[Gmod-gbrowse] [Gmod-help] Re: gbrowse

Wed Oct 1 14:22:09 EDT 2008

I fixed the DB_File issue by adding the tcool repository to the list of
repositories that the installer adds but I'm currently unable to commit, so
I'm attaching the install script to this email.  I'll do the check for perl
5.10 next.

Scott

On Wed, Oct 1, 2008 at 12:45 PM, Scott Cain <cain.cshl at gmail.com> wrote:

> I still don't know what happened to DB_File from ActiveState for perl
> 5.8--it used to be there and google doesn't turn up and explanation.  For
> perl 5.10, it is supposed to be distributed with core, but it isn't present
> either.  When 5.10 does get DB_File in core, it should support GBrowse
> fine.  Until then, I looks like we'll have to add another repository to the
> preinstall so that DB_File can be found:  there is a ppm version of DB_File
> at ppm.tcool.org that appears to work.  I'll update the installer and do
> some testing.
>
> Scott
>
>
>
> On Wed, Oct 1, 2008 at 11:12 AM, Scott Cain <cain.cshl at gmail.com<https://mail.google.com/mail?view=cm&tf=0&to=cain.cshl@gmail.com>
> > wrote:
>
>> Darn it.  I tried ActiveState perl 5.10 since I read that there cpan shell
>> problems were fixed, but it doesn't have a DB_File either.  It is baffling
>> to me that ActiveState could have screwed up such an important module.
>>
>> Scott
>>
>>
>>
>> On Wed, Oct 1, 2008 at 10:40 AM, Chris Fields <cjfields at illinois.edu<https://mail.google.com/mail?view=cm&tf=0&to=cjfields@illinois.edu>
>> > wrote:
>>
>>> That's scary.  I wonder how this might affect bioperl tests and
>>> installation.
>>>
>>> chris
>>>
>>>
>>> On Oct 1, 2008, at 8:58 AM, Scott Cain wrote:
>>>
>>>  Somebody (perhaps Remi) submitted a bug report about this:
>>>>
>>>>
>>>> https://sourceforge.net/tracker/?func=detail&atid=391291&aid=2138884&group_id=27707
>>>>
>>>> I was just working on it.  The bug report has a link to a suggested fix
>>>> when DB_File doesn't install.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Wed, Oct 1, 2008 at 9:54 AM, Lincoln Stein <lincoln.stein at gmail.com<https://mail.google.com/mail?view=cm&tf=0&to=lincoln.stein@gmail.com>>
>>>> wrote:
>>>> Hi Remi,
>>>>
>>>> ActivePerl 5.10 has known problems with missing modules. I suggest that
>>>> you uninstall it and try version 5.8, which is just as good.
>>>>
>>>> Lincoln
>>>>
>>>> On Wed, Oct 1, 2008 at 9:46 AM, Rémi Emans <remi.emans at univ-perp.fr<https://mail.google.com/mail?view=cm&tf=0&to=remi.emans@univ-perp.fr>>
>>>> wrote:
>>>> Lincoln Stein a écrit :
>>>>
>>>> Hi Remi,
>>>>
>>>> This means that your version of Perl does not have the DB_File module
>>>> installed. This is odd, because DB_File is a standard part of most Perl
>>>> distributions. From your error message, it looks like you are using Perl on
>>>> a Windows platform. Are you using the ActiveState distribution, or a
>>>> different one? Which version of the distribution are you using?
>>>>
>>>> Lincoln
>>>> Thank you to answer me so quickly...
>>>> I've installed Active Perl 5.10 which seem to be the last package...
>>>>
>>>> Rémi
>>>>
>>>>
>>>> --
>>>> Biologie & Ecologie Tropicale & Méditerranéenne
>>>> Service Informatique UMR 5244
>>>> CNRS/EPHE/Université de Perpignan
>>>> 52, Avenue Paul Alduy
>>>> 66860 Perpignan
>>>> Tel 33 (0)468662055
>>>> Fax 33 (0)468503686
>>>> http://cbetm.univ-perp.fr
>>>>
>>>>
>>>> --
>>>> Ce message a été vérifié par MailScanner
>>>> pour des virus ou des polluriels et rien de
>>>> suspect n'a été trouvé.
>>>> CRI UPVD http://www.univ-perp.fr
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Lincoln D. Stein
>>>>
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca<https://mail.google.com/mail?view=cm&tf=0&to=Stacey.Quinn@oicr.on.ca>
>>>> >
>>>>
>>>> Cold Spring Harbor Laboratory
>>>> 1 Bungtown Road
>>>> Cold Spring Harbor, NY 11724 USA
>>>> (516) 367-8380
>>>> Assistant: Sandra Michelsen <michelse at cshl.edu<https://mail.google.com/mail?view=cm&tf=0&to=michelse@cshl.edu>
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.
>>>> cain.cshl at gmail.com<https://mail.google.com/mail?view=cm&tf=0&to=cain.cshl@gmail.com>
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
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>>>>
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Marie-Claude Hofmann
>>> College of Veterinary Medicine
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   cain.cshl at gmail.com<https://mail.google.com/mail?view=cm&tf=0&to=cain.cshl@gmail.com>
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   cain.cshl at gmail.com<https://mail.google.com/mail?view=cm&tf=0&to=cain.cshl@gmail.com>
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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