Add-on compilation errors in GRASS 7

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
16 messages Options
Reply | Threaded
Open this post in threaded view
|

Add-on compilation errors in GRASS 7

geo-joe

Hi all,

I am really struggling to to use the r.geomorphon (or indeed any) add-on in GRASS 7 (it's not available in 6) and I have spent a great many hours trying to get this working before seeking advice here. Any help would be hugely appreciated. I really am a GRASS novice so I may well have missed something obvious, despite trying to be thorough. This is also my first post here so I hope it's up to scratch.

First, system Info:                                                                     
GRASS version: 7.0.0beta3                                                       
GRASS SVN Revision: 61541                                                       
Build Date: 2014-09-08                                                          
Build Platform: x86_64-unknown-linux-gnu                                        
GDAL/OGR: 1.11.0                                                                
PROJ.4: 4.8.0                                                                   
GEOS: 3.4.2                                                                     
SQLite: 3.8.2                                                                   
Python: 2.7.6                                                                   
wxPython: 2.8.12.1                                                              
Platform: Linux-3.13.0-35-generic-x86_64-with-Ubuntu-14.04-trusty               
            
How I got to this stage:
As you can see from System Info, I compiled GRASS GIS 7.0.0beta3 from source code via "svn checkout http://svn.osgeo.org/grass/grass/tags/release_20140806_grass_7_0_0beta3", but I had also tried it via "svn co https://svn.osgeo.org/grass/grass/trunk" before, with the same negative result. I cannot use the stable version of GRASS GIS 7 (I tried that first) because of the issue with g.extension, which is fixed in these later versions (see http://lists.osgeo.org/pipermail/grass-user/2014-June/070480.html). I've compiled and installed GRASS 7 using the instructions from the OSGeo Ubuntu Wiki page (http://grasswiki.osgeo.org/wiki/Compile_and_Install_Ubuntu#GRASS_GIS) and have been sure run the commands under 'Dependencies'.


The compilation set-up that I've used is as follows (this does not produce any errors):
CFLAGS="-O2 -Wall" LDFLAGS="-s" ./configure \
--enable-largefile=yes \
--with-nls \
--with-cxx \
--with-python=yes \
--with-wxwidgets \
--with-cairo \
--with-freetype=yes \
--with-freetype-includes="/usr/include/freetype2/" \
--with-opengl-libs=/usr/include/GL \
--with-postgres=yes \
--with-postgres-includes="/usr/include/postgresql" \
--with-sqlite=yes \
--with-mysql=yes \
--with-mysql-includes="/usr/include/mysql" \
--with-odbc=no \
--with-geos=yes

And here's the summary once compiled (does anything stand out as being missing?):
  BLAS support:                no
  C++ support:                  yes
  Cairo support:                yes
  DWG support:                no
  FFMPEG support:          no
  FFTW support:               yes
  FreeType support:         yes
  GDAL support:               yes
  GEOS support:               yes
  LAPACK support:           no
  Large File support (LFS):   yes
  libLAS support:              no
  MySQL support:            yes
  NetCDF support:           no
  NLS support:                 yes
  ODBC support:              yes
  OGR support:                yes
  OpenCL support:           no
  OpenGL support:           yes
  OpenMP support:           no
  PNG support:                 yes
  POSIX thread support:  no
  PostgreSQL support:    yes
  Readline support:          no
  Regex support:              yes
  SQLite support:             yes
  TIFF support:               yes
  wxWidgets support:     yes
  X11 support:                yes

Finally, here's the output upon attempting to install r.geomorphon via g.extension (g.extension extension=r.geomorphon svnurl=http://svn.osgeo.org/grass/grass-addons/grass7). I've also put another couple of error-filled outputs from other add-ons below. Many thanks in advance, Joe

