lcalc
     rubiks
-    flintqs
     jdk # only needed for `jmol` which may be replaced in the future
     less # needed to prevent transient test errors until https://github.com/ipython/ipython/pull/11864 is resolved
   ]

pkgs/applications/science/math/sage/sage-with-env.nix

···
 , gmp
 , gfan
 , python3
-, flintqs
 , eclib
 , ntl
 , ecm
···
     gfan
     maxima
     eclib
-    flintqs
     ntl
     ecm
   ];

pkgs/applications/science/math/singular/default.nix

···
 , doxygen
 , graphviz
 , latex2html
-# upstream generates docs with texinfo 4. later versions of texinfo
-# use letters instead of numbers for post-appendix chapters, and we
-# want it to match the upstream format because sage depends on it.
-, texinfo4
+, texinfo
 , texliveSmall
-, enableDocs ? true
+, enableDocs ? !stdenv.isDarwin
 , enableGfanlib ? true
 }:
 
···
     doxygen
     graphviz
     latex2html
-    texinfo4
+    texinfo
     texliveSmall
   ] ++ lib.optionals stdenv.isDarwin [ getconf ];
   depsBuildBuild = [ buildPackages.stdenv.cc ];

pkgs/development/libraries/fflas-ffpack/default.nix

···
   doCheck = true;
 
   meta = with lib; {
-    broken = stdenv.isDarwin;
     description = "Finite Field Linear Algebra Subroutines";
     mainProgram = "fflas-ffpack-config";
     license = licenses.lgpl21Plus;

pkgs/development/libraries/flint/3.nix

···
 { lib
 , stdenv
+, fetchpatch
 , fetchurl
 , gmp
 , mpfr
···
     url = "https://www.flintlib.org/flint-${version}.tar.gz";
     sha256 = "sha256-ezEaAFA6hjiB64F32+uEMi8pOZ89fXLzsaTJuh1XlLQ=";
   };
+
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/flintlib/flint/commit/e7d005c369754243cba32bd782ea2a5fc874fde5.diff";
+      hash = "sha256-IqEtYEpNVXfoTeerh/0ig+eDqUpAlGdBB3uO8ShYh3o=";
+    })
+  ];
 
   nativeBuildInputs = [
     autoconf

pkgs/development/libraries/fplll/default.nix

···
 { lib, stdenv
 , fetchFromGitHub
+, fetchpatch
 , pkg-config
 , gettext
 , autoreconfHook
···
     rev = version;
     sha256 = "sha256-taSS7jpVyjVfNe6kSuUDXMD2PgKmtG64V5MjZyQzorI=";
   };
+
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/fplll/fplll/commit/317cf70893eebfb2625da12e5377189908c36240.diff";
+      sha256 = "sha256-GbYSolBgv/he4QzjuRFdg93wHJABVHvA9x3PjpJTSRE=";
+    })
+  ];
 
   nativeBuildInputs = [
     pkg-config

pkgs/development/libraries/givaro/default.nix

···
       url = "https://github.com/linbox-team/givaro/commit/c7744bb133496cd7ac04688f345646d505e1bf52.patch";
       hash = "sha256-aAA5o8Va10v0Pqgcpx7qM0TAZiNQgXoR6N9xecj7tDA=";
     })
+    (fetchpatch {
+      name = "clang-16.patch";
+      url = "https://github.com/linbox-team/givaro/commit/a81d44b3b57c275bcb04ab00db79be02561deaa2.patch";
+      hash = "sha256-sSk+VWffoEjZRTJcHRISLHPyW6yuvI1u8knBOfxNUIE=";
+    })
   ];
 
   enableParallelBuilding = true;

pkgs/development/libraries/linbox/default.nix

···
 { lib, stdenv
 , fetchFromGitHub
+, fetchpatch
 , autoreconfHook
 , givaro
 , pkg-config
···
     rev = "v${version}";
     sha256 = "sha256-mW84a98KPLqcHMjX3LIYTmVe0ngUdz6RJLpoDaAqKU8=";
   };
+
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/linbox-team/linbox/commit/4be26e9ef0eaf36a9909e5008940e8bf7dc625b6.patch";
+      sha256 = "PX0Tik7blXOV2vHUq92xMxaADkNoNGiax4qrjQyGK6U=";
+    })
+  ];
 
