[Bioperl-l] in desperate: please help me with this installation problem

[Hilmar Lapp]

zhenyisong wrote:
> 
> I have to send this letter again.I remember someone has asked the same question before, but  I cannot find them in web archive.
> 
> feel dismayed when i installed bio-perl

You don't need to feel dismayed, and neither do you have to worry.
See below.


> platform: RH7.2 bioperl bioperl-0.7.2
> 
> When I instlall bioperl as root,make test:
> 
> t/DB................ok 39/47Warning: Couldn't connect to Genbank with Bio::DB::GenBank.pm!  (why??)
> t/DB................ok, 8/47 skipped: unknown reason

Some DB tests frequently fail for reasons we don't know exactly
(NCBI sort-of refuses connection).

> t/SearchDist........ok, 3/3 skipped: unknown reason

You don't have the bioperl-ext module installed. You don't need it
unless you want to use SearchDist.pm or pSW.pm.

> 
> t/StandAloneBlast...ok 2/8[blastall] WARNING: Could not find index files for database /usr/local/bin/data/ecoli.nt

You have blast installed, but you didn't set the required
environment variables correctly. Check the POD of
Bio::Tools::Run::StandAloneBlast.


	-hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
San Diego, Ca. 92130                     phone: +1 858 812 1757
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