Mauricio Herrera Cuadra | 1 Dec 01:56 2006
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Re: [Root-l] Intermittent MySQL problems on BioPerl wiki

Chris & Chris,

I've run the maintenance scripts for MediaWiki (just in case they 
weren't run in the upgrade to 1.8.2), restarted Apache (with no 
significant changes on website response), then rebooted the machine 
(seems like MySQL restart didn't do the trick) and apparently its 
behaving much better. Please check if the reported error still happens.

Regards,
Mauricio.

Chris Dagdigian wrote:
> Reports like this need to go to support <at> helpdesk.open-bio.org so that  
> they enter our RT helpdesk queue --  the main reason is that  
> sometimes emails to the root-l <at> open-bio.org administrators mailing  
> list can get lost in the shuffle.
> 
> I am going to bounce this message into RT and will restart mysql on  
> the portal box. This is probably something we should be doing anyway  
> to free up memory -- the wikis in particular seem to be pretty hard  
> on mysql and free memory.
> 
> -Chris
> 
> On Nov 30, 2006, at 2:11 PM, Chris Fields wrote:
> 
>> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and
>> WinXP):
>>
>> Database error
(Continue reading)

Nathan S. Haigh | 1 Dec 08:47 2006
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Re: Upgrading my BioPerl RC via ppm?

Caitlin wrote:
> Hi all.
>
> I'm currently using BioPerl 1.5.2 RC2 but I've seen multiple references
> to 1.5.2 RC5. Can anyone tell me how to upgrade to the latest version?
> The ppm GUI (ActivePerl Build 819) doesn't include any BioPerl packages
> among those deemed upgradable.
>
> Thanks,
>
> ~Katie
>
>
>   

Hi Katie,

Currently there is not an RC5 PPM package available - we are hoping to
have the official 1.5.2 release out pretty soon and there will
definitely be a PPM package for that! Are you experiencing any problems
with your current version of bioperl? If not, there is no need to worry,
once we've released an updated PPM package your PPM GUI should then be
able to see it as an upgrade - hopefully! :o)

Sendu, I know you were working on automatically generating PPM packages
- what is the current situation with regards to this?

Nath

---
(Continue reading)

Sendu Bala | 1 Dec 10:00 2006
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Re: BLASTing with a seqio/seq object...

Samantha Thompson wrote:

You missed a step...

> use strict;
> use Bio::Perl;
> use Bio::Seq;
> use Bio::SeqIO;
> 
> use Bio::Tools::Run::RemoteBlast;
> use Bio::SearchIO;
> 
> #seq bit
> 
> #$seq_obj = Bio::Seq->new(-format => 'fasta');
> 
> my $seqio_obj = Bio::SeqIO->new(-file => 
> "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta');
> 
> my $seq_obj = $seqio_obj->next_seq;
> 
> 
> 
> #blast bit
> 
> my $remote_blast = Bio::Tools::Run::RemoteBlast->new (
>          -prog => 'blastp', -db => 'nr', -expect => '1e-15' );
> 
> my $blast_report = $remote_blast->submit_blast($seq_obj);

(Continue reading)

Sendu Bala | 1 Dec 10:03 2006
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Re: Error with supplied lineages importing uniprot data

pelikan <at> cs.pitt.edu wrote:
> Hello all,
> 
>  I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows,
> without Cygwin. The "make test"s have all completed without error. This
> is my first time dealing with bioperl, so bear with me.
> 
>    I've successfully loaded the most recent taxonomy information using the
> biosql-schema scripts. After this, I attempted to load the most recent
> release of the uniprot flat file dataset with the following command:
> 
> load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass
> ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat
> 
> I am subsequently greeted by many of the following errors:
> 
> Could not store Q7N3Q6:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: The supplied lineage does not start near 'Photorhabdus luminescens
> subsp. laumondii'

In your uniprot_sprot.dat file there'll be some kind of entry with that 
Photorhabdus species. Can you post that entry (sans sequence if it has 
one) so I can take a look at it? Maybe post a few that cause problems, 
and a few that don't.
Sendu Bala | 1 Dec 10:19 2006
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Re: Bioperl 1.5.2 RC5 install on WinXP ActivePerl5.8.8.819

Chris Fields wrote:
>> Nathan S. Haigh wrote:
>>> More updates:
>>>
>>> After the failed install I updating Module::Build, and re-ran the 
>>> install, I get:
>>>
>>> -- snip --
>>> Creating new 'Build' script for 'bioperl' version '1.005002005'
>>> Warning: while trying to determine prerequisites for 
>>> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of 
>>> Module::Build the following error occurred: 'Failed to re-load 
>>> 'ModuleBuildBiope
>>> rl': Can't locate ModuleBuildBioperl.pm in  <at> INC ( <at> INC contains: 
>>> _build\lib C:\Perl\site\lib C:\
>>> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1.
>>> '
>>>
>>> Falling back to META.yml for prerequisites 'YAML' not installed, 
>>> cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml'
>>> -- snip --
>> I had that problem fleetingly and it drove me crazy because 
>> later I couldn't reproduce it. Is it reproducible on your end?
> 
> During Module::Build installation I see this:
> 
> ...
> t\metadata........ok
>         8/43 skipped: YAML_support feature is not enabled

(Continue reading)

Nathan S. Haigh | 1 Dec 10:26 2006
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Re: Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819

