BioPerl Core 1.6.1 PPM now available

[Chris Fields-5]

The first cut at the ActivePerl PPM distribution for BioPerl core  
1.6.1 is now available.  Instructions for installing on Windows are  
here:

http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows

I have made this installation architecture-independent, but it has  
only been testing on WinXP using ActivePerl 5.10.1.1006.  A couple of  
modules may give warnings (specifically SOAP::Lite and  
XML::SAX::Writer), but the installation should proceed.  We would  
appreciate feedback on trying to install this with other versions of  
ActivePerl or on more recent versions of Windows (Vista, Win7).

Enjoy!

chris
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[Mark A. Jensen]

Hey Chris-
I'm trying this out from the ppm-shell. I see that bioperl-1.4 is considered a
dependency and is loaded and installed. Not sure yet what happens to it, seems
strange. I'm using repos activestate, trouchelle58, and uwinnipeg58. More as
this develops.
MAJ
----- Original Message -----
From: "Chris Fields" <cjfields@...>
To: "BioPerl List" <bioperl-l@...>
Sent: Saturday, October 10, 2009 1:24 AM
Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available

> The first cut at the ActivePerl PPM distribution for BioPerl core  1.6.1 is
> now available.  Instructions for installing on Windows are  here:
>
> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>
> I have made this installation architecture-independent, but it has  only been
> testing on WinXP using ActivePerl 5.10.1.1006.  A couple of  modules may give
> warnings (specifically SOAP::Lite and  XML::SAX::Writer), but the installation
> should proceed.  We would  appreciate feedback on trying to install this with
> other versions of  ActivePerl or on more recent versions of Windows (Vista,
> Win7).
>
> Enjoy!
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

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[Mark A. Jensen]

(P.S. - my current worry is that Bio::ASN1::EntrezGene is enforcing bioperl-1.4
dependency)
----- Original Message -----
From: "Chris Fields" <cjfields@...>
To: "BioPerl List" <bioperl-l@...>
Sent: Saturday, October 10, 2009 1:24 AM
Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available

> The first cut at the ActivePerl PPM distribution for BioPerl core  1.6.1 is
> now available.  Instructions for installing on Windows are  here:
>
> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>
> I have made this installation architecture-independent, but it has  only been
> testing on WinXP using ActivePerl 5.10.1.1006.  A couple of  modules may give
> warnings (specifically SOAP::Lite and  XML::SAX::Writer), but the installation
> should proceed.  We would  appreciate feedback on trying to install this with
> other versions of  ActivePerl or on more recent versions of Windows (Vista,
> Win7).
>
> Enjoy!
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

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[Mark A. Jensen]

More detail:

The setup:

To install BioPerl via ppm, we require the following in order
to get a working DB_File for 5.8:

 (possibly required:
 
 C:> ppm install PPM-Repositories
 
 then...
 )

 C:> ppm repo add http://bioperl.org/DIST
 C:> ppm repo add trouchelle58

 We try

 C:> ppm install BioPerl

 (case is important -- not 'bioperl' eg), but this borks.

When BioPerl is installed, Bundle-BioPerl-Core is subinstalled,
bioperl-1.4 is installed. Pops back up to BioPerl 1.6.1 installation.
HTML is generated, then "Updating files in site area." Here
ppm borks when it tries to make a ppm backup for the first BioPerl
module it finds, since the file it wants to make already exists.

  * theory: Bio::ASN1::EntrezGene (one of the deps installed by
    Bundle-BioPerl-Core) requires Bio::Index::EntrezGene, so obtains a
    provider that submits bioperl-1.4

The following procedure succeeds:

Install Bundle-BioPerl-Core explicitly first:

 C:> ppm install Bundle-BioPerl-Core

This succeeds, but now

 C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"
 1.4

Now install BioPerl

 C:> ppm install BioPerl

and we end up with

 C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"
 1.006001

MAJ
----- Original Message -----
From: "Chris Fields" <cjfields@...>
To: "BioPerl List" <bioperl-l@...>
Sent: Saturday, October 10, 2009 1:24 AM
Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available

> The first cut at the ActivePerl PPM distribution for BioPerl core  
> 1.6.1 is now available.  Instructions for installing on Windows are  
> here:
>
> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>
> I have made this installation architecture-independent, but it has  
> only been testing on WinXP using ActivePerl 5.10.1.1006.  A couple of  
> modules may give warnings (specifically SOAP::Lite and  
> XML::SAX::Writer), but the installation should proceed.  We would  
> appreciate feedback on trying to install this with other versions of  
> ActivePerl or on more recent versions of Windows (Vista, Win7).
>
> Enjoy!
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

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[Chris Fields-5]

