[Bioperl-l] Installing Bioperl using PPM

[Chris Fields]

I think he means that you should do the following:

1) use "search bioperl"
2) pick the number of the correct bioperl from the list (NOT the version 
number) and type "install #"

Here's what it looks like get when I use PPM3

C:\Documents and Settings\Chris Fields>ppm
PPM - Programmer's Package Manager version 3.1.
Copyright (c) 2001 ActiveState SRL. All Rights Reserved.

Entering interactive shell. Using Term::ReadLine::Stub as readline library.

Type 'help' to get started.

ppm> rep
Repositories:
[1] bioperl
[ ] ActiveState Package Repository
[ ] ActiveState PPM2 Repository
[ ] gmod
[ ] kobes
[ ] local
ppm> search bioperl
Searching in Active Repositories
   1. Bioperl-1.2     [1.2] Bioperl 1.2 PPM3 Archive
   2. Bioperl-1.2.1 [1.2.1] Bioperl 1.2.1 PPM3 Archive
   3. Bioperl-1.2.3 [1.2.3] Bioperl 1.2.3 PPM3 Archive
   4. Bioperl-1.4     [1.4] Bioperl 1.4 PPM3 Archive
ppm> install 4

<Should install bioperl 1.4 unless already installed>
....


Chris


At 05:35 PM 1/20/2005, Tim Alcon wrote:
>Typing "install 1.4" didn't work, but typing "install Bioperl-1.4" did.
>Thanks.
>
>Tim
>
>
>
>Nathan Haigh wrote:
>
>>Please read this even if you think you know how to install modules via PPM!
>>
>>This is just a note on what to do to install the latest version of 
>>Bioperl (or any other module) via PPM:
>>Because of inconsistencies (see ActiveStates comments on this at the 
>>bottom) with the way PPM determines modules names/versions etc
>>it is NOT WISE to install modules by going:
>>    "install bioperl"
>>OR
>>    "upgrade bioperl"
>>
>>You are very likely NOT to install the most recent version of a 
>>particular module by doing this! Instead you should do the
>>following:
>>    "search bioperl"
>>This gives a numbered list of the available modules in the repository's 
>>searched by your PPM (you can add additional repositories in
>>addition to the defaults given during installation - and this is 
>>advised). Chose the number of the correct module to install from
>>the list and do:
>>    "install <number>"
>>Where <number> is the number of the module you wish to install. This way 
>>you will ensure you install the correct module/version YOU
>>want not the arbitrary module that PPM seems to want to install most of 
>>the time!
>>
>>As soon as the official Bioperl 1.5 is released, I'll make the ppd and 
>>tar.gz files so it can be installed via PPM.
>>
>>Nathan
>>
>>ActiveStates comment on PPM's inconsistencies for determining module 
>>name/versions:
>>"Sorry for the confusion, ppm3 is kind of inconsistent in spots."
>>
>>
>>
>>
>>>-----Original Message-----
>>>From: bioperl-l-bounces at portal.open-bio.org 
>>>[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Tim Alcon
>>>Sent: 18 January 2005 22:20
>>>To: bioperl-l at portal.open-bio.org
>>>Subject: [Bioperl-l] accessing GenBank
>>>
>>>I seem unable to access GenBank.  When running bptutorial.exe, it seems
>>>like all the other examples run fine except that one.  Anyone know why
>>>that would be?  I'm using ActivePerl on Windows XP.  I have whichever
>>>version of bioperl is the current default using ppm (it's at least
>>>1.0).   When I run the exact same code from my campus Unix account, it
>>>works fine.
>>>
>>>Tim
>>>
>>>_______________________________________________
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>>>Bioperl-l at portal.open-bio.org
>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
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>>>
>>
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>>
>>
>>
>>
>>_______________________________________________
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>>
>>
>>
>
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__________________________________

Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer

Address:

University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
600 S. Mathews Ave.
Urbana, IL 61801

Phone : (217) 333-7098
Fax : (217) 244-5858