Sendu Bala wrote:
> Chris Fields wrote:
>>
>> I know that setting up the PPM is a pain, but I have to say it is 
>> much faster, and all required PPMs are available.  Which makes me 
>> curious: why bother with trying out a CPAN installation process at 
>> this point, especially when you have to use PPM to install some of 
>> the prereqs properly anyway?
>
> Firstly, problems discovered and resulting fixes will help all 
> platforms, not just Windows. So thanks for trying it out and reporting 
> back. Secondly, the PPM method, like Bundle::BioPerl, is 
> all-or-nothing. The CPAN installation method allows an interactive 
> choice of which optional things to install.
>
> If what you say about DB_File is true, then that's a great shame!
>
>
> So I can do further trouble-shooting of my own, what is the sure-fire 
> way to completely clean-out an ActivePerl install, including any 
> modules you might have installed with PPMs or CPAN?
>
>

In addition, using CPAN allows you to run the test suite easily without 
the need to download it separately and run it after a PPM install.

I don't know of a way to clean out ActivePerl - I use VMWare Workstation 
and have a virtual machine with a fresh install of WinXP and ActivePerl 
5.8.8.819 - maybe someone else has ideas?
(Continue reading)

Sendu Bala | 1 Dec 10:13 2006
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Re: Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819

Chris Fields wrote:
> 
> I know that setting up the PPM is a pain, but I have to say it is much 
> faster, and all required PPMs are available.  Which makes me curious: 
> why bother with trying out a CPAN installation process at this point, 
> especially when you have to use PPM to install some of the prereqs 
> properly anyway?

Firstly, problems discovered and resulting fixes will help all 
platforms, not just Windows. So thanks for trying it out and reporting 
back. Secondly, the PPM method, like Bundle::BioPerl, is all-or-nothing. 
The CPAN installation method allows an interactive choice of which 
optional things to install.

If what you say about DB_File is true, then that's a great shame!

So I can do further trouble-shooting of my own, what is the sure-fire 
way to completely clean-out an ActivePerl install, including any modules 
you might have installed with PPMs or CPAN?
Chris Fields | 1 Dec 15:08 2006
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Re: Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819


On Dec 1, 2006, at 3:13 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> I know that setting up the PPM is a pain, but I have to say it is  
>> much faster, and all required PPMs are available.  Which makes me  
>> curious: why bother with trying out a CPAN installation process at  
>> this point, especially when you have to use PPM to install some of  
>> the prereqs properly anyway?
>
> Firstly, problems discovered and resulting fixes will help all  
> platforms, not just Windows. So thanks for trying it out and  
> reporting back. Secondly, the PPM method, like Bundle::BioPerl, is  
> all-or-nothing. The CPAN installation method allows an interactive  
> choice of which optional things to install.

Yes, I understand that.  My point is, you are generally forced to use  
PPM anyway due to several modules not installing properly (all the  
'trouble' distributions, like DB_File, are available via PPM).  I can  
see using CPAN as an alternative way of installing Bioperl for a  
distribution, or as the primary method via CVS or manually, but not  
for distributions.  At least not until the kinks are worked out for  
Windows users.

What are the significant issues for a bioperl PPM installation, based  
on the last PPM Nathan set up?  If there is a redirection problem,  
could we just modify the installation docs to address that ('due to  
problem X, you must install the following modules prior to installing  
BioPerl 1.5.2...').

(Continue reading)

Chris Fields | 1 Dec 15:10 2006
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Re: Bioperl 1.5.2 RC5 install on WinXP ActivePerl5.8.8.819


On Dec 1, 2006, at 3:19 AM, Sendu Bala wrote:

> You were pointing out the YAML issue? I think I'm less concerned  
> with that (solution: install YAML) and much more concerned with why  
> it can't reload ModuleBuildBioperl (claiming it isn't in  <at> INC). The  
> module in question is in the same dir as the Build script, so it  
> should be found automatically.
>
> The only thing I can think of is that CPAN doesn't manage to chdir  
> to the directory. Hopefully I'll be able to reproduce this and then  
> I can investigate further.

My thought was the two were related in some way.  I'm not sure to  
tell the truth.

-chris
Sendu Bala | 1 Dec 15:17 2006
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Re: Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819

Chris Fields wrote:
> 
> On Dec 1, 2006, at 3:13 AM, Sendu Bala wrote:
> 
>> Chris Fields wrote:
>>> I know that setting up the PPM is a pain, but I have to say it is 
>>> much faster, and all required PPMs are available.  Which makes me 
>>> curious: why bother with trying out a CPAN installation process at 
>>> this point, especially when you have to use PPM to install some of 
>>> the prereqs properly anyway?
>>
>> Firstly, problems discovered and resulting fixes will help all 
>> platforms, not just Windows. So thanks for trying it out and reporting 
>> back. Secondly, the PPM method, like Bundle::BioPerl, is 
>> all-or-nothing. The CPAN installation method allows an interactive 
>> choice of which optional things to install.
> 
> Yes, I understand that.  My point is, you are generally forced to use 
> PPM anyway due to several modules not installing properly (all the 
> 'trouble' distributions, like DB_File, are available via PPM).  I can 
> see using CPAN as an alternative way of installing Bioperl for a 
> distribution, or as the primary method via CVS or manually, but not for 
> distributions.  At least not until the kinks are worked out for Windows 
> users.

CPAN isn't being suggested as the primary or preferred installation 
method for Windows. That will still be PPM. I'm mentioning CPAN / manual 
installation in the Windows INSTALL docs for the benefit of anyone who 
wants a simple install and test environment when checking out from CVS.

(Continue reading)


Gmane