[Bioperl-l] Installation Failed Tests

[Simon Wagstaff]

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