Hi Dave, Chris, Cassandra and others,
I was following the wonderful directions that Dave wrote and have made it to an almost similar end as Cassandra.
ncfa-2-3502-ap3:~ Vi$ perl -e "use Bio::SeqIO;"
Base class package "Bio::Root::Root" is empty.
(Perhaps you need to 'use' the module which defines that package first.)
at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.
Compilation failed in require at (eval 1) line 3.
...propagated at /System/Library/Perl/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Simple.pm line 87.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.
Compilation failed in require at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
I see that there are many items that were not compiled "aborted", is that something I need to do separately? I'm sorry but I got lost when Dave and Chris began discussing the stuff at the bottom of this chain. So if someone could explain a solution simply I
would greatly appreciate it!
On Tuesday, February 7, 2012 3:38:12 PM UTC-6, Dave Messina wrote:
I will take the opportunity to shamelessly pimp my no-install install
instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
Casandra is just looking to get started with BioPerl, messing with external
libs and configs is probably overkill.
There’s a quickie, “zero-install” way to get BioPerl on your system.
1) Okay, click here to download bioperl as a zip file:
when it's done downloading, unzip it if your computer hasn’t done it
automatically. On the
command line, you would do:
or whatever the file is called. You should then have a folder with some
ugly name like
3) rename that to
4) move that folder to wherever you want to keep it. I keep mine in a
directory called src in my
So on my computer if I go to the command line and cd to that folder and
type pwd I get:
5) in the terminal, cd to your home directory.
6) see if you have a file named .bash_profile by typing
ls -l ~/.bash_profile
7) if so, open that file in your favorite editor. if the file doesn't
exist, just create the file.
8) put this line in your .bash_profile
(obviously replacing my path info with wherever you chose to put
9) save and close your .bash_profile
10) open a new terminal window so that the change will take effect.
11) on the command line of the new terminal, type
perl -e "use Bio::SeqIO;"
If that works, then you have "installed" bioperl. Yay!
On Tue, Feb 7, 2012 at 22:12, Scott Cain <sc... <at> scottcain.net> wrote:
> 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 <cjfi... <at> illinois.edu>
> > I guess one key question is where these CPAN installation instructions
> > from. They're a bit odd, and if this is from the wiki we need to do some
> > updating.
> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> > single perl version.
> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
> > 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.
> > https://metacpan.org/module/perlbrew
> > https://metacpan.org/module/cpanm
> > chris
> > 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
> >> Scott
> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasa... <at> gmail.com> wrote:
> >>> Hi,
> >>> 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
> >>> so...
> >>> 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
> >>> cpan>q
> >>> * Install/upgrade Module::Build, and make it your preferred
> >>> installer:
> >>> >cpan
> >>> cpan>install Module::Build
> >>> cpan>o conf prefer_installer MB
> >>> cpan>o conf commit
> >>> cpan>q
> >>> * 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
> >>> cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> >>> EXPATINCPATH=/non-standard/include"
> >>> cpan>o conf commit
> >>> --------------
> >>> And I think I did "Upgrade CPAN properly" but when I tried the next one
> >>> it
> >>> started asking too many things to me, and finally it stopped due to
> >>> 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
> >>> .tar
> >>> 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
> >>> MAC.
> >>> * I went to Fink webpage and what I expected to see was "hello!
> >>> 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
> >>> Bioperl
> >>> but I have no people to ask it face to face.
> >>> Thank you so much,
> >>> Casandra
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Biop... <at> lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > _______________________________________________
> > Bioperl-l mailing list
> > Biop... <at> lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 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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