Mark,

Definitely suboptimal.  Are you using ActivePerl 5.8? (I used 5.10.1)

I'm wondering if there are a few Bio::ASN1::EntrezGene out there  
floating around in other repos.  The one in the bioperl PPM repo  
doesn't have that requirement.  The only way I can think of to direct  
installation of the BioPerl PPM for Bio::ASN1::EntrezGene is to  
indicate the bioperl repo needs to be first in the repo list.

chris

On Oct 10, 2009, at 4:53 PM, Mark A. Jensen wrote:

> More detail:
>
> The setup:
>
> To install BioPerl via ppm, we require the following in order to get  
> a working DB_File for 5.8:
>
> (possibly required:
> C:> ppm install PPM-Repositories
> then...
> )
>
> C:> ppm repo add http://bioperl.org/DIST
> C:> ppm repo add trouchelle58
>
> We try
>
> C:> ppm install BioPerl
>
> (case is important -- not 'bioperl' eg), but this borks.
>
> When BioPerl is installed, Bundle-BioPerl-Core is subinstalled,
> bioperl-1.4 is installed. Pops back up to BioPerl 1.6.1  
> installation. HTML is generated, then "Updating files in site area."  
> Here
> ppm borks when it tries to make a ppm backup for the first BioPerl
> module it finds, since the file it wants to make already exists.
>
> * theory: Bio::ASN1::EntrezGene (one of the deps installed by
>   Bundle-BioPerl-Core) requires Bio::Index::EntrezGene, so obtains a
>   provider that submits bioperl-1.4
>
> The following procedure succeeds:
>
> Install Bundle-BioPerl-Core explicitly first:
>
> C:> ppm install Bundle-BioPerl-Core
>
> This succeeds, but now
>
> C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"
> 1.4
>
> Now install BioPerl
>
> C:> ppm install BioPerl
>
> and we end up with
>
> C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"
> 1.006001
>
> MAJ
> ----- Original Message ----- From: "Chris Fields" <cjfields@...
> >
> To: "BioPerl List" <bioperl-l@...>
> Sent: Saturday, October 10, 2009 1:24 AM
> Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available
>
>
>> The first cut at the ActivePerl PPM distribution for BioPerl core  
>> 1.6.1 is now available.  Instructions for installing on Windows  
>> are  here:
>> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>> I have made this installation architecture-independent, but it has  
>> only been testing on WinXP using ActivePerl 5.10.1.1006.  A couple  
>> of  modules may give warnings (specifically SOAP::Lite and  
>> XML::SAX::Writer), but the installation should proceed.  We would  
>> appreciate feedback on trying to install this with other versions  
>> of  ActivePerl or on more recent versions of Windows (Vista, Win7).
>> Enjoy!
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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[Mark A. Jensen]

Yeah-- It is 5.8-- I'll try with 5.10. The Bio::ASN1::EntrezGene package
contains the  Bio::ASN1::EntrezGene::Indexer module, which has the bioperl
dependency-- What I'm going for (for a class I'm teaching) is a ppm installation
that will transparently include B::A::E, since we'll be doing some DB and EUtils
stuff that I believe needs NCBIHelper. (Agggh...). I'm trying to make the
install
as painless as possible for the participants....
cheers
----- Original Message -----
From: "Chris Fields" <cjfields@...>
To: "Mark A. Jensen" <maj@...>
Cc: "BioPerl List" <bioperl-l@...>
Sent: Saturday, October 10, 2009 6:45 PM
Subject: Re: [Bioperl-l] BioPerl Core 1.6.1 PPM now available

