Test failure on i386: ""No usable version of RAxML could be found."

[tillea]

Hi, the Debian packaged gubbins has trouble to use RaXML. As you can see in the complete build log it runs into

======================================================================
ERROR: test_raxml_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_treebuilders.py", line 91, in test_raxml_convert_raw_ancestral_states_to_fasta
    raxml = treebuilders.RAxML(8)
  File "/<<PKGBUILDDIR>>/python/gubbins/treebuilders.py", line 147, in __init__
    sys.exit("No usable version of RAxML could be found.")
SystemExit: No usable version of RAxML could be found.

The i386 Debian package just contains /usr/bin/raxmlHPC but if I'm reading line 142 of file python/gubbins/treebuilders.py in gubbins source

142         self.single_threaded_executables = ['raxmlHPC-AVX2', 'raxmlHPC-AVX', 'raxmlHPC-SSE3', 'raxmlHPC']
143         self.multi_threaded_executables = ['raxmlHPC-PTHREADS-AVX2', 'raxmlHPC-PTHREADS-AVX',
144                                            'raxmlHPC-PTHREADS-SSE3', 'raxmlHPC-PTHREADS']
145         self.executable = self.select_executable_based_on_threads()
146         if self.executable is None:
147             sys.exit("No usable version of RAxML could be found.")

correctly this should be a valid single trheaded executable. Any hint how we can pass the test suite also on i386?

Kind regards, Andreas.

[puethe]

Hi Andreas, thanks for still building the debian package, this is great. Looking at the tests, the number of threads is set to 8 (for whatever reason), so it's looking for one of the multi-threaded executables. Which means that you'd need to install one of them to get the tests passing. Is that a possible solution for you? Or alternatively, could you live with some broken tests? Gubbins should still run fine in single-threaded mode. Best wishes, Christoph