[Bioperl-l] Q: cpan installation fails for "core.t"

[Cerebron Emtadrat]

Hi Scott,

Frankly speaking I'm new to BioPerl and don't know if I'll be using assembly modules. I want to write a script that allows me to parse patent sequence protocols according to WIPO standard 25 (i.e the parser is ready, I only need the Bio::Perl objects to put the results into), and to save the results in a SQLite database. So I rather trust that I'll have to use Bio/Root/IO.

But thanks anyway!

Best regards



----- Ursprüngliche Message -----
Von: Scott Cain <scott at scottcain.net>
An: Cerebron Emtadrat <emtadrat at yahoo.de>
CC: "bioperl-l at bioperl.org" <bioperl-l at bioperl.org>
Gesendet: 15:19 Donnerstag, 6.Juni 2013
Betreff: Re: [Bioperl-l] Q: cpan installation fails for "core.t"

Hi Celebron,

Are those the only failures and are you planning on using the assembly modules of BioPerl?  If you aren't planning on using them, yes it's safe to install. 

Scott


Sent from my iPhone

On Jun 5, 2013, at 5:32 AM, Cerebron Emtadrat <emtadrat at yahoo.de> wrote:

> Dear mailing list,
> 
> I'm trying to install Bioperl on a Windows 7 machine running Strawberry Perl. I've started installation using the cpan tool as described on the bioperl.org wiki "Installing BioPerl on Unix". One of the failed tests worries me:
> 
> t/Assembly/core.t ............................ 1/890
> --------------------- WARNING ---------------------
> MSG: Setting end to equal start[1]
> ---------------------------------------------------
> 
> --------------------- WARNING ---------------------
> MSG: Setting end to equal start[1]
> ---------------------------------------------------
> 
> --------------------- WARNING ---------------------
> MSG: Setting end to equal start[1]
> ---------------------------------------------------
> 
> --------------------- WARNING ---------------------
> MSG: Setting end to equal start[1]
> ---------------------------------------------------
> 
> --------------------- WARNING ---------------------
> MSG: Setting end to equal start[1]
> ---------------------------------------------------
> t/Assembly/core.t ............................ 246/890 Can't do inplace edit without backup at Bio/Root/IO.pm line 513.
> # Looks like you planned 890 tests but ran 246.
> # Looks like your test exited with 25 just after 246.
> t/Assembly/core.t ............................ Dubious, test returned 25 (wstat 6400, 0x1900)
> Failed 644/890 subtests
> 
> Is it ok to install Bioperl anyway?
> 
> Thanks for your help!
> 
> Cerebron Emtadrat
> 
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