Updated patch attached which also works with older NetCDF.
Kind Regards,
Bas
--
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diff -Nru minc-tools-2.3.00+dfsg/debian/patches/netcdf-4.9.3.patch
minc-tools-2.3.00+dfsg/debian/patches/netcdf-4.9.3.patch
--- minc-tools-2.3.00+dfsg/debian/patches/netcdf-4.9.3.patch 1970-01-01
01:00:00.000000000 +0100
+++ minc-tools-2.3.00+dfsg/debian/patches/netcdf-4.9.3.patch 2025-02-08
10:56:30.000000000 +0100
@@ -0,0 +1,124 @@
+Description: Replace _FillValue by NC_FillValue for NetCDF 4.9.3.
+Author: Bas Couwenberg <sebas...@debian.org>
+
+--- a/progs/mincgen/ncgentab.y
++++ b/progs/mincgen/ncgentab.y
+@@ -14,6 +14,10 @@
+ #include "ncgen.h"
+ #include "genlib.h" /* for grow_darray() et al */
+
++#if defined(_FillValue) && !defined(NC_FillValue)
++#define NC_FillValue _FillValue
++#endif
++
+ YYSTYPE symlist; /* symbol table: linked list */
+
+ extern int derror_count; /* counts errors in netcdf definition */
+@@ -68,7 +72,7 @@ static void *rec_start; /* start of spa
+ NETCDF /* keyword declaring netcdf name */
+ HDF5 /* keyword declaring hdf5 name */
+ DATA /* keyword starting data section, if any */
+- FILLVALUE /* fill value, from _FillValue attribute or default */
++ FILLVALUE /* fill value, from NC_FillValue attribute or default */
+
+ %start ncdesc /* start symbol for grammar */
+
+@@ -204,7 +208,7 @@ varspec: var
+ vars[nvars].lname = decodify($1->name);
+ vars[nvars].type = type_code;
+ /* set default fill value. You can override this with
+- * the variable attribute "_FillValue". */
++ * the variable attribute "NC_FillValue". */
+ nc_getfill(type_code, &vars[nvars].fill_value);
+ vars[nvars].has_data = 0; /* has no data (yet) */
+ }
+@@ -275,14 +279,14 @@ attdecl: att
+ /* shrink space down to what was really needed */
+ att_space = erealloc(att_space,
valnum*nctypesize(valtype));
+ atts[natts].val = att_space;
+- if (STREQ(atts[natts].name, _FillValue) &&
++ if (STREQ(atts[natts].name, NC_FillValue) &&
+ atts[natts].var != NC_GLOBAL) {
+ nc_putfill(atts[natts].type,
+ atts[natts].val,
+ &vars[atts[natts].var].fill_value);
+ if(atts[natts].type != vars[atts[natts].var].type) {
+ derror("variable %s: %s type mismatch",
+- vars[atts[natts].var].name, _FillValue);
++ vars[atts[natts].var].name, NC_FillValue);
+ }
+ }
+ natts++;
+--- a/progs/mincdump/mincdump.c
++++ b/progs/mincdump/mincdump.c
+@@ -19,6 +19,10 @@
+ #include "dumplib.h"
+ #include "vardata.h"
+
++#if defined(_FillValue) && !defined(NC_FillValue)
++#define NC_FillValue _FillValue
++#endif
++
+ static void usage(void);
+ static char* name_path(const char* path);
+ static char* type_name(nc_type type);
+@@ -475,20 +479,20 @@ do_ncdump(char *path, struct fspec* spec
+ vdims[id] = dims[var.dims[id]].size;
+ var.has_fillval = 1; /* by default, but turn off for bytes */
+
+- /* get _FillValue attribute */
++ /* get NC_FillValue attribute */
+ old_nc_opts = ncopts;
+ ncopts = 0;
+- nc_status =
ncattinq(ncid,varid,_FillValue,&att.type,&att.len);
++ nc_status =
ncattinq(ncid,varid,NC_FillValue,&att.type,&att.len);
+ ncopts = old_nc_opts;
+ if(nc_status == NC_NOERR &&
+ att.type == var.type && att.len == 1) {
+ if(var.type == NC_CHAR) {
+ char fillc;
+- ncattget(ncid, varid, _FillValue, &fillc );
++ ncattget(ncid, varid, NC_FillValue, &fillc );
+ var.fillval = fillc;
+ }
+ else {
+- ncattget(ncid, varid, _FillValue, &var.fillval);
++ ncattget(ncid, varid, NC_FillValue, &var.fillval);
+ }
+ } else {
+ switch (var.type) {
+--- a/progs/mincdump/mincdump.man1
++++ b/progs/mincdump/mincdump.man1
+@@ -52,8 +52,8 @@ and shapes; attribute names and values;
+ data for all variables or selected variables in a netCDF file.
+ .LP
+ \fBmincdump\fP uses `_' to represent data values that are equal to the
+-`_FillValue' attribute for a variable, intended to represent data that
+-has not yet been written. If a variable has no `_FillValue' attribute, the
++`NC_FillValue' attribute for a variable, intended to represent data that
++has not yet been written. If a variable has no `NC_FillValue' attribute, the
+ default fill value for the variable type is used if the variable is not of
+ byte type.
+ .SH OPTIONS
+--- a/progs/mincgen/mincgen.man1
++++ b/progs/mincgen/mincgen.man1
+@@ -167,7 +167,7 @@ arrays, the last dimension varies fastes
+ column order is used for matrices. If fewer values are supplied than
+ are needed to fill a variable, it is extended with a type-dependent
+ `fill value', which can be overridden by supplying a value for a
+-distinguished variable attribute named `_FillValue'. The
++distinguished variable attribute named `NC_FillValue'. The
+ types of constants need not match the type declared for a variable;
+ coercions are done to convert integers to floating point, for example.
+ The constant `_' can be used to designate the fill value for a variable.
+--- a/progs/mincgen/ncgen.h
++++ b/progs/mincgen/ncgen.h
+@@ -39,7 +39,7 @@ extern struct vars {
+ nc_type type;
+ int ndims;
+ int *dims; /* array of dimension ids */
+- union generic fill_value; /* set to value of _FillValue attribute */
++ union generic fill_value; /* set to value of NC_FillValue attribute */
+ int has_data; /* 1 if data specified, 0 otherwise */
+ size_t nrecs; /* for record variables, number of records
+ * of data in CDL */
diff -Nru minc-tools-2.3.00+dfsg/debian/patches/series
minc-tools-2.3.00+dfsg/debian/patches/series
--- minc-tools-2.3.00+dfsg/debian/patches/series 2024-12-29
23:39:42.000000000 +0100
+++ minc-tools-2.3.00+dfsg/debian/patches/series 2025-02-08
10:56:30.000000000 +0100
@@ -5,3 +5,4 @@
fix_manpages.patch
fix-gcc10-build.patch
mnc2nii-use-size-t.patch
+netcdf-4.9.3.patch
