Unverified Commit 3502abb8 authored by Aleksana's avatar Aleksana Committed by GitHub
Browse files

[Backport release-25.11] {ebtks,n3,inormalize}: update and fix build with CMake >= 4 (#466531)

parents a62fea28 dbc45029

pkgs/by-name/ar/arguments/package.nix

+12 −17
Original line number Diff line number Diff line
@@ -5,36 +5,31 @@ 
  cmake,

}:



stdenv.mkDerivation rec {

stdenv.mkDerivation {

  pname = "arguments";

  version = "unstable-2015-11-30";



  owner = "BIC-MNI";

  version = "1.4.60-unstable-2023-01-18";



  src = fetchFromGitHub {

    inherit owner;

    owner = "BIC-MNI";

    repo = "arguments";

    rev = "b3aad97f6b6892cb8733455d0d448649a48fa108";

    sha256 = "1ar8lm1w1jflz3vdmjr5c4x6y7rscvrj78b8gmrv79y95qrgzv6s";

    rev = "ed7c4c126b800d4312469e3cd3999a31e96fed0e";

    hash = "sha256-1QxVZ17zSqx5P9nGAXHf7Fj86fuGn17PllGXFqyYJUo=";

  };



  nativeBuildInputs = [ cmake ];



  #cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBICPL_DIR=${bicpl}/lib" ];



  doCheck = false;

  # internal_volume_io.h: No such file or directory

  doCheck = false; # test binary not built by cmake



  postPatch = ''

    substituteInPlace CMakeLists.txt \

      --replace-fail "CMAKE_MINIMUM_REQUIRED(VERSION 2.6)" "cmake_minimum_required(VERSION 3.10)"

      --replace-fail "CMAKE_MINIMUM_REQUIRED(VERSION 3.1)" "cmake_minimum_required(VERSION 3.10)"

  '';



  meta = with lib; {

    homepage = "https://github.com/${owner}/arguments";

  meta = {

    homepage = "https://github.com/BIC-MNI/arguments";

    description = "Library for argument handling for MINC programs";

    maintainers = with maintainers; [ bcdarwin ];

    platforms = platforms.unix;

    license = licenses.gpl2Plus;

    maintainers = with lib.maintainers; [ bcdarwin ];

    platforms = lib.platforms.unix;

    license = lib.licenses.gpl2Plus;

  };

}

pkgs/by-name/eb/ebtks/package.nix

+7 −17
Original line number Diff line number Diff line
@@ -8,35 +8,25 @@ 


stdenv.mkDerivation {

  pname = "ebtks";

  version = "unstable-2017-09-23";

  version = "1.6.40-unstable-2025-05-06";



  src = fetchFromGitHub {

    owner = "BIC-MNI";

    repo = "EBTKS";

    rev = "67e4e197d8a32d6462c9bdc7af44d64ebde4fb5c";

    hash = "sha256-+MIRE2NdRH7IQrstK3WRqft6l9I+UGD6j0G7Q6LhOKg=";

    rev = "7317b54d79bd7d80b5361dc44a7966709d9a8b36";

    hash = "sha256-kp3uPvsIker8918stsVUdMC72A6Jz0K7r5PFDLbWqNo=";

  };



  # error: use of undeclared identifier 'finite'; did you mean 'isfinite'?

  postPatch = ''

    substituteInPlace templates/EBTKS/SimpleArray.h \

      --replace "#define FINITE(x) finite(x)" "#define FINITE(x) isfinite(x)"

  ''

  # error: ISO C++17 does not allow 'register' storage class specifier

  + ''

    find . -type f -exec sed -i -e 's/register //g' {} +

  '';



  nativeBuildInputs = [ cmake ];

  buildInputs = [ libminc ];



  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];



  meta = with lib; {

  meta = {

    homepage = "https://github.com/BIC-MNI/EBTKS";

    description = "Library for working with MINC files";

    maintainers = with maintainers; [ bcdarwin ];

    platforms = platforms.unix;

    license = licenses.free;

    maintainers = with lib.maintainers; [ bcdarwin ];

    platforms = lib.platforms.unix;

    license = lib.licenses.free;

  };

}

pkgs/by-name/in/inormalize/lgmask-interp.patch

deleted100644 → 0
+0 −10
Original line number Diff line number Diff line 
diff --git a/lgmask.in b/lgmask.in

index 17dbe4d..2195d91 100644

--- a/lgmask.in

+++ b/lgmask.in

@@ -1,4 +1,4 @@

-#! @PERL@

+#! /usr/bin/env perl

 

 #---------------------------------------------------------------------------

 #@COPYRIGHT :

pkgs/by-name/in/inormalize/nu_correct_norm-interp.patch

deleted100644 → 0
+0 −10
Original line number Diff line number Diff line 
diff --git a/nu_correct_norm.in b/nu_correct_norm.in

index 1dc84ac..1bc6235 100644

--- a/nu_correct_norm.in

+++ b/nu_correct_norm.in

@@ -1,4 +1,4 @@

-#! @PERL@

+#! /usr/bin/perl

  

 #---------------------------------------------------------------------------

 #@COPYRIGHT :

pkgs/by-name/in/inormalize/package.nix

+13 −17
Original line number Diff line number Diff line
@@ -11,38 +11,34 @@ 


stdenv.mkDerivation {

  pname = "inormalize";

  version = "unstable-2014-10-21";

  version = "1.2.00-unstable-2023-01-19";



  src = fetchFromGitHub {

    owner = "BIC-MNI";

    repo = "inormalize";

    rev = "79cea9cdfe7b99abfd40afda89ab2253b596ad2f";

    sha256 = "1ahqv5q0ljvji99a5q8azjkdf6bgp6nr8lwivkqwqs3jm0k5clq7";

    rev = "4928e573165d76551c3d273ccf0c46f4fbab11fc";

    hash = "sha256-ZxTsPBsaL/5BWC7ew57um8LPb96hytI30JE8saBBNw8=";

  };



  patches = [

    ./lgmask-interp.patch

    ./nu_correct_norm-interp.patch

  ];



  postPatch = ''

    substituteInPlace inormalize.cc \

      --replace "clamp" "::clamp"

    substituteInPlace CMakeLists.txt \

      --replace-fail "CMAKE_MINIMUM_REQUIRED(VERSION 3.1)" "CMAKE_MINIMUM_REQUIRED(VERSION 3.10)"

  '';



  nativeBuildInputs = [

    cmake

    makeWrapper

  ];



  buildInputs = [

    libminc

    ebtks

  ];

  propagatedBuildInputs = with perlPackages; [

  ]

  ++ (with perlPackages; [

    perl

    GetoptTabular

    MNI-Perllib

  ];

  ]);



  cmakeFlags = [

    "-DLIBMINC_DIR=${libminc}/lib/cmake"
@@ -55,11 +51,11 @@ stdenv.mkDerivation { 
    done

  '';



  meta = with lib; {

  meta = {

    homepage = "https://github.com/BIC-MNI/inormalize";

    description = "Program to normalize intensity of MINC files";

    maintainers = with maintainers; [ bcdarwin ];

    platforms = platforms.unix;

    license = licenses.free;

    maintainers = with lib.maintainers; [ bcdarwin ];

    platforms = lib.platforms.unix;

    license = lib.licenses.free;

  };

}