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On Sun, 23 Mar 2008, Aaron Darling wrote:

I made some further changes yesterday to move libmuscle into a c++ namespace in order to avoid global namespace pollution. A new diff is here:
The diff does not include source for files I added, such as the thread storage class and the anchored profile-profile alignment function.

I'll have a look at this soon.

that's good news, it seems we are progressing :)

Yep.  It would be really great if this would go upstream to
MUSCLE because this would reduce the effort to make consistent
packages drastically.

Hmmm, that's unfortunate. Yes, I had come across their project before but never really considered that it might cause naming conflicts. Perhaps they would want to rename to something like mauve-test? Or maybe the aligner could be renamed mauve-aligner? I'd prefer to avoid wisc-mauve since I'm now at the University of Queensland and Mauve may move at some point.

Well, mauve-aligner is an alternative, but my plan was to put the
mauveAligner into a separate package of this name.

As for the mauve build error, some further investigation suggests that the PropertyFile task lives inside ant-nodeps.jar, which should be included in the ant-optional debian package. Perhaps ant can't find /usr/share/ant/lib/ant-nodeps.jar ? If that file exists you might try running:
ant -lib /usr/share/ant/lib/ant-nodeps.jar
and if that works, then ant may not know where $ANT_HOME is, or $ANT_HOME may not be set to /usr/share/ant.

I think I have to enhance my Java skills a little bit.

Kind regards



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