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crystfel: enable aarch64-* and external filter plugins on Darwin
This commit is contained in:
Philipp Middendorf
parent
fca0501c76
commit
da46337f0e
116
pkgs/applications/science/physics/crystfel/add-meson-build.patch
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116
pkgs/applications/science/physics/crystfel/add-meson-build.patch
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@ -0,0 +1,116 @@
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diff --git a/meson.build b/meson.build
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new file mode 100644
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index 0000000..8fc0631
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--- /dev/null
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+++ b/meson.build
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@@ -0,0 +1,110 @@
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+# Meson file for libccp4c (CCP4 core libraries, C part only)
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+project('libccp4c', 'c', version: '8.0.0', meson_version: '>=0.49.0', license: 'LGPL-3.0-or-later')
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+
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+cc = meson.get_compiler('c')
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+mdep = cc.find_library('m', required: false)
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+
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+# Note that the source code assumes that datadir='share'.
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+# If it is not, programs using the library will not be able
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+# to find 'environ.def'.
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+datadir = get_option('datadir') / 'ccp4'
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+
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+add_project_arguments('-DPACKAGE_ROOT="@0@"'.format(get_option('prefix')), language: 'c')
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+add_project_arguments(
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+ cc.get_supported_arguments(
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+ '-Wno-uninitialized',
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+ '-Wno-unused-function',
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+ '-Wno-stringop-truncation',
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+ '-Wno-stringop-overflow',
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+ '-Wno-format-overflow',
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+ '-Wno-misleading-indentation',
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+ '-Wno-pointer-compare',
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+ ),
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+ language: 'c',
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+)
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+
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+# C library
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+libccp4c = library(
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+ 'ccp4c',
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+ 'ccp4/ccp4_array.c',
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+ 'ccp4/cmap_accessor.c',
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+ 'ccp4/cmap_open.c',
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+ 'ccp4/csymlib.c',
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+ 'ccp4/pack_c.c',
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+ 'ccp4/ccp4_general.c',
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+ 'ccp4/cmap_close.c',
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+ 'ccp4/cmap_skew.c',
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+ 'ccp4/cvecmat.c',
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+ 'ccp4/ccp4_parser.c',
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+ 'ccp4/cmap_data.c',
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+ 'ccp4/cmap_stats.c',
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+ 'ccp4/library_err.c',
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+ 'ccp4/ccp4_program.c',
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+ 'ccp4/cmap_header.c',
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+ 'ccp4/cmap_symop.c',
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+ 'ccp4/library_file.c',
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+ 'ccp4/ccp4_unitcell.c',
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+ 'ccp4/cmap_labels.c',
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+ 'ccp4/cmtzlib.c',
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+ 'ccp4/library_utils.c',
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+ dependencies: mdep,
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+ install: true,
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+)
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+
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+# CCP4 headers are included with prefix: <ccp4/header.h>
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+incdir = include_directories('.')
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+
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+install_headers(
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+ 'ccp4/ccp4_file_err.h',
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+ 'ccp4/ccp4_program.h',
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+ 'ccp4/ccp4_unitcell.h',
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+ 'ccp4/cmap_errno.h',
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+ 'ccp4/cmap_stats.h',
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+ 'ccp4/csymlib.h',
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+ 'ccp4/library_file.h',
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+ 'ccp4/ccp4_fortran.h',
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+ 'ccp4/ccp4_spg.h',
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+ 'ccp4/ccp4_utils.h',
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+ 'ccp4/cmap_header.h',
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+ 'ccp4/cmaplib.h',
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+ 'ccp4/cvecmat.h',
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+ 'ccp4/mtzdata.h',
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+ 'ccp4/ccp4_array.h',
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+ 'ccp4/ccp4_general.h',
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+ 'ccp4/ccp4_sysdep.h',
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+ 'ccp4/ccp4_vars.h',
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+ 'ccp4/cmap_labels.h',
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+ 'ccp4/cmaplib_f.h',
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+ 'ccp4/overview.h',
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+ 'ccp4/ccp4_errno.h',
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+ 'ccp4/ccp4_parser.h',
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+ 'ccp4/ccp4_types.h',
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+ 'ccp4/cmap_data.h',
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+ 'ccp4/cmap_skew.h',
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+ 'ccp4/cmtzlib.h',
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+ 'ccp4/pack_c.h',
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+ subdir: 'ccp4',
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+)
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+
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+# Data files
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+install_data(
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+ 'data/atomsf_electron.lib',
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+ 'data/atomsf.lib',
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+ 'data/atomsf_neutron.lib',
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+ 'data/syminfo.lib',
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+ 'data/symop.lib',
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+ install_dir: datadir,
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+)
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+
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+# pkg-config file
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+pkg = import('pkgconfig')
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+pkg.generate(
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+ libccp4c,
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+ filebase: 'libccp4c',
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+ description: 'CCP4 core C libraries',
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+)
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+
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+libccp4c_dep = declare_dependency(
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+ include_directories: incdir,
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+ link_with: libccp4c,
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+)
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@ -6,7 +6,6 @@
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, cmake
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, lz4
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, bzip2
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, gfortran
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, m4
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, hdf5
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, gsl
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@ -38,14 +37,12 @@
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let
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libccp4 = stdenv.mkDerivation rec {
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pname = "libccp4";
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version = "6.5.1";
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version = "8.0.0";
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src = fetchurl {
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# Original mirror, now times out
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# url = "ftp://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
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url = "https://deb.debian.org/debian/pool/main/libc/${pname}/${pname}_${version}.orig.tar.gz";
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sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8";
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url = "http://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
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hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";
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};
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nativeBuildInputs = [ gfortran m4 ];
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nativeBuildInputs = [ meson ninja ];
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buildInputs = [ hdf5 gsl ];
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configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];
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@ -53,15 +50,12 @@ let
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# libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility.
