Package: release.debian.org
Severity: normal
User: release.debian....@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
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 <sebas...@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 <pwes...@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
