[GRASS-dev] [GRASS GIS] #3978: r.kappa: Segmentation fault

GRASS GRASS developer
1

#3978: r.kappa: Segmentation fault
---------------------+-------------------------
Reporter: sbl | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 7.8.2
Component: Imagery | Version: svn-trunk
Keywords: r.kappa | CPU: Unspecified
Platform: Linux |
---------------------+-------------------------
In trunk (and 7.8.0) I observed an issue with r.kappa which segfaults at
the end of the process.
Therefore, stdout is not written in the GUI console and kappa estimates
are not written to file. On command line kappa estimates are written
before the segfault occurs.

Example from the manual:

{{{
r.kappa -w classification=landuse96_28m reference=landclass96
}}}

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3978&gt;
GRASS GIS <https://grass.osgeo.org>

2

#3978: r.kappa: Segmentation fault
--------------------------+-------------------------
  Reporter: sbl | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.8.2
Component: Imagery | Version: svn-trunk
Resolution: | Keywords: r.kappa
       CPU: Unspecified | Platform: Linux
--------------------------+-------------------------

Comment (by neteler):

It works nicely here (F30) - did you try to `make distclean` and
recompile?

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3978#comment:1&gt;
GRASS GIS <https://grass.osgeo.org>

3

#3978: r.kappa: Segmentation fault
--------------------------+-------------------------
  Reporter: sbl | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.8.2
Component: Imagery | Version: svn-trunk
Resolution: | Keywords: r.kappa
       CPU: Unspecified | Platform: Linux
--------------------------+-------------------------

Comment (by hellik):

tested with in the GUI

{{{
System Info
GRASS version: 7.8.1
Code revision: c865432c9
Build date: 2019-11-10
Build platform: x86_64-w64-mingw32
GDAL: 3.0.2
PROJ: 6.2.1
GEOS: 3.8.0
SQLite: 3.29.0
Python: 3.7.0
wxPython: 4.0.3
Platform: Windows-10-10.0.18362-SP0 (OSGeo4W)
}}}

{{{
r.kappa -w classification=landuse96_28m@PERMANENT
reference=landclass96@PERMANENT
                         ACCURACY ASSESSMENT
LOCATION: nc_spm_08_grass7 Wed Nov 20
21:12:55 2019
MASK: none
MAPS: MAP1 = South-West Wake county: Simplified landuse classes
(landclass96@PERMANENT in PERMANENT)
       MAP2 = South-West Wake county: NC Land Use 1996 clipped
(landuse96_28m@PERMANENT in PERMANENT)
Error Matrix
Panel #1 of 2
                           MAP1
      cat# 1 2 3 4 5 6 7 8
9
  M 1 34931 38146 0 0 0 0 0 0
0
  A 2 0 0 2137 0 0 0 0 0
0
  P 3 0 0 0 25488 0 30 0 0
0
  2 4 0 0 0 0 0 0 16464
320 45
        5 0 0 0 0 0 0 0 0
0
        6 0 0 0 0 0 0 0 0
0
        7 0 0 0 0 0 0 0 0
0
        8 0 0 0 0 0 0 0 0
0
        9 0 0 0 0 0 0 0 0
0
       10 0 0 0 0 0 0 0 0
0
       11 0 0 0 0 0 0 0 0
0
       15 0 0 0 0 0 0 0 0
0
       18 0 0 0 0 0 0 0 0
0
       20 0 0 0 0 0 0 0 0
0
       21 0 0 0 0 0 0 0 0
0
Col Sum 34931 38146 2137 25488 0 30 16464
320 45
Panel #2 of 2
                           MAP1
      cat# 10 11 15 18 20 21 Row Sum
  M 1 0 0 0 0 0 0 73077
  A 2 0 0 0 0 0 0 2137
  P 3 0 0 0 0 0 0 25518
  2 4 0 0 0 0 0 0 16829
        5 7893 19733 64774 33865 0 0 126265
        6 0 0 0 0 5303 0 5303
        7 0 0 0 0 0 194 194
        8 0 0 0 0 0 0 0
        9 0 0 0 0 0 0 0
       10 0 0 0 0 0 0 0
       11 0 0 0 0 0 0 0
       15 0 0 0 0 0 0 0
       18 0 0 0 0 0 0 0
       20 0 0 0 0 0 0 0
       21 0 0 0 0 0 0 0
Col Sum 7893 19733 64774 33865 5303 194 249323
Cats % Commission % Ommission Estimated Kappa
1 52.199735 0.000000 0.392953
2 100.000000 100.000000 -0.180635
3 100.000000 100.000000 -0.008645
4 100.000000 100.000000 -0.113870
5 NA NA NA
6 100.000000 100.000000 -0.000120
7 100.000000 100.000000 -0.070704
8 NA NA NA
9 NA NA NA
10 NA NA NA
11 NA NA NA
15 NA NA NA
18 NA NA NA
20 NA NA NA
21 NA NA NA
Kappa Kappa Variance
0.094648 0.000001
Obs Correct Total Obs % Observed Correct
34931 249323 14.010340
MAP1 Category Description
1: developed
2: agriculture
3: herbaceous
4: shrubland
5: forest
6: water
7: sediment
8: (no description)
9: (no description)
10: (no description)
11: (no description)
15: (no description)
18: (no description)
20: (no description)
21: (no description)
MAP2 Category Description
1: High Intensity Developed
2: Low Intensity Developed
3: Cultivated
4: Managed Herbaceous Cover
5: Upland Herbaceous
6: Riverine/Estuarine Herbaceous
7: Evergreen Shrubland
8: Deciduous Shrubland
9: Mixed Shrubland
10: Mixed Hardwoods
11: Bottomland Hardwoods/Hardwood Swamps
15: Southern Yellow Pine
18: Mixed Hardwoods/Conifers
20: Water Bodies
21: Unconsolidated Sediment
(Wed Nov 20 21:12:55 2019) Command finished (0 sec)
}}}

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Ticket URL: <https://trac.osgeo.org/grass/ticket/3978#comment:2&gt;
GRASS GIS <https://grass.osgeo.org>

4

#3978: r.kappa: Segmentation fault
--------------------------+-------------------------
  Reporter: sbl | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: normal | Milestone: 7.8.3
Component: Imagery | Version: svn-trunk
Resolution: | Keywords: r.kappa
       CPU: Unspecified | Platform: Linux
--------------------------+-------------------------
Comment (by marisn):

There is an invalid memory access in calc_kappa.c that might result in a
segfault.

I'll try to deal with this issue in PR
https://github.com/OSGeo/grass/pull/2573
--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3978#comment:5&gt;
GRASS GIS <https://grass.osgeo.org>

5

#3978: r.kappa: Segmentation fault
--------------------------+-------------------------
  Reporter: sbl | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: normal | Milestone:
Component: Imagery | Version: svn-trunk
Resolution: fixed | Keywords: r.kappa
       CPU: Unspecified | Platform: Linux
--------------------------+-------------------------
Changes (by marisn):

* status: new => closed
* resolution: => fixed
* milestone: 7.8.3 =>

Comment:

The issue is fixed in 8.4.0.
--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3978#comment:6&gt;
GRASS GIS <https://grass.osgeo.org>