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<div>All,</div>
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<div>The master branch on github is undergoing significant changes that <b>will break your code</b>; 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.</div>
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<div>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).</div>
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<div>chris</div>
<br>
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<div>On Aug 1, 2014, at 1:20 PM, Tess Cherlin <<a href="mailto:tess.cherlin@gmail.com">tess.cherlin@gmail.com</a>> wrote:</div>
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<div dir="ltr">Hi Dave, Chris, Cassandra and others,<br>
<br>
I was following the wonderful directions that Dave wrote and have made it to an almost similar end as Cassandra.<br>
<br>
<br>
ncfa-2-3502-ap3:~ Vi$ perl -e "use Bio::SeqIO;"<br>
Base class package "Bio::Root::Root" is empty.<br>
(Perhaps you need to 'use' the module which defines that package first.)<br>
at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80<br>
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80.<br>
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.<br>
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.<br>
Compilation failed in require at (eval 1) line 3.<br>
...propagated at /System/Library/Perl/5.8.8/base.pm line 85.<br>
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Simple.pm line 87.<br>
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.<br>
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.<br>
Compilation failed in require at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.<br>
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.<br>
Compilation failed in require at -e line 1.<br>
BEGIN failed--compilation aborted at -e line 1.<br>
ncfa-2-3502-ap3:~ Vi$<span class="Apple-converted-space"> </span><br>
<br>
<br>
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!<br>
<br>
Thank you!<br>
<br>
Tess<br>
<br>
On Tuesday, February 7, 2012 3:38:12 PM UTC-6, Dave Messina wrote:
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I will take the opportunity to shamelessly pimp my no-install install<br>
instructions (below and<span class="Apple-converted-space"> </span><a href="http://seqxml.org/xml/BioPerl.html" target="_blank">http://seqxml.org/xml/BioPerl.<wbr>html</a>). IMHO if<br>
Casandra is just looking to get started with BioPerl, messing with external<br>
libs and configs is probably overkill.
<p>Best,<br>
Dave</p>
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<p> There’s a quickie, “zero-install” way to get BioPerl on your system.</p>
<p> 1) Okay, click here to download bioperl as a zip file:</p>
<p> <span class="Apple-converted-space"> </span><a href="https://github.com/bioperl/bioperl-live/zipball/master" target="_blank">https://github.com/bioperl/<wbr>bioperl-live/zipball/master</a></p>
<p><br>
when it's done downloading, unzip it if your computer hasn’t done it<br>
automatically. On the<br>
command line, you would do:</p>
<p> unzip bioperl-live-bioperl-release-<wbr>1-5-1-rc4-4318-g342e587.zip</p>
<p> or whatever the file is called. You should then have a folder with some<br>
ugly name like</p>
<p> bioperl-bioperl-live-558467a</p>
<p> 3) rename that to</p>
<p> bioperl-live</p>
<p> 4) move that folder to wherever you want to keep it. I keep mine in a<br>
directory called src in my<br>
home directory.</p>
<p> So on my computer if I go to the command line and cd to that folder and<br>
type pwd I get:</p>
<p> /Users/dave/src/bioperl-live</p>
<p> 5) in the terminal, cd to your home directory.</p>
<p> 6) see if you have a file named .bash_profile by typing</p>
<p> ls -l ~/.bash_profile</p>
<p> 7) if so, open that file in your favorite editor. if the file doesn't<br>
exist, just create the file.</p>
<p> 8) put this line in your .bash_profile</p>
<p> export PERL5LIB=/Users/dave/src/<wbr>bioperl-live</p>
<p> (obviously replacing my path info with wherever you chose to put<br>
bioperl)</p>
<p> 9) save and close your .bash_profile</p>
