[Biopython-dev] 1.62b test coverage report

[Eric Talevich]

On Fri, Aug 2, 2013 at 2:31 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Thanks for these details Ben - it sounds like a mixture of real
> test failures, and mere warnings that an external tool wasn't
> found.
>
> On Fri, Aug 2, 2013 at 3:20 AM, Ben Fulton <ben at benfulton.net> wrote:
> > My test machine was running Ubuntu 12.04.
> >
> > For fasttree I installed version 2.1.4-1~ubuntu12.04.1 using apt-get, and
> > got this error:
> > ApplicationError: Command 'fasttree -out temp_test.tree
> > Quality/example.fasta' returned non-zero exit status 1, 'Unknown or
> > incorrect use of option -out'
>
> I don't seem to have fasttree installed at all, and from the
> test and wrapper it is not explicit about which version is
> was originally written for.
>

I pushed a patch to not use the potentially problematic '-out' flag:
https://github.com/biopython/biopython/commit/771c1ed23bbb39dcf37805b4cb7bb23ffcb0c46a

According to FastTree's changelog (
http://www.microbesonline.org/fasttree/ChangeLog), the -out option was
added in version 2.1.5, released August 30, 2012. So the 'fasttree' package
on the stable Ubuntu (12.04) does not have the -out flag, but the package
in subsequent Ubuntus and other Debian derivatives does.

-Eric