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# We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a
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# preprocessor flag.
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preBuild = ''
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makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"')
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export NIX_LDFLAGS="-L${gfortran.cc}/lib64 -L${gfortran.cc}/lib $NIX_LDFLAGS";
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'';
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makeFlags = [ "CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"" ];
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env.NIX_CFLAGS_COMPILE = "-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/ccp4/syminfo.lib\"";
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patches = [
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# This circumvents the original autoconf/CMake based build and uses meson instead
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./add-meson-build.patch
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./libccp4-use-hardcoded-syminfo-lib.patch
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./0002-fix-ftbfs-with-gcc-10.patch
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];
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};
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# This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult
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@ -143,10 +137,10 @@ let
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pname = "HDF5-External-Filter-Plugins";
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version = "0.1.0";
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src = fetchFromGitHub {
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owner = "nexusformat";
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owner = "spanezz";
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repo = pname;
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rev = "d469f175e5273c1d488e71a6134f84088f57d39c";
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sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9";
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rev = "master";
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hash = "sha256-Lkhhfhs0dIEplTAod1VBeO4vWH5/MIdfRvhAI3bCgD4=";
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};
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nativeBuildInputs = [ cmake ];
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@ -184,13 +178,14 @@ stdenv.mkDerivation rec {
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] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]
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++ lib.optionals stdenv.isDarwin [
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argp-standalone
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] ++ lib.optionals (stdenv.isDarwin && !stdenv.isAarch64) [
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memorymappingHook
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]
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# hdf5-external-filter-plugins doesn't link on Darwin
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++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ];
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++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];
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patches = [
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./link-to-argp-standalone-if-needed.patch
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./disable-fmemopen-on-aarch64-darwin.patch
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(fetchpatch {
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url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff";
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hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc=";
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@ -204,7 +199,7 @@ stdenv.mkDerivation rec {
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sed -i -e 's#execlp("mosflm"#execl("${mosflm}/bin/mosflm"#' libcrystfel/src/indexers/mosflm.c;
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'';
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postInstall = lib.optionalString (withBitshuffle && !stdenv.isDarwin) ''
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postInstall = lib.optionalString withBitshuffle ''
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for file in $out/bin/*; do
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wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins
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done
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@ -224,7 +219,7 @@ stdenv.mkDerivation rec {
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downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";
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license = licenses.gpl3Plus;
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maintainers = with maintainers; [ pmiddend ];
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platforms = [ "x86_64-linux" "x86_64-darwin" ];
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platforms = [ "x86_64-linux" "x86_64-darwin" "aarch64-linux" "aarch64-darwin" ];
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};
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}
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@ -0,0 +1,13 @@
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diff --git a/libcrystfel/src/image-cbf.c b/libcrystfel/src/image-cbf.c
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index b8f09a1f..f8a15c1b 100644
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--- a/libcrystfel/src/image-cbf.c
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+++ b/libcrystfel/src/image-cbf.c
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@@ -287,7 +287,7 @@ static float *read_cbf_data(const char *filename, int gz, int *w, int *h)
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} else {
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- #ifdef HAVE_ZLIB
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+ #if defined(HAVE_ZLIB) && !(defined(__aarch64__) && defined(__APPLE__))
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gzFile gzfh;
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int len_read;
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size_t len;
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