scott at scottcain.net
Tue Feb 7 16:12:19 EST 2012
Yes, but those doc don't address exactly the problem Cassandra is
having, that she wants to use local::lib, but there need to be some
prereqs installed, but they can't be because she chose to use
local::lib, and it's not installed. That's all fine if you're not a
newbie and know how to properly install the prereqs before using the
cpan shell, but when following instructions that say "use local::lib",
I find that the instructions are completely insufficient in actually
getting the desired software installed. Thus the need for a good
On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfields at illinois.edu> wrote:
> I guess one key question is where these CPAN installation instructions come
> from. They're a bit odd, and if this is from the wiki we need to do some
> Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> single perl version.
> In my case I use perlbrew (which is all local by default, and allows
> switching between perl versions). Highly recommend using either simple
> local::lib or perlbrew in combination with cpanm.
> On 02/07/2012 02:55 PM, Scott Cain wrote:
>> hi Cassandra,
>> I don't have an answer for you at the moment. It seems to me that
>> using local::lib is a good idea, but I've never found a good tutorial
>> for using it, so I haven't. Perhaps someone else on the list can
>> suggest one.
>> The other thing I just wanted to mention as the admin that approved
>> your message--I came very close to deleting it from the queue without
>> looking at it because it is not unusual for spam messages to have
>> generic subjects like "help!" (just for future reference :-)
>> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com> wrote:
>>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>> installed becaused I have already write some scripts but I'm biologist
>>> not pretty sure about what messages say.
>>> My perl version:
>>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>> My computer:
>>> Mac OS X Vesion 10.5.8
>>> I was following this preliminary steps:
>>> PRELIMINARY PREPARATION
>>> This is optional, but regardless of your subsequent choice of
>>> installation method, it will help to carry out the following steps.
>>> They will increase the likelyhood of installation success
>>> (especially of optional dependencies).
>>> * Upgrade CPAN:
>>> >perl -MCPAN -e shell
>>> cpan>install Bundle::CPAN
>>> * Install/upgrade Module::Build, and make it your preferred
>>> cpan>install Module::Build
>>> cpan>o conf prefer_installer MB
>>> cpan>o conf commit
>>> * Install the expat library by whatever method is
>>> appropriate for your system.
>>> * If your expat library is installed in a non-standard location,
>>> tell CPAN about it:
>>> cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>> cpan>o conf commit
>>> And I think I did "Upgrade CPAN properly" but when I tried the next one
>>> started asking too many things to me, and finally it stopped due to "some
>>> problems". In text file you can see the whole process.
>>> What did I do wrong?
>>> After solving these preliminary steps, what should I do? What exactly
>>> or .whatever should I download to install?
>>> I don't see the difference between installing it through "built.PL" or
>>> CPAN. And I don't know if I should do this or that "Fink*" stuff for
>>> * I went to Fink webpage and what I expected to see was "hello! download
>>> Bioperl simply clicking here!" but far from this, what it seems is that
>>> first I have to download some kinf of Fink-program before starting with
>>> Bioperl... is it something close to this?
>>> I'm sorry, too many questions... But I really want to learn to use
>>> but I have no people to ask it face to face.
>>> Thank you so much,
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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