[Bioperl-l] Installation problems: solaris

[Jason Stajich]

Denise - You haven't reported which version of bioperl you having this
trouble with. It has nothing to do with solaris - but rather with that
version of bioperl and the NCBI Entrez server URL changing.  All releases
after 0.7.2 contain the appropriate URL in them - if you need
Bio::DB functionality immedietely you should install the developer release
0.9.3 - otherwise await the 1.0 release at the end of the month.

-jason
On Fri, 1 Feb 2002, Denise Abbott wrote:

>
> When installing on this system:
> SunOS terra 5.8 Generic_108528-06 sun4u sparc SUNW,Ultra-4
> This is perl, v5.6.1 built for sun4-solaris
>
> I receive this error while doing make test:
>
> t/DB...................ok 5/33 Batch access test failed.
> Error: -------------------- EXCEPTION --------------------
> MSG: WebDBSeqI Error - check query sequences!
>
> STACK Bio::DB::WebDBSeqI::get_seq_stream blib/lib/Bio/DB/WebDBSeqI.pm:296
> STACK Bio::DB::NCBIHelper::get_Stream_by_batch
>                                         blib/lib/Bio/DB/NCBIHelper.pm:205
> STACK (eval) t/DB.t:73
> STACK toplevel t/DB.t:72
> -------------------------------------------
>
> t/DB................ok 38/33Warning: Couldn't connect to Genbank with
> Bio::DB::GenPept.pm!
>
> t/DB................ok 46/33Warning: Couldn't connect to Genbank with
> Bio::DB::GenBank.pm!
>
> Don't know which tests failed: got 46 ok, expected 33
>
> The make test continues on from there and at the end says that it has
> errors and won't install unless forced.  I looked a bit at the code there
> to see if it was some error that I could see, but I don't have time to
> look deeper into it, so I was wondering if anyone else could offer some
> hints of what to change or whether or not it really IS a problem with the
> sequences make test tries to use.
>
> Thanks.
> Denise Abbott
>
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>

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