debian/changelog

-gmt (5.4.5+dfsg-2) UNRELEASED; urgency=medium
+gmt (5.4.5+dfsg-2) unstable; urgency=medium
 
   * Remove package name from lintian overrides.
+  * Add upstream patch to fix segfault with NetCDF 4.6.3.
+    (closes: #929264)
 
- -- Bas Couwenberg <sebastic@debian.org>  Fri, 15 Mar 2019 15:22:04 +0100
+ -- Bas Couwenberg <sebastic@debian.org>  Tue, 21 May 2019 09:39:24 +0200
 
 gmt (5.4.5+dfsg-1) unstable; urgency=medium
 

debian/patches/0001-Same-fix-as-for-masters-but-for-5.4-542.patch

+Description: Avoid passing stride = NULL to io_nc_varm_grdfloat.
+ netCDF introduced a bug in 4.6.2 and fixed it in 4.6.3.  However,
+ macports just now released 4.6.2 and GMT scripts involving netcdf grids
+ would in some cases crash do to the bug.  A fix is to not pass a stride
+ of NULL (which was meant that netCDF would create unit strides - but
+ that is the bug) and instead pass thje unit strides directly.  Closes # 512.
+Author: Paul Wessel <pwessel@hawaii.edu>
+Origin: https://github.com/GenericMappingTools/gmt/commit/1a5a11a29eaa242258d088fdf2690c0452986988
+Bug: https://github.com/GenericMappingTools/gmt/issues/512
+Bug-Debian: https://bugs.debian.org/
+
+--- a/src/gmt_nc.c
++++ b/src/gmt_nc.c
+@@ -177,6 +177,7 @@ GMT_LOCAL int gmtnc_io_nc_grid (struct G
+ 	size_t start[5] = {0,0,0,0,0}, count[5] = {1,1,1,1,1};
+ 	size_t n_contiguous_chunk_rows = 0;  /* that are processed at once, 0 = all */
+ 	ptrdiff_t imap[5] = {1,1,1,1,1}; /* mapping between dims of netCDF and in-memory grid */
++	const ptrdiff_t onestride[5] = {1,1,1,1,1};	/* Passing this instead of NULL bypasses netCDF bug in 4.6.2 */
+ 
+ 	/* catch illegal io_mode in debug */
+ 	assert (io_mode == k_put_netcdf || io_mode == k_get_netcdf);
+@@ -223,7 +224,7 @@ GMT_LOCAL int gmtnc_io_nc_grid (struct G
+ #endif
+ 			/* get/put chunked rows */
+ 			if (stride)
+-				status = io_nc_varm_float (header->ncid, header->z_id, start, count, NULL, imap, grid, io_mode);
++				status = io_nc_varm_float (header->ncid, header->z_id, start, count, onestride, imap, grid, io_mode);
+ 			else
+ 				status = io_nc_vara_float (header->ncid, header->z_id, start, count, grid, io_mode);
+ 
+@@ -244,7 +245,7 @@ GMT_LOCAL int gmtnc_io_nc_grid (struct G
+ 					++row_num, start[yx_dim[0]], count[yx_dim[0]]);
+ #endif
+ 			if (stride)
+-				status = io_nc_varm_float (header->ncid, header->z_id, start, count, NULL, imap, grid, io_mode);
++				status = io_nc_varm_float (header->ncid, header->z_id, start, count, onestride, imap, grid, io_mode);
+ 			else
+ 				status = io_nc_vara_float (header->ncid, header->z_id, start, count, grid, io_mode);
+ 		}
+@@ -254,7 +255,7 @@ GMT_LOCAL int gmtnc_io_nc_grid (struct G
+ 		count[yx_dim[0]] = height_t;
+ 		count[yx_dim[1]] = width_t;
+ 		if (stride)
+-			status = io_nc_varm_float (header->ncid, header->z_id, start, count, NULL, imap, grid, io_mode);
++			status = io_nc_varm_float (header->ncid, header->z_id, start, count, onestride, imap, grid, io_mode);
+ 		else
+ 			status = io_nc_vara_float (header->ncid, header->z_id, start, count, grid, io_mode);
+ 	}

debian/patches/series

 disable-triangle.patch
 manpage-section.patch
 spelling-errors.patch
+0001-Same-fix-as-for-masters-but-for-5.4-542.patch