g.extension extension=r.geomorphon svnurl=http://svn.osgeo.org/grass/grass-addons/grass7
Fetching <r.geomorphon> from GRASS-Addons SVN (be patient)...
Compiling...
geom.c: In function ‘ternary_rotate’:
geom.c:22:9: warning: unused variable ‘res’ [-Wunused-
variable]
     int res;
         ^
geom.c: At top level:
geom.c:2:15: warning: ‘dirs’ defined but not used
[-Wunused-variable]
 static double dirs[8] = { 0.7854, 0., 5.4978, 4.7124,
3.9270, 3.1416, 2.3562, 1.5708 }; /* radians */
               ^
geom.c: In function ‘shape’:
geom.c:252:26: warning: ‘rymax’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
  rymax = ry > rymax ? ry : rymax;
                          ^
geom.c:251:26: warning: ‘rymin’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
  rymin = ry < rymin ? ry : rymin;
                          ^
geom.c:250:26: warning: ‘rxmax’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
  rxmax = rx > rxmax ? rx : rxmax;
                          ^
geom.c:249:26: warning: ‘rxmin’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
  rxmin = rx < rxmin ? rx : rxmin;
                          ^
geom.c:232:15: warning: ‘avg_x_square’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
  avg_x_square += pattern->x[i] * pattern->x[i];
               ^
main.c: In function ‘main’:
main.c:312:20: warning: unused variable ‘formC’
[-Wunused-variable]
  int formA, formB, formC;
                    ^
main.c:312:13: warning: unused variable ‘formB’
[-Wunused-variable]
  int formA, formB, formC;
             ^
main.c:312:6: warning: unused variable ‘formA’
[-Wunused-variable]
  int formA, formB, formC;
      ^
main.c:93:28: warning: unused variable ‘radius’
[-Wunused-variable]
     int row, cur_row, col, radius;
                            ^
main.c:91:15: warning: unused variable ‘n’ [-Wunused-
variable]
     int i, j, n;
               ^
main.c:91:12: warning: unused variable ‘j’ [-Wunused-
variable]
     int i, j, n;
            ^
main.c:553:1: warning: control reaches end of non-void
function [-Wreturn-type]
 }
 ^
memory.c: In function ‘open_map’:
memory.c:10:9: warning: unused variable ‘bufsize’
[-Wunused-variable]
     int bufsize;
         ^
memory.c:7:9: warning: unused variable ‘fd’ [-Wunused-
variable]
     int fd;
         ^
memory.c: In function ‘shift_buffers’:
memory.c:75:39: warning: unused variable ‘aspect_tmp’
[-Wunused-variable]
     FCELL *tmp_elev_buf, *slope_tmp, *aspect_tmp;
                                       ^
memory.c:75:27: warning: unused variable ‘slope_tmp’
[-Wunused-variable]
     FCELL *tmp_elev_buf, *slope_tmp, *aspect_tmp;
                           ^
memory.c: In function ‘write_contrast_colors’:
memory.c:131:23: warning: unused variable ‘cats’
[-Wunused-variable]
     struct Categories cats;
                       ^
multires.c: In function ‘pattern_matching’:
multires.c:23:29: warning: suggest parentheses around
comparison in operand of ‘&’ [-Wparentheses]
     return (result & source == source) ? 1 : 0;
                             ^
pattern.c: In function ‘calc_pattern’:
pattern.c:134:24: warning: ‘nadir_distance’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
   pattern->distance[i] = nadir_distance;
                        ^
pattern.c:128:24: warning: ‘zenith_distance’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
   pattern->distance[i] = zenith_distance;
                        ^
pattern.c:133:25: warning: ‘nadir_height’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
   pattern->elevation[i] = nadir_height; //ZMIANA!
                         ^
pattern.c:127:25: warning: ‘zenith_height’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
   pattern->elevation[i] = zenith_height; //ZMIANA!
                         ^
Installing...
Updating metadata file...
WARNING: Unable to parse 'http://grass.osgeo.org/addons/grass7/modules.xml'. Metadata file not updated.
Installation of <r.geomorphon> successfully finished



-- END of OUTPUT 1 --        

I also get errors when attempting to install other add-ons, e.g. r.bioclim:

g.extension extension=r.bioclim svnurl=http://svn.osgeo.org/grass/grass-addons/grass7
Fetching <r.bioclim> from GRASS-Addons SVN (be patient)...
Compiling...
/bin/sh: 1: cannot create /usr/local/grass-7.0.0beta3/locale
/scriptstrings/r.bioclim_to_translate.c: Directory
nonexistent
make: [/usr/local/grass-7.0.0beta3/locale/scriptstrings/r.bi
oclim_to_translate.c] Error 2 (ignored)
Installing...
Updating metadata file...
WARNING: Unable to parse 'http://grass.osgeo.org/addons/grass7/modules.xml'. Metadata file not updated.
Installation of <r.bioclim> successfully finished



 -- END of OUTPUT 2 --        

e.g. r.stream.basins:

Fetching <r.stream.basins> from GRASS-Addons SVN (be patient)...
Compiling...
io.c: In function ‘ram_write_map’:
io.c:221:10: warning: ‘c’ may be used uninitialized in
this function [-Wmaybe-uninitialized]
   G_debug(1, "ram_null:Cannot convert to null at: %d %d",
r, c);
          ^
io.c: In function ‘seg_write_map’:
io.c:531:12: warning: ‘c’ may be used uninitialized in
this function [-Wmaybe-uninitialized]
   G_warning(_("Unable to convert to null at: %d %d"), r,
            ^
Installing...
Updating metadata file...
WARNING: Unable to parse 'http://grass.osgeo.org/addons/grass7/modules.xml'. Metadata file not updated.
Installation of <r.stream.basins> successfully finished

 -- END of OUTPUT 3 --
 --- END  ---


   


_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user

Joe B
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

Martin Landa
Hi,

2014-09-08 22:48 GMT+02:00 Joseph Bailey <[hidden email]>:

> WARNING: Unable to parse 'http://grass.osgeo.org/addons/grass7/modules.xml'.
> Metadata file not updated.
> Installation of <r.geomorphon> successfully finished

it's related to the problem on the server where modules.xml is
generated. I am working on solving it.