<p> 10) open a new terminal window so that the change will take effect.</p>
<p> 11) on the command line of the new terminal, type</p>
<p> perl -e "use Bio::SeqIO;"</p>
<p> If that works, then you have "installed" bioperl. Yay!</p>
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<p><br>
On Tue, Feb 7, 2012 at 22:12, Scott Cain <<a target="_blank" gdf-obfuscated-mailto="1zxcapOb3FEJ">sc...@</a><a href="http://scottcain.net/">scottcain.net</a>> wrote:</p>
<p>> Yes, but those doc don't address exactly the problem Cassandra is<br>
> having, that she wants to use local::lib, but there need to be some<br>
> prereqs installed, but they can't be because she chose to use<br>
> local::lib, and it's not installed. That's all fine if you're not a<br>
> newbie and know how to properly install the prereqs before using the<br>
> cpan shell, but when following instructions that say "use local::lib",<br>
> I find that the instructions are completely insufficient in actually<br>
> getting the desired software installed. Thus the need for a good<br>
> tutorial.<br>
><br>
> Scott<br>
><br>
><br>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <<a target="_blank" gdf-obfuscated-mailto="1zxcapOb3FEJ">cjfi...@</a><a href="http://illinois.edu/">illinois.edu</a>><br>
> wrote:<br>
> > I guess one key question is where these CPAN installation instructions<br>
> come<br>
> > from. They're a bit odd, and if this is from the wiki we need to do some<br>
> > updating.<br>
> ><br>
> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a<br>
> > single perl version.<br>
> ><br>
> ><span class="Apple-converted-space"> </span><a href="https://metacpan.org/module/local::lib#The-bootstrapping-technique" target="_blank">https://metacpan.org/module/<wbr>local::lib#The-bootstrapping-<wbr>technique</a><br>
> ><br>
> > In my case I use perlbrew (which is all local by default, and allows<br>
> > switching between perl versions). Highly recommend using either simple<br>
> > local::lib or perlbrew in combination with cpanm.<br>
> ><br>
> ><span class="Apple-converted-space"> </span><a href="https://metacpan.org/module/perlbrew" target="_blank">https://metacpan.org/module/<wbr>perlbrew</a><br>
> ><span class="Apple-converted-space"> </span><a href="https://metacpan.org/module/cpanm" target="_blank">https://metacpan.org/module/<wbr>cpanm</a><br>
> ><br>
> > chris<br>
> ><br>
> ><br>
> ><br>
> > On 02/07/2012 02:55 PM, Scott Cain wrote:<br>
> >><br>
> >> hi Cassandra,<br>
> >><br>
> >> I don't have an answer for you at the moment. It seems to me that<br>
> >> using local::lib is a good idea, but I've never found a good tutorial<br>
> >> for using it, so I haven't. Perhaps someone else on the list can<br>
> >> suggest one.<br>
> >><br>
> >> The other thing I just wanted to mention as the admin that approved<br>
> >> your message--I came very close to deleting it from the queue without<br>
> >> looking at it because it is not unusual for spam messages to have<br>
> >> generic subjects like "help!" (just for future reference :-)<br>
> >><br>
> >> Scott<br>
> >><br>
> >><br>
> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<<a target="_blank" gdf-obfuscated-mailto="1zxcapOb3FEJ">kasa...@</a><a href="http://gmail.com/">gmail.com</a>> wrote:<br>
> >>><br>
> >>> Hi,<br>
> >>><br>
> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl<br>
> >>> installed becaused I have already write some scripts but I'm biologist<br>
> >>> so...<br>
> >>> not pretty sure about what messages say.<br>
> >>><br>
> >>> My perl version:<br>
> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level<br>
> >>> My computer:<br>
> >>> Mac OS X Vesion 10.5.8<br>
> >>><br>
> >>> I was following this preliminary steps:<br>
> >>><br>
> >>> --------------<br>
> >>><br>
> >>> PRELIMINARY PREPARATION<br>
> >>><br>
> >>> This is optional, but regardless of your subsequent choice of<br>
> >>> installation method, it will help to carry out the following steps.<br>
> >>> They will increase the likelyhood of installation success<br>
> >>> (especially of optional dependencies).<br>
> >>><br>
