[Bioperl-l] Installation Failed Tests

Simon Wagstaff Simon.Wagstaff at liverpool.ac.uk
Tue Jun 15 07:21:41 EDT 2004

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
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
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

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,


Dr. Simon Wagstaff
Alistair Reid Venom Research Unit,
Liverpool School of Tropical Medicine,
Pembroke Place,
L3 5QA,
Tel: +44(0)151 705 3164
Fax: +44 (0)151 705 3371
email: simonw at liv.ac.uk

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