   nativeBuildInputs = [
     autoreconfHook

pkgs/development/libraries/science/math/flintqs/default.nix

···
-{ lib, stdenv
-, fetchFromGitHub
-, autoreconfHook
-, gmp
-}:
-
-stdenv.mkDerivation rec {
-  version = "1.0";
-  pname = "flintqs";
-
-  src = fetchFromGitHub {
-    owner = "sagemath";
-    repo = "FlintQS";
-    rev = "v${version}";
-    sha256 = "1f0lnayz6j6qgasx8pbq61d2fqam0wwhsmh6h15l4vq58l1vvbwj";
-  };
-
-  preAutoreconf = ''
-    touch ChangeLog
-  '';
-
-  buildInputs = [
-    gmp
-  ];
-
-  nativeBuildInputs = [
-    autoreconfHook
-  ];
-
-  doCheck = true;
-
-  meta = with lib; {
-    description = "Highly optimized multi-polynomial quadratic sieve for integer factorization";
-    homepage = "https://github.com/sagemath/FlintQS";
-    license = with licenses; [ gpl2 ];
-    maintainers = teams.sage.members;
-    mainProgram = "QuadraticSieve";
-    platforms = platforms.all;
-  };
-}

pkgs/development/libraries/science/math/m4rie/default.nix

···
     m4ri
   ];
 
+  # does not compile correctly with -O2 on LLVM clang; see
+  # https://bitbucket.org/malb/m4rie/issues/23/trying-to-compile-on-apple-m1
+  makeFlags = [] ++ lib.optionals stdenv.isDarwin [ "CFLAGS=-O0" ];
   nativeBuildInputs = [
     autoreconfHook
   ];
···
     license = licenses.gpl2Plus;
     maintainers = teams.sage.members;
     platforms = platforms.unix;
-    # never built on aarch64-darwin since first introduction in nixpkgs
-    broken = stdenv.isDarwin && stdenv.isAarch64;
   };
 }

pkgs/development/libraries/science/math/rubiks/default.nix

···
 , fetchurl
 , fetchpatch
 , coreutils
+, dos2unix
 }:
 
 stdenv.mkDerivation rec {
···
     "PREFIX=$(out)"
   ];
 
+  nativeBuildInputs = [ dos2unix ];
+
+  prePatch = ''
+    find ./dietz/ -type f -exec dos2unix {} \;
+  '';
+
   patches = [
     # Fix makefiles which use all the variables in all the wrong ways and
     # hardcode values for some variables.
     (fetchpatch {
-      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-cu2-Makefile.patch";
-      sha256 = "1ry3w1mk9q4jqd91zlaa1bdiiplld4hpfjaldbhlmzlgrrc99qmq";
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/dietz-cu2-Makefile.patch";
+      sha256 = "bRU7MJ/6BgCp2PUqZOragJhm38Q3E8ShStXQIYwIjvw=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/dietz-mcube-Makefile.patch";
+      sha256 = "f53z4DogXKax1vUNkraOTt3TQ4bvT7CdQK/hOaaBS38=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/dietz-solver-Makefile.patch";
+      sha256 = "7gMC8y9elyIy2KvXYcp7YjPBNqn9PVhUle+/GrYAAdE=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/reid-Makefile.patch";
+      sha256 = "rp3SYtx02vVBtSlg1vJpdIoXNcdBNKDLCLqLAKwOYeQ=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-1-rubiks-includes.patch";
+      sha256 = "QYJ1KQ73HTEGY/beMVbcU215g/B8rHDjYD1YM2WZ7sk=";
     })
     (fetchpatch {
-      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-mcube-Makefile.patch";
-      sha256 = "0zsbh6k3kqdg82fv0kzghr1x7pafisv943gmssqscp107bhg77bz";
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-2-rubiks-ansi-c.patch";
+      sha256 = "Rnu7uphE9URxnbg2K8mkymnB61magweH+WxVWR9JC4s=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-3-rubiks-prototypes.patch";
+      sha256 = "Wi038g+y7No1TNMiITtAdipjRi0+g6h0Sspslm5rZGU=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-4-rubiks-longtype.patch";
+      sha256 = "6pNuxFM69CZ/TQGZfHXLlCN5g5lf3RiYYZKzMvLJwkw=";
     })
     (fetchpatch {
-      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-solver-Makefile.patch";
-      sha256 = "0vhw70ylnmydgjhwx8jjlb2slccj4pfqn6vzirkyz1wp8apsmfhp";
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-5-rubiks-signed.patch";
+      sha256 = "CCGXBMYvSjTm4YKQZAQMi6pWGjyHDYYQzdMZDSW2vFE=";
     })
     (fetchpatch {
-      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/reid-Makefile.patch";
-      sha256 = "1r311sn012xs135s0d21qwsig2kld7rdcq19nm0zbnklviid57df";
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-6-rubiks-attributes.patch";
+      sha256 = "RhlzMb33iaLfeBoF7Y0LIgEzOB/EC+AoWMSkRPCICaU=";
     })
   ];
 

