xml_parse / yxml_parse errors: octave, ubuntu 2204LTS

[andregouws]

Hi -

When running PALM (alpha 119, and a 2021 version) through octave 6.4 or 7.2 I am getting the same errror:

On first install I get (when I run)

palm -i myelin_data_R.func.gii -d design.mat -t design.con -o ALL_corrMyelin_results_R_CLUSTER -Cstat mass -C 2.31 -s R_midthick_average.surf.gii R_area.func.gii -precision double -save1-p -zstat

error ends:

...
Loading surface 1/1: R_midthick_average.surf.gii
error: A compiled version of "xml_parser" is not available for your platform.
error: called from
xml_parser at line 37 column 1
gifti_read at line 14 column 3
gifti at line 105 column 22
palm_miscread at line 249 column 13
palm_takeargs at line 1565 column 20
palm_core at line 33 column 12
palm at line 81 column 1

So I then recompile the xml_parser file as there is no xml_parser.mex in the distro:

mkoctfile --mex ./xml_parser.c

which generates and xml_parser.mex

Now we get past the previous error but get :

...
Loading surface 1/1: R_midthick_average.surf.gii
error: /home/vagrant/Software/palm_alpha119/fileio/@gifti/private/xml_parser.mex: failed to load
Incompatible version or missing dependency?
/home/vagrant/Software/palm_alpha119/fileio/@gifti/private/xml_parser.mex: undefined symbol: yxml_parse
error: called from
gifti_read at line 14 column 3
gifti at line 105 column 22
palm_miscread at line 249 column 13
palm_takeargs at line 1565 column 20
palm_core at line 33 column 12
palm at line 81 column 1

.. as if yxml_parse is not in scope?

So I then tried to recompile ALL mex files in the distro tree for my architecture but still get the same error.

I mean, I can just go back to MATLAB but I was hoping to get away from that.

Any help would be appreciated.

Best wishes and thank you for the software.

Andre'

[gllmflndn]

Hi @andregouws

You need to compile the MEX file with:

mkoctfile --mex xml_parser.c yxml.c