Martin

--
Martin Landa * http://geo.fsv.cvut.cz/gwiki/Landa
_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

geo-joe
In reply to this post by geo-joe

Thanks for the quick reply; much appreciated. I was partly hoping it was something I was doing wrong so that it was fixable. Not to worry. Is there anything that I can do in the meantime so that I can use the add-on, please? Is it possible to compile locally from the source code (https://svn.osgeo.org/grass/grass-addons/grass7/raster/r.geomorphon/), for example? The add-on does load and runs but produces no output and doesn't appear in the 'installed add-ons' list as it is, despite saying "Installation ... successfully finished".

Many thanks,

Joe

Joe B
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

Martin Landa
Hi,

2014-09-09 9:04 GMT+02:00 geo-joe <[hidden email]>:
>
> Thanks for the quick reply; much appreciated. I was partly hoping it was
> something I was doing wrong so that it was fixable. Not to worry. Is there
> anything that I can do in the meantime so that I can use the add-on, please?

this warning (modules.xml) has nothing to do the with the
functionality of addons module...

> Is it possible to compile locally from the source code
> (https://svn.osgeo.org/grass/grass-addons/grass7/raster/r.geomorphon/), for
> example? The add-on does load and runs but produces no output and doesn't
> appear in the 'installed add-ons' list as it is, despite saying
> "Installation ... successfully finished".

Can you launch the module or not?

Martin

--
Martin Landa * http://geo.fsv.cvut.cz/gwiki/Landa
_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

geo-joe
Hello,
r.geomorphon launches and presents the GUI when I type 'r.geomorphon' into the command line. I can launch the module's GUI and enter the inputs but it doesn't produce an output when it runs, which I assumed was to do with the warning following compilation.
Thanks,
Joe

Joe B
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

geo-joe
I just thought, does that final warning on the parsing issue relate to the previous warnings or are they separate issues? I was assuming that it did but maybe not, considering what you say. Could these be caused by missing components during GRASS compilation?
e.g.
geom.c: In function ‘ternary_rotate’:
geom.c:22:9: warning: unused variable ‘res’ [-Wunused-
variable]
     int res;
         ^
Thanks,
Joe

Joe B
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

Martin Landa
Hi,

2014-09-09 9:43 GMT+02:00 geo-joe <[hidden email]>:
> I just thought, does that final warning on the parsing issue relate to the
> previous warnings or are they separate issues? I was assuming that it did

right, completely separated issues. The first part comes from
compilation (such warnings/errors should be fixed by an author of the
module). Warning about broken modules.xml is related to g.extension
which tries to keep metadata about installed modules [1]. This will be
fixed by me since the generation of modules.xml file is done on our
university server (CTU in Prague).

> but maybe not, considering what you say. Could these be caused by missing
> components during GRASS compilation?
> e.g.
> geom.c: In function 'ternary_rotate':
> geom.c:22:9: warning: unused variable 'res' [-Wunused-
> variable]
>      int res;
>          ^

No, such warnings are harmless and have no impact on functionality of
the module.

Martin

[1] http://trac.osgeo.org/grass/wiki/AddOnsManagement
_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

geo-joe
Hi,
Ok, sorry, my lack of GRASS know-how is being highlighted here!
So, if I've understood correctly, the module should work, despite the separate 'Wunused' and 'broken modules.xml' warnings received? It would be great to get this ironed out. I'll contact the module's authors and link through to this thread.
Thanks for your time on this,
Joe

Joe B
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

Martin Landa
In reply to this post by geo-joe
Hi,

2014-09-08 22:48 GMT+02:00 Joseph Bailey <[hidden email]>:

> /bin/sh: 1: cannot create /usr/local/grass-7.0.0beta3/locale
> /scriptstrings/r.bioclim_to_translate.c: Directory
> nonexistent
> make: [/usr/local/grass-7.0.0beta3/locale/scriptstrings/r.bi
> oclim_to_translate.c] Error 2 (ignored)

this issue has been fixed after beta3 [1], could you try out more
recent version from SVN [2]?