pkgs/development/libraries/tachyon/default.nix

···
          # see https://github.com/NixOS/nixpkgs/pull/117465
          if stdenv.hostPlatform.system == "aarch64-linux"  then "linux-arm"     else
          if stdenv.hostPlatform.system == "armv7l-linux"   then "linux-arm"     else
+         if stdenv.hostPlatform.system == "aarch64-darwin" then "macosx"        else
          if stdenv.hostPlatform.system == "x86_64-darwin"  then "macosx-thr"    else
          if stdenv.hostPlatform.system == "i686-darwin"    then "macosx-64-thr" else
          if stdenv.hostPlatform.system == "i686-cygwin"    then "win32"         else

pkgs/development/python-modules/fpylll/default.nix

···
       url = "https://github.com/fplll/fpylll/commit/fc432b21fa7e4b9891f5b761b3539989eb958f2b.diff";
       hash = "sha256-+UidQ5xnlmjeVeVvR4J2zDzAuXP5LUPXCh4RP4o9oGA=";
     })
+    (fetchpatch {
+      url = "https://github.com/fplll/fpylll/commit/cece9c9b182dc3ac2c9121549cb427ccf4c4a9fe.diff";
+      hash = "sha256-epJb8gorQ7gEEylZ2yZFdM9+EZ4ys9mUUUPiJ2D0VOM=";
+    })
   ];
 
   nativeBuildInputs = [

pkgs/top-level/aliases.nix

···
   fitnesstrax = throw "fitnesstrax was removed from nixpkgs because it disappeared upstream and no longer compiles"; # added 2023-07-04
   flashrom-stable = flashprog;   # Added 2024-03-01
   flatbuffers_2_0 = flatbuffers; # Added 2022-05-12
+  flintqs = throw "FlintQS has been removed due to lack of maintenance and security issues; use SageMath or FLINT instead"; # Added 2024-03-21
   flutter2 = throw "flutter2 has been removed because it isn't updated anymore, and no packages in nixpkgs use it. If you still need it, use flutter.mkFlutter to get a custom version"; # Added 2023-07-03
   flutter37 = throw "flutter37 has been removed because it isn't updated anymore, and no packages in nixpkgs use it. If you still need it, use flutter.mkFlutter to get a custom version"; # Added 2023-07-03
   foldingathome = fahclient; # Added 2020-09-03

pkgs/top-level/all-packages.nix

···
 
   ecos = callPackage ../development/libraries/science/math/ecos { };
 
-  flintqs = callPackage ../development/libraries/science/math/flintqs { };
-
   getdp = callPackage ../applications/science/math/getdp { };
 
   gurobi = callPackage ../applications/science/math/gurobi {