> >>> * Upgrade CPAN:<br>
> >>><br>
> >>> >perl -MCPAN -e shell<br>
> >>> cpan>install Bundle::CPAN<br>
> >>> cpan>q<br>
> >>><br>
> >>> * Install/upgrade Module::Build, and make it your preferred<br>
> >>> installer:<br>
> >>><br>
> >>> >cpan<br>
> >>> cpan>install Module::Build<br>
> >>> cpan>o conf prefer_installer MB<br>
> >>> cpan>o conf commit<br>
> >>> cpan>q<br>
> >>><br>
> >>> * Install the expat library by whatever method is<br>
> >>> appropriate for your system.<br>
> >>><br>
> >>> * If your expat library is installed in a non-standard location,<br>
> >>> tell CPAN about it:<br>
> >>><br>
> >>> >cpan<br>
> >>> cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/<wbr>lib<br>
> >>> EXPATINCPATH=/non-standard/<wbr>include"<br>
> >>> cpan>o conf commit<br>
> >>><br>
> >>> --------------<br>
> >>><br>
> >>> And I think I did "Upgrade CPAN properly" but when I tried the next one<br>
> >>> it<br>
> >>> started asking too many things to me, and finally it stopped due to<br>
> "some<br>
> >>> problems". In text file you can see the whole process.<br>
> >>> What did I do wrong?<br>
> >>><br>
> >>><br>
> >>> After solving these preliminary steps, what should I do? What exactly<br>
> >>> .tar<br>
> >>> or .whatever should I download to install?<br>
> >>><br>
> >>> I don't see the difference between installing it through "built.PL" or<br>
> >>> CPAN. And I don't know if I should do this or that "Fink*" stuff for<br>
> >>> MAC.<br>
> >>><br>
> >>> * I went to Fink webpage and what I expected to see was "hello!<br>
> download<br>
> >>> Bioperl simply clicking here!" but far from this, what it seems is that<br>
> >>> first I have to download some kinf of Fink-program before starting with<br>
> >>> Bioperl... is it something close to this?<br>
> >>><br>
> >>> I'm sorry, too many questions... But I really want to learn to use<br>
> >>> Bioperl<br>
> >>> but I have no people to ask it face to face.<br>
> >>><br>
> >>> Thank you so much,<br>
> >>><br>
> >>> Casandra<br>
> >>><br>
> >>> ______________________________<wbr>_________________<br>
> >>> Bioperl-l mailing list<br>
> >>><span class="Apple-converted-space"> </span><a target="_blank" gdf-obfuscated-mailto="1zxcapOb3FEJ">Biop...@</a><a href="http://lists.open-bio.org/">lists.open-bio.org</a><br>
> >>><span class="Apple-converted-space"> </span><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_blank">http://lists.open-bio.org/<wbr>mailman/listinfo/bioperl-l</a><br>
> >><br>
> >><br>
> >><br>
> >><br>
> ><br>
> > ______________________________<wbr>_________________<br>
> > Bioperl-l mailing list<br>
> ><span class="Apple-converted-space"> </span><a target="_blank" gdf-obfuscated-mailto="1zxcapOb3FEJ">Biop...@</a><a href="http://lists.open-bio.org/">lists.open-bio.org</a><br>
> ><span class="Apple-converted-space"> </span><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_blank">http://lists.open-bio.org/<wbr>mailman/listinfo/bioperl-l</a><br>
><br>
><br>
><br>
> --<br>
> ------------------------------<wbr>------------------------------<wbr>------------<br>
> Scott Cain, Ph. D. scott at scottcain<br>
> dot net<br>
> GMOD Coordinator (<a href="http://gmod.org/" target="_blank">http://gmod.org/</a>) 216-392-3087<br>
> Ontario Institute for Cancer Research<br>
><br>
> ______________________________<wbr>_________________<br>
> Bioperl-l mailing list<br>
><span class="Apple-converted-space"> </span><a target="_blank" gdf-obfuscated-mailto="1zxcapOb3FEJ">Biop...@</a><a href="http://lists.open-bio.org/">lists.open-bio.org</a><br>
><span class="Apple-converted-space"> </span><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_blank">http://lists.open-bio.org/<wbr>mailman/listinfo/bioperl-l</a><br>
></p>
<p>______________________________<wbr>_________________<br>
Bioperl-l mailing list<br>
<a target="_blank" gdf-obfuscated-mailto="1zxcapOb3FEJ">Biop...@</a><a href="http://lists.open-bio.org/">lists.open-bio.org</a><br>
<a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_blank">http://lists.open-bio.org/<wbr>mailman/listinfo/bioperl-l</a></p>
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