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

[Scott Cain]

I suspect you'll be fine.

Scott


Sent from my iPad

On Jun 17, 2013, at 4:04 AM, Cerebron Emtadrat <emtadrat at yahoo.de> wrote:

> 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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