netcdf: 4.9.2 -> 4.9.3 (#380393)

pkgs/applications/science/biology/minc-tools/default.nix

@@ -50,6 +50,8 @@ stdenv.mkDerivation rec {
     "-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti"
   ];
 
+  env.NIX_CFLAGS_COMPILE = "-D_FillValue=NC_FillValue";
+
   postFixup = ''
     for prog in minccomplete minchistory mincpik; do
       wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB
@@ -62,5 +64,6 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
     license = licenses.free;
+    broken = stdenv.hostPlatform.isDarwin;
   };
 }

pkgs/by-name/ne/netcdf/package.nix

@@ -20,11 +20,11 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "netcdf" + lib.optionalString mpiSupport "-mpi";
-  version = "4.9.2";
+  version = "4.9.3";
 
   src = fetchurl {
     url = "https://downloads.unidata.ucar.edu/netcdf-c/${version}/netcdf-c-${version}.tar.gz";
-    hash = "sha256-zxG6u725lj8J9VB54LAZ9tA3H1L44SZKW6jp/asabEg=";
+    hash = "sha256-pHQUmETmFEVmZz+s8Jf+olPchDw3vAp9PeBH3Irdpd0=";
   };
 
   postPatch = ''

pkgs/by-name/ne/netcdfcxx4/netcdf.patch

@@ -0,0 +1,49 @@
+From b819b3616b96352d23cdf0840df9e6674437948c Mon Sep 17 00:00:00 2001
+From: Orion Poplawski <orion@nwra.com>
+Date: Mon, 17 Feb 2025 15:17:28 -0700
+Subject: [PATCH] Use HAVE_NC_SET_LOG_LEVEL to determine usage of
+ nc_set_log_level (fixes #161)
+
+---
+ cxx4/test_filter.cpp                | 2 ++
+ examples/pres_temp_4D_plugin_wr.cpp | 4 ++++
+ 2 files changed, 6 insertions(+)
+
+diff --git a/cxx4/test_filter.cpp b/cxx4/test_filter.cpp
+index 879ba71..f442c64 100644
+--- a/cxx4/test_filter.cpp
++++ b/cxx4/test_filter.cpp
+@@ -30,7 +30,9 @@ int main()
+   try
+     {
+       NcFile test("pres_temp_plugin_4D.nc", NcFile::replace);
++#ifdef HAVE_NC_SET_LOG_LEVEL
+       nc_set_log_level(5);
++#endif
+       // Define the dimensions. NetCDF will hand back an ncDim object for
+       // each.
+       NcDim latDim = test.addDim(LAT_NAME, NLAT);
+diff --git a/examples/pres_temp_4D_plugin_wr.cpp b/examples/pres_temp_4D_plugin_wr.cpp
+index 832d2a6..584e8be 100644
+--- a/examples/pres_temp_4D_plugin_wr.cpp
++++ b/examples/pres_temp_4D_plugin_wr.cpp
+@@ -71,7 +71,9 @@ string LON_UNITS = "degrees_east";
+ 
+ int main()
+ {
++#ifdef HAVE_NC_SET_LOG_LEVEL
+   nc_set_log_level(5);
++#endif
+   // We will write latitude and longitude fields.
+    float lats[NLAT],lons[NLON];
+ 
+@@ -103,7 +105,9 @@ int main()
+ 
+       // Create the file.
+       NcFile test(FILE_NAME, NcFile::replace);
++#ifdef HAVE_NC_SET_LOG_LEVEL
+       nc_set_log_level(5);
++#endif
+       // Define the dimensions. NetCDF will hand back an ncDim object for
+       // each.
+       NcDim lvlDim = test.addDim(LVL_NAME, NLVL);

pkgs/by-name/ne/netcdfcxx4/package.nix

@@ -22,6 +22,7 @@ stdenv.mkDerivation rec {
   patches = [
     # This fix is included upstream, remove with next upgrade
     ./cmake-h5free.patch
+    ./netcdf.patch
   ];
 
   preConfigure = ''