[BioRuby] PhyloXML and libxml-ruby

[Clayton Wheeler]

Hi all,

It appears that the native extension for libxml-ruby is not building reliably under JRuby, causing Travis-CI runs to fail as seen at:

http://travis-ci.org/#!/ngoto/bioruby/jobs/1356992

I'm not having much luck identifying exactly why it builds in some JRuby environments and not others, but I've been able to reproduce the Travis-CI problem on a test Linux machine and don't see an obvious fix.

If we're going to repackage PhyloXML into a separate gem, I think the safest course of action would be to revert to calling for libxml-jruby in the Travis-CI Gemfiles (i.e. back out http://bit.ly/JmNjDY). Using libxml-ruby instead of libxml-jruby doesn't solve the PhyloXML problems on JRuby in 1.9 mode anyway, and 1.9 mode will soon be the default in JRuby. The PhyloXML gem can be explicitly declared to depend on libxml-ruby, and moving it out of the core BioRuby gem will remove this whole issue, as far as the unit tests go. Then PhyloXML's library requirements can be addressed separately.

Thoughts?

Clayton Wheeler
cswh at umich.edu