Bug#929304: unblock: gmt/5.4.5+dfsg-2

[Bas Couwenberg]

Package: release.debian.org
Severity: normal
User: release.debian.org at packages.debian.org
Usertags: unblock

Please unblock package gmt

It includes the upstream patch to fix the segfault with NetCDF 4.6.3 reported in #929264.

unblock gmt/5.4.5+dfsg-2

Kind Regards,

Bas
-------------- next part --------------
diff -Nru gmt-5.4.5+dfsg/debian/changelog gmt-5.4.5+dfsg/debian/changelog
--- gmt-5.4.5+dfsg/debian/changelog	2019-01-05 08:50:08.000000000 +0100
+++ gmt-5.4.5+dfsg/debian/changelog	2019-05-21 09:39:24.000000000 +0200
@@ -1,3 +1,11 @@
+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 at debian.org>  Tue, 21 May 2019 09:39:24 +0200
+
 gmt (5.4.5+dfsg-1) unstable; urgency=medium
 
   * New upstream release.
diff -Nru gmt-5.4.5+dfsg/debian/gmt-common.lintian-overrides gmt-5.4.5+dfsg/debian/gmt-common.lintian-overrides
--- gmt-5.4.5+dfsg/debian/gmt-common.lintian-overrides	2015-11-04 21:12:27.000000000 +0100
+++ gmt-5.4.5+dfsg/debian/gmt-common.lintian-overrides	2019-03-15 15:21:48.000000000 +0100
@@ -1,3 +1,3 @@
 # Man pages are automatically generated with sphinx
-gmt-common: manpage-has-errors-from-man *
+manpage-has-errors-from-man *
 
diff -Nru gmt-5.4.5+dfsg/debian/gmt.lintian-overrides gmt-5.4.5+dfsg/debian/gmt.lintian-overrides
--- gmt-5.4.5+dfsg/debian/gmt.lintian-overrides	2015-11-04 21:12:27.000000000 +0100
+++ gmt-5.4.5+dfsg/debian/gmt.lintian-overrides	2019-03-15 15:21:50.000000000 +0100
@@ -1,6 +1,6 @@
 # User scripts rely on the extension
-gmt: script-with-language-extension usr/bin/gmt_shell_functions.sh
+script-with-language-extension usr/bin/gmt_shell_functions.sh
 
 # False positive due to language extension
-gmt: binary-without-manpage usr/bin/gmt_shell_functions.sh
+binary-without-manpage usr/bin/gmt_shell_functions.sh
 
diff -Nru gmt-5.4.5+dfsg/debian/patches/0001-Same-fix-as-for-masters-but-for-5.4-542.patch gmt-5.4.5+dfsg/debian/patches/0001-Same-fix-as-for-masters-but-for-5.4-542.patch
--- gmt-5.4.5+dfsg/debian/patches/0001-Same-fix-as-for-masters-but-for-5.4-542.patch	1970-01-01 01:00:00.000000000 +0100
+++ gmt-5.4.5+dfsg/debian/patches/0001-Same-fix-as-for-masters-but-for-5.4-542.patch	2019-05-21 09:09:50.000000000 +0200
@@ -0,0 +1,48 @@
+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 at 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);
+ 	}
diff -Nru gmt-5.4.5+dfsg/debian/patches/series gmt-5.4.5+dfsg/debian/patches/series
--- gmt-5.4.5+dfsg/debian/patches/series	2018-10-26 16:05:02.000000000 +0200
+++ gmt-5.4.5+dfsg/debian/patches/series	2019-05-21 09:09:46.000000000 +0200
@@ -1,3 +1,4 @@
 disable-triangle.patch
 manpage-section.patch
 spelling-errors.patch
+0001-Same-fix-as-for-masters-but-for-5.4-542.patch
diff -Nru gmt-5.4.5+dfsg/debian/source/lintian-overrides gmt-5.4.5+dfsg/debian/source/lintian-overrides
--- gmt-5.4.5+dfsg/debian/source/lintian-overrides	2018-07-31 16:26:28.000000000 +0200
+++ gmt-5.4.5+dfsg/debian/source/lintian-overrides	2019-03-15 15:45:42.000000000 +0100
@@ -1,5 +1,5 @@
 # Download archive not available over HTTPS
-gmt source: debian-watch-uses-insecure-uri ftp://ftp.soest.hawaii.edu/gmt/
+debian-watch-uses-insecure-uri ftp://ftp.soest.hawaii.edu/gmt/
 
 # Not worth the effort
 testsuite-autopkgtest-missing