> Mark,
>
> Definitely suboptimal.  Are you using ActivePerl 5.8? (I used 5.10.1)
>
> I'm wondering if there are a few Bio::ASN1::EntrezGene out there  floating
> around in other repos.  The one in the bioperl PPM repo  doesn't have that
> requirement.  The only way I can think of to direct  installation of the
> BioPerl PPM for Bio::ASN1::EntrezGene is to  indicate the bioperl repo needs
> to be first in the repo list.
>
> chris
>
> On Oct 10, 2009, at 4:53 PM, Mark A. Jensen wrote:
>
>> More detail:
>>
>> The setup:
>>
>> To install BioPerl via ppm, we require the following in order to get  a
>> working DB_File for 5.8:
>>
>> (possibly required:
>> C:> ppm install PPM-Repositories
>> then...
>> )
>>
>> C:> ppm repo add http://bioperl.org/DIST
>> C:> ppm repo add trouchelle58
>>
>> We try
>>
>> C:> ppm install BioPerl
>>
>> (case is important -- not 'bioperl' eg), but this borks.
>>
>> When BioPerl is installed, Bundle-BioPerl-Core is subinstalled,
>> bioperl-1.4 is installed. Pops back up to BioPerl 1.6.1  installation. HTML
>> is generated, then "Updating files in site area."  Here
>> ppm borks when it tries to make a ppm backup for the first BioPerl
>> module it finds, since the file it wants to make already exists.
>>
>> * theory: Bio::ASN1::EntrezGene (one of the deps installed by
>>   Bundle-BioPerl-Core) requires Bio::Index::EntrezGene, so obtains a
>>   provider that submits bioperl-1.4
>>
>> The following procedure succeeds:
>>
>> Install Bundle-BioPerl-Core explicitly first:
>>
>> C:> ppm install Bundle-BioPerl-Core
>>
>> This succeeds, but now
>>
>> C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"
>> 1.4
>>
>> Now install BioPerl
>>
>> C:> ppm install BioPerl
>>
>> and we end up with
>>
>> C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION"
>> 1.006001
>>
>> MAJ
>> ----- Original Message ----- From: "Chris Fields" <cjfields@...
>> >
>> To: "BioPerl List" <bioperl-l@...>
>> Sent: Saturday, October 10, 2009 1:24 AM
>> Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available
>>
>>
>>> The first cut at the ActivePerl PPM distribution for BioPerl core   1.6.1 is
>>> now available.  Instructions for installing on Windows  are  here:
>>> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>>> I have made this installation architecture-independent, but it has   only
>>> been testing on WinXP using ActivePerl 5.10.1.1006.  A couple  of  modules
>>> may give warnings (specifically SOAP::Lite and   XML::SAX::Writer), but the
>>> installation should proceed.  We would   appreciate feedback on trying to
>>> install this with other versions  of  ActivePerl or on more recent versions
>>> of Windows (Vista, Win7).
>>> Enjoy!
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@...
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>

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[Mark A. Jensen]

I find with the 5.10 install that the ActiveState repo borks on an install of
SOAP::Lite 0.71 ("no provider of Apache:: found for package SOAP::Lite").
The message makes me think the .ppd is wrong on their end.  
The trouchelle and uwinnipeg repo versions (both 0.69) install find;
maybe a workaround is to specify version 0.69 in the Bundle-BioPerl-Core
spec.
cheers MAJ
----- Original Message -----
From: "Chris Fields" <cjfields@...>
To: "BioPerl List" <bioperl-l@...>
Sent: Saturday, October 10, 2009 1:24 AM
Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available

> The first cut at the ActivePerl PPM distribution for BioPerl core  
> 1.6.1 is now available.  Instructions for installing on Windows are  
> here:
>
> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>
> I have made this installation architecture-independent, but it has  
> only been testing on WinXP using ActivePerl 5.10.1.1006.  A couple of  
> modules may give warnings (specifically SOAP::Lite and  
> XML::SAX::Writer), but the installation should proceed.  We would  
> appreciate feedback on trying to install this with other versions of  
> ActivePerl or on more recent versions of Windows (Vista, Win7).
>
> Enjoy!
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

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[Chris Fields-5]

Mark,

That might work, though I think that indicates the minimal version,  
not requiring a specific version.  Makes me think we should have a  
local PPM for SOAP::Lite as well that doesn't ask for this.  One would  
think the automated process ActiveState has for building PPMs would  
have pointed this out!

chris

On Oct 13, 2009, at 9:53 AM, Mark A. Jensen wrote:

> I find with the 5.10 install that the ActiveState repo borks on an  
> install of SOAP::Lite 0.71 ("no provider of Apache:: found for  
> package SOAP::Lite").
> The message makes me think the .ppd is wrong on their end.  The  
> trouchelle and uwinnipeg repo versions (both 0.69) install find;  
> maybe a workaround is to specify version 0.69 in the Bundle-BioPerl-
> Core
> spec. cheers MAJ
> ----- Original Message ----- From: "Chris Fields" <cjfields@...
> >
> To: "BioPerl List" <bioperl-l@...>
> Sent: Saturday, October 10, 2009 1:24 AM
> Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available
>
>
>> The first cut at the ActivePerl PPM distribution for BioPerl core  
>> 1.6.1 is now available.  Instructions for installing on Windows  
>> are  here:
>> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>> I have made this installation architecture-independent, but it has  
>> only been testing on WinXP using ActivePerl 5.10.1.1006.  A couple  
>> of  modules may give warnings (specifically SOAP::Lite and  
>> XML::SAX::Writer), but the installation should proceed.  We would  
>> appreciate feedback on trying to install this with other versions  
>> of  ActivePerl or on more recent versions of Windows (Vista, Win7).
>> Enjoy!
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>

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