[Bioperl-l] Windows "index" installation failure

[Jason Eric Stajich]

Yep, some of the Index stuff is not really compatible in ActiveState, this
has to do with filehandles and DBM stuff as best I could tell when I ran
tests for the 07 series earlier this year.  Need someone to debug this on
a windows machine and figure out a workaround.  Since these cause errors
and tests fail you have to do the force install - solutions in the short
term would be to detect these errors AND that one was running on Windows
and cause these tests to be skipped.  Perhaps a windows user/dev would be
willing to do this?


-jason

On Wed, 14 Nov 2001, Jonathan Epstein wrote:

> Hi,
>
> While I had successfully installed BioPerl 0.70 on a previous Windows 2000 machine, it failed on my current machine (in the end I did 'force install' to get around this, since I don't currently use the indexing feature).  This error occurs for me both with 0.70 and 0.71.
>
>
> bash-2.05$ perl -v
>
> This is perl, v5.6.1 built for MSWin32-x86-multi-thread
> (with 1 registered patch, see perl -V for more detail)
>
> Copyright 1987-2001, Larry Wall
>
> Binary build 630 provided by ActiveState Tool Corp. http://www.ActiveState.com
> Built 20:29:41 Oct 31 2001
>
>
> -----excerpt from CPAN output ------
>
> t\HTML..............ok
> t\Index.............HSMETOO - retrieved length '0' doesn't match known length
> 34'
> t\Index.............ok 1/10i|238775|bbs|65126 - retrieved length '0' doesn't m
> ch known length '70'
> MMWHISK - retrieved length '0' doesn't match known length '62'
> Didn't get sequence 'HSEARLOBE' from index
> t\Index.............ok 5/10-------------------- EXCEPTION --------------------
> MSG: EMBL stream with no ID. Not embl in my book
> STACK Bio::SeqIO::embl::next_seq C:/users/epstein/.cpan/build/bioperl-0.7.1/bl
> /lib/Bio/SeqIO/embl.pm:152
> STACK Bio::Index::AbstractSeq::fetch C:/users/epstein/.cpan/build/bioperl-0.7.
> blib/lib/Bio/Index/AbstractSeq.pm:144
> STACK toplevel t\Index.t:103
> -------------------------------------------
> t\Index.............dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 2, 6-10
>         Failed 6/10 tests, 40.00% okay
> t\largefasta........ok
> t\largepseq.........ok
>
> ----- end excerpt -----
>
> Is anyone familiar with this code and/or the error?
>
> - Jonathan
>
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu