[Bioperl-l] Installation Failed Tests

[Jason Stajich]

As was posted on the list earlier this month I believe - you can ignore
these failed tests and force the install.

The Variation_IO one has to do with differences in XML::Writer 0.4 and 0.5
and extra newlines in the output.

The DB.t was a problem in the released code as well.  I believe the DB.t
problem has been fixed on the 1.4 branch while the Variation_IO still
needs some massaging to either handle both variants from XML::Writer by
making the diff strategy more intelligent to the extra newline, require
XML::Writer 0.5 only, or just dump the tests which do the diffing.

-jason

On Tue, 15 Jun 2004, Simon Wagstaff wrote:

> Dear Helpdesk,
>
> I have installed via CPN bioperl bundle 1.4 returning default values when
> prompted and encountered the following failed tests/errors.
>
> t/Variation_IO...............FAILED tests 15, 20, 25
>         Failed 3/25 tests, 88.00% okay
> t/WABA.......................ok
> t/XEMBL_DB...................ok
> Failed Test      Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t/DB.t                         78   ??       %  ??
> t/Variation_IO.t               25    3  12.00%  15 20 25
> 121 subtests skipped.
> Failed 2/179 test scripts, 98.88% okay. -6/8122 subtests failed, 100.07% okay.
> make: *** [test_dynamic] Error 29
>   /usr/bin/make test -- NOT OK
> Running make install
>   make test had returned bad status, won't install without force
>
> also missing is:
>
> GD or Text::Shellwords
> Graph.pm
> t/registry DB_file and BerkleyDB
>
> MSG: sorted sublocation doesn't define seq_id....
>
> I have installed (I think) all the external dependencies such as GD, BerkleyDB,
> MySQL and expat according to the install instruction provided with these
> dependencies.
>
> The machine I am running is a Dual Xeon Processor (2.8Ghz) Dell Precision 450
> Workstation with Redhat Enterprise Linux WS version 3 OS. I was hoping to
> install bioperl in order to run BioLinux 3 which I have installed as an image
> from the EGTDC server,
>
> Your advice is greatly appreciated,
>
> Many Thanks in anticipation,
>
> Simon
>
>
> --
> Dr. Simon Wagstaff
> Alistair Reid Venom Research Unit,
> Liverpool School of Tropical Medicine,
> Pembroke Place,
> Liverpool,
> L3 5QA,
> UK
> Tel: +44(0)151 705 3164
> Fax: +44 (0)151 705 3371
> email: simonw at liv.ac.uk
> _______________________________________________
> Bioperl-l mailing list
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu