<div dir="ltr">Could you switch master into a feature branch, and put master back to some last-known-good commit?</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jun 25, 2014 at 6:09 PM, Fields, Christopher J <span dir="ltr"><<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Jay.<br>
<br>
We’ve been working on splitting out BioPerl modules, including Bio::Root, into separate distributions. So yes you are catching us in the middle of a (very long and drawn out) transition.<br>
<br>
If you want the old version, it is on the v1.6.x branch, which still includes the Root modules.<br>
<br>
chris<br>
<div class="HOEnZb"><div class="h5"><br>
On Jun 25, 2014, at 4:07 PM, Jay Hannah <<a href="mailto:jay@jays.net">jay@jays.net</a>> wrote:<br>
<br>
> Hi BioPerl!<br>
><br>
> I've been gone a long time. I'm sitting here at YAPC, someone mentioned <a href="http://rosalind.info/" target="_blank">http://rosalind.info/</a> Cool! Hey, I'll do some of these with BioPerl, just for fun! Woot!<br>
><br>
> I'm surprised, sad, that I'm having a hard time using BioPerl on my laptop. I just wanted to use Bio::Seq:<br>
><br>
> BioPerl-Rosalind git:(master) $ perl <a href="http://dna.pl" target="_blank">dna.pl</a><br>
> Can't locate Bio/Seq.pm in @INC ...<br>
><br>
> Oh, right. No problem, I'll just add BioPerl to my PERL5LIB:<br>
><br>
> BioPerl-Rosalind git:(master) $ export PERL5LIB=~/src/bioperl-live<br>
> BioPerl-Rosalind git:(master) $ perl <a href="http://dna.pl" target="_blank">dna.pl</a><br>
> Base class package "Bio::Root::Root" is empty. ...<br>
><br>
> Uhh... what? Do I have to install BioPerl? That's a bummer, well, OK, I guess if I HAVE TO install, I will:<br>
><br>
> bioperl-live git:(master) $ perl Build.PL<br>
> Can't locate Bio/Root/Build.pm in @INC ...<br>
> bioperl-live git:(master) $ find ./ -name "Build.pm"<br>
> bioperl-live git:(master) $<br>
><br>
> Wait... what? Years ago I used BioPerl from github for years... Have I completely forgotten how everything works?<br>
><br>
> If I "fix" it would I be breaking it?<br>
><br>
> Chris: Are you in the middle of some transition?<br>
><br>
> -------------------------------------------------------------<br>
> bioperl-live git:(master) $ git log Build.PL<br>
> commit a747f2054b2a85526eda382baf498a945a9817d2<br>
> Author: Chris Fields <<a href="mailto:cjfields@bioperl.org">cjfields@bioperl.org</a>><br>
> Date: Tue May 27 10:33:21 2014 -0500<br>
><br>
> Revert "Move Build.pm out of Root into an install-specific directory; this will"<br>
><br>
> This reverts commit 268b046514e9e4cd7b67f346c524ff04b8a3aa5e.<br>
><br>
> commit 268b046514e9e4cd7b67f346c524ff04b8a3aa5e<br>
> Author: Chris Fields <<a href="mailto:cjfields@bioperl.org">cjfields@bioperl.org</a>><br>
> Date: Tue May 27 00:54:25 2014 -0500<br>
><br>
> Move Build.pm out of Root into an install-specific directory; this will<br>
> eventually lead up to factoring as much out of it as possible (and maybe<br>
> deprecating it altogether)<br>
> -------------------------------------------------------------<br>
><br>
> ...<br>
><br>
> To my shock and horror (j/k lolz), I've been coding Perl for almost 20 years, yet BioPython Just Works:<br>
><br>
> biopython git:(master) $ python setup.py build<br>
> biopython git:(master) $ python setup.py test<br>
><br>
> Why is Python easier to use than Perl, when I'm a Perl guy and don't know squat about Python?<br>
><br>
> ... Can I help fix things?<br>
><br>
> Thanks,<br>
><br>
> j<br>
> <a href="http://www.bioperl.org/wiki/Jay_Hannah" target="_blank">http://www.bioperl.org/wiki/Jay_Hannah</a><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
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