[Bioperl-l] After Checkout of Bioperl-live version doesn'tseem to change

Wed Feb 3 18:10:09 UTC 2010

The practicality of it is that you can do a simple float comparision to check
for prerequisites and such:

if ($Bio::Perl::VERSION < 1.006900) {
    die "You ain't got the freshest."
}

Harder if you're comparing strings "1.6" to "1.6.9".
MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
Cc: <bioperl-l at lists.open-bio.org>; "Scott Cain" <scott at scottcain.net>
Sent: Wednesday, February 03, 2010 12:58 PM
Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn'tseem to 
change

> If I were to choose a versioning scheme I would probably go with simple 
> bipartite ones, but (by legacy) BioPerl is based on the perl tripartite 
> versioning scheme:
>
> http://www.perl.com/pub/a/2000/04/whatsnew.html#Version_Tuples
>
> For instance, with perl 5.10.1 the vstring v5.10.1 would be 5.010001.  BioPerl 
> 1.6.0 is 1.006000, so you either have an older lingering CPAN installation of 
> 1.6.0 or you are installing that one (I'm guessing the former, as the latest 
> from CPAN is now 1.6.1, or 1.006001).  Effectively, svn trunk is v1.6.900 
> (roughly the 900th point release).
>
> The reason trunk is set at 1.6.9 is simple, it supercedes any current CPAN 
> release version, and it's very unlikely we'll release another 898 point 
> releases of BioPerl.  It also tags the main trunk as pre-1.7.  I can 
> cherry-pick off trunk into the properly designated 1.6 branch (now at 1.6.1), 
> bump the release there, and push to CPAN.  Once we actively start on 1.7 we'll 
> probably bump trunk up to something higher.  It also enables one to 
> distinguish between a CPAN release of BioPerl vs. the SVN version, as 
> installing from svn has unfortunately become very common practice.  Comes in 
> useful in cases like yours, where we're trying to distinguish what version is 
> being called.
>
> chris
>
> On Feb 3, 2010, at 11:32 AM, Lacey Sanderson wrote:
>
>> It returned "1.006"... unfortunately no 9 at the end... Any idea why it 
>> doesn't seem to be picking up the bioperl-live checkout?
>>
>> PS. Why do the distributions have version numbers like 1.5.2 and 1.6 and yet 
>> the bioperl-live (which I take to be the most current version of bioperl) 
>> returns 1.069?
>>
>> Lacey
>>
>> On 3-Feb-10, at 11:08 AM, Scott Cain wrote:
>>
>>> Hi Lacey,
>>>
>>> Did it return "1.006" or 1.0069 exactly, which is what it should
>>> return if you are using bioperl-live?  As for older versions of
>>> BioPerl, if you go down the install route (which is what I generally
>>> do), you can do the standard build procedure:
>>>
>>> perl Build.PL
>>> ./Build
>>> ./Build test
>>> sudo ./Build install --uninst 1
>>>
>>> and that last part (--uninst 1) will remove older versions of the
>>> modules installed elsewhere.  If you want to hunt down where GBrowse
>>> installed bioperl, first you could look in the typical linuxy places,
>>> like /usr/share/perl or /usr/lib/perl for the Bio directory, but
>>> deleting that directory will also delete Bio::Graphics, which isn't
>>> part of bioperl anymore.
>>>
>>> Using PERL5LIB will put your specified bioperl at the front of the
>>> list for when things get used, so even if you have bioperl installed
>>> elsewhere, that one should get used.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Feb 3, 2010 at 10:32 AM, Lacey Sanderson
>>> <laceyanne_sanderson at shaw.ca> wrote:
>>>> Hi,
>>>>
