[Bioperl-l] Re: CPAN install

Brian Osborne brian_osborne at cognia.com
Wed Feb 25 10:42:47 EST 2004


No idea, though when I do "perl t/DB.t" I also get failures. You can always
do the "force install" and thoroughly investigate after installation. The
Perl.t failure is odd, I'm guessing it's the RefSeq retrieval, but I'm not
sure. I don't think it has to do with your local installation. Same thing
for the RestrictionIO.t failure.

>It might be worth documenting this in the install instructions or fixing
>the distribution so it's not necessary.


Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Dave Howorth
Sent: Wednesday, February 25, 2004 9:33 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Re: CPAN install

I wrote:
> I'm trying to upgrade my bioperl installation to 1.4.
> (2) What is the name of the distribution?

I got a little further. It is necessary to type:

  install B/BI/BIRNEY/bioperl-1.4.tar.gz

It might be worth documenting this in the install instructions or fixing
the distribution so it's not necessary.

But now I get test failures:

Failed Test       Stat Wstat Total Fail  Failed  List of Failed
t/DB.t                          78    8  10.26%  55 79-85
t/Perl.t                        14    1   7.14%  13
t/RestrictionIO.t               14    1   7.14%  10
121 subtests skipped.
Failed 3/179 test scripts, 98.32% okay. -4/8268 subtests failed, 100.05%
make: *** [test_dynamic] Error 11
   /usr/bin/make test -- NOT OK
Running make install
   make test had returned bad status, won't install without force

My system is Debian Woody with a bunch of backports. Perl 5.6.1.

Any thoughts on why these tests are failing?

Thanks, Dave
Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960

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