Merge pull request #218968 from pmiddend/crystfel-aarch64

Description: Fixing argument mismatches in Fortran code, addressing #957430.

Author: Andrius Merkys <merkys@debian.org>

Forwarded: ccp4-dev@dl.ac.uk

--- a/fortran/pack_f.f

+++ b/fortran/pack_f.f

@@ -106,7 +106,7 @@

          endif

  10   continue

       filnarray(len(filn) + 1) = 0

-      call pack_wordimage_f(data, x, y, filnarray)

+      call pack_longimage_f(data, x, y, filnarray)

       return

       end

@@ -138,7 +138,7 @@

          endif

  10   continue

       filnarray(len(filn) + 1) = 0

-      call v2pack_wordimage_f(data, x, y, filnarray)

+      call v2pack_longimage_f(data, x, y, filnarray)

       return

       end

--- a/fortran/lgglib.f

+++ b/fortran/lgglib.f

@@ -1236,7 +1236,7 @@

       B3(2) = XYZ(2) * CELL(2)

       B3(3) = XYZ(3) * CELL(3)

 C

-      CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)

+      CALL matmult(3,3,3,1,ORTH,B3,XYZ)

       END

 c

 c

@@ -1274,7 +1274,7 @@

       B3(1) = XYZ(1)

       B3(2) = XYZ(2)

       B3(3) = XYZ(3)

-      CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)

+      CALL matmult(3,3,3,1,ORTH,B3,XYZ)

       END

       character*80 function getnam(filnam)

       character*(*) filnam

, fetchurl

, fetchFromGitHub

, fetchpatch

, fetchzip

, cmake

, lz4

, bzip2

, gfortran

, m4

, hdf5

, gsl

let

  libccp4 = stdenv.mkDerivation rec {

    pname = "libccp4";

    version = "6.5.1";

    version = "8.0.0";

    src = fetchurl {

      # Original mirror, now times out

      # url = "ftp://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";

      url = "https://deb.debian.org/debian/pool/main/libc/${pname}/${pname}_${version}.orig.tar.gz";

      sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8";

      url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";

      hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";

    };

    nativeBuildInputs = [ gfortran m4 ];

    nativeBuildInputs = [ meson ninja ];

    buildInputs = [ hdf5 gsl ];

    configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];

    # libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility.

    # We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a

    # preprocessor flag.

    preBuild = ''

      makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"')

      export NIX_LDFLAGS="-L${gfortran.cc}/lib64 -L${gfortran.cc}/lib $NIX_LDFLAGS";

    '';

    makeFlags = [ "CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"" ];

    env.NIX_CFLAGS_COMPILE = "-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/ccp4/syminfo.lib\"";

    patches = [

      ./libccp4-use-hardcoded-syminfo-lib.patch

      ./0002-fix-ftbfs-with-gcc-10.patch

    ];

    postPatch =

      let

        mesonPatch = fetchzip {

          url = "https://wrapdb.mesonbuild.com/v2/libccp4c_8.0.0-1/get_patch#somefile.zip";

          hash = "sha256-ohskfKh+972Pl56KtwAeWwHtAaAFNpCzz5vZBAI/vdU=";

        };

      in

      ''

        cp ${mesonPatch}/meson.build .

      '';

  };

  # This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult

  # since the build process is very hard-coded for a specific machine, architecture, and libraries.

    src = fetchFromGitHub {

      owner = "nexusformat";

      repo = pname;

      rev = "d469f175e5273c1d488e71a6134f84088f57d39c";

      sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9";

      rev = "49e3b65eca772bca77af13ba047d8b577673afba";

      hash = "sha256-bEzfWdZuHmb0PDzCqy8Dey4tLtq+4coO0sT0GzqrTYI=";

    };

    patches = [

      (fetchpatch {

        url = "https://github.com/spanezz/HDF5-External-Filter-Plugins/commit/6b337fe36da97a3ef72354393687ce3386c0709d.patch";

        hash = "sha256-wnBEdL/MjEyRHPwaVtuhzY+DW1AFeaUQUmIXh+JaRHo=";

      })

    ];

    nativeBuildInputs = [ cmake ];

    buildInputs = [ hdf5 lz4 bzip2 ];

  ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]

  ++ lib.optionals stdenv.isDarwin [

    argp-standalone

  ] ++ lib.optionals (stdenv.isDarwin && !stdenv.isAarch64) [

    memorymappingHook

  ]

  # hdf5-external-filter-plugins doesn't link on Darwin

  ++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ];

  ++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];

  patches = [

    ./link-to-argp-standalone-if-needed.patch

    ./disable-fmemopen-on-aarch64-darwin.patch

    (fetchpatch {

      url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff";

      hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc=";

    sed -i -e 's#execlp("mosflm"#execl("${mosflm}/bin/mosflm"#' libcrystfel/src/indexers/mosflm.c;

  '';

  postInstall = lib.optionalString (withBitshuffle && !stdenv.isDarwin) ''

  postInstall = lib.optionalString withBitshuffle ''

    for file in $out/bin/*; do

      wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins

    done

    downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";

    license = licenses.gpl3Plus;

    maintainers = with maintainers; [ pmiddend ];

    platforms = [ "x86_64-linux" "x86_64-darwin" ];

    platforms = platforms.unix;

  };

}

diff --git a/libcrystfel/src/image-cbf.c b/libcrystfel/src/image-cbf.c

index b8f09a1f..f8a15c1b 100644

--- a/libcrystfel/src/image-cbf.c

+++ b/libcrystfel/src/image-cbf.c

@@ -287,7 +287,7 @@ static float *read_cbf_data(const char *filename, int gz, int *w, int *h)

 	} else {

-		#ifdef HAVE_ZLIB

+		#if defined(HAVE_ZLIB) && !(defined(__aarch64__) && defined(__APPLE__))

 		gzFile gzfh;

 		int len_read;

 		size_t len;