[Bioperl-l] help!

Fields, Christopher J cjfields at illinois.edu
Mon Aug 4 21:05:04 UTC 2014


All,

The master branch on github is undergoing significant changes that will break your code; in short, it is missing several modules that were removed due to our work on modularization.  If you really need to grab the latest stable code, I recommend either getting the latest CPAN release (v1.6.924, just released a month ago) or using the ‘v1.6.x’ branch on GitHub, which we have been routinely patching with fixes to the main branch.

If needed we can switch the default checkout branch to ‘v1.6.x' to make things easier (so far there has been no consensus about this, so I am leaving it as is for the time being).

chris

On Aug 1, 2014, at 1:20 PM, Tess Cherlin <tess.cherlin at gmail.com<mailto:tess.cherlin at gmail.com>> wrote:

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.
ncfa-2-3502-ap3:~ Vi$


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!

Thank you!

Tess

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.

Best,
Dave


 There’s a quickie, “zero-install” way to get BioPerl on your system.

    1) Okay, click here to download bioperl as a zip file:

    https://github.com/bioperl/bioperl-live/zipball/master

    when it's done downloading, unzip it if your computer hasn’t done it
automatically. On the
    command line, you would do:

         unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip

    or whatever the file is called. You should then have a folder with some
ugly name like

    bioperl-bioperl-live-558467a

    3) rename that to

    bioperl-live

    4) move that folder to wherever you want to keep it. I keep mine in a
directory called src in my
        home directory.

    So on my computer if I go to the command line and cd to that folder and
type pwd I get:

    /Users/dave/src/bioperl-live

    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

             export PERL5LIB=/Users/dave/src/bioperl-live

    (obviously replacing my path info with wherever you chose to put
bioperl)

    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<http://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
> tutorial.
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfi... at illinois.edu<http://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
> > 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<http://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
> "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
> >>> .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!
> 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
> >>> 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/>
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Biop... at lists.open-bio.org<http://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
>
> _______________________________________________
> Bioperl-l mailing list
> Biop... at lists.open-bio.org<http://lists.open-bio.org/>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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