Martin

[1] http://trac.osgeo.org/grass/changeset/61713/grass/branches/releasebranch_7_0/scripts/g.extension/g.extension.py
[2] http://trac.osgeo.org/grass/wiki/DownloadSource#GRASS7.0

--
Martin Landa * http://geo.fsv.cvut.cz/gwiki/Landa
_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

Martin Landa
In reply to this post by Martin Landa
2014-09-09 10:08 GMT+02:00 Martin Landa <[hidden email]>:
> module). Warning about broken modules.xml is related to g.extension
> which tries to keep metadata about installed modules [1]. This will be
> fixed by me since the generation of modules.xml file is done on our
> university server (CTU in Prague).

hopefully fixed.

g.extension r.geomorphon
Fetching <r.geomorphon> from GRASS-Addons SVN repository (be patient)...
Compiling...
geom.c: In function 'ternary_rotate':
geom.c:22:9: warning: unused variable 'res' [-Wunused-variable]
...
Installing...
Updating metadata file...
Installation of <r.geomorphon> successfully finished

Martin

--
Martin Landa * http://geo.fsv.cvut.cz/gwiki/Landa
_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

peifer
Martin Landa wrote
2014-09-09 10:08 GMT+02:00 Martin Landa <[hidden email]>:
> module). Warning about broken modules.xml is related to g.extension
> which tries to keep metadata about installed modules [1]. This will be
> fixed by me since the generation of modules.xml file is done on our
> university server (CTU in Prague).

hopefully fixed.
Thanks for fixing. Installation works fine now [1]. I will close my ticket from earlier today [2].

r.geomorphon seems to work fine for me and creates a forms output map as expected. I'm using svn/grass7_releasebranch

Hermann

[1]

[GRASS:test]> g.extension r.geomorphon
Fetching <r.geomorphon> from GRASS-Addons SVN repository (be patient)...
Compiling...
Installing...
Updating metadata file...
Installation of <r.geomorphon> successfully finished
[GRASS:test]> g.extension -l
List of available extensions (modules):
r.geomorphon
[GRASS:test]>


[2] https://trac.osgeo.org/grass/ticket/2411
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

geo-joe
In reply to this post by Martin Landa
Ah yes, the parsing error is now gone. The others are still present, however, and the add-on isn't working... I'll try a clean install and maybe contact the author of the tool when I'm sure it's not something that I'm doing. Thanks again for all of this, Joe

Joe B
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

peifer
In reply to this post by Martin Landa
On 2014-09-09 8:57, Martin Landa wrote:
>
> it's related to the problem on the server where modules.xml is
> generated. I am working on solving it.
>

Hi Martin,

I assume that at some point, there will be a full-size modules.xml file
for grass7, i.e. comparable to
http://grass.osgeo.org/addons/grass6/modules.xml

Any idea when this will be?

Thanks in advance, Hermann

_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

Martin Landa
Hi,

2014-09-10 8:06 GMT+02:00 Hermann Peifer <[hidden email]>:

> I assume that at some point, there will be a full-size modules.xml file for
> grass7, i.e. comparable to http://grass.osgeo.org/addons/grass6/modules.xml
>
> Any idea when this will be?

hm, it's broken again, strangely only when launched via cronjobs (this
happens after I reinstalled the server where it's running). Manually
launched scripts simply work. Will fix it manually right now, and I
will try to find out what is wrong with cronjob which should work in
the same way as launching scripts manually.

Martin

--
Martin Landa * http://geo.fsv.cvut.cz/gwiki/Landa
_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

Martin Landa
2014-09-10 9:23 GMT+02:00 Martin Landa <[hidden email]>:

> launched scripts simply work. Will fix it manually right now, and I
> will try to find out what is wrong with cronjob which should work in

it's back. I will test cronjobs and try to fix the real problem behind. Martin

--
Martin Landa * http://geo.fsv.cvut.cz/gwiki/Landa
_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user
Reply | Threaded
Open this post in threaded view
|

Re: Add-on compilation errors in GRASS 7

Martin Landa
Hi,

2014-09-10 10:11 GMT+02:00 Martin Landa <[hidden email]>:
>> launched scripts simply work. Will fix it manually right now, and I
>> will try to find out what is wrong with cronjob which should work in
>
> it's back. I will test cronjobs and try to fix the real problem behind. Martin

the problem was that the path defined by crontab lacked
`/usr/local/bin`. I have fixed that, hopefully the next call (this
night) will be finally OK.

Martin

--
Martin Landa * http://geo.fsv.cvut.cz/gwiki/Landa
_______________________________________________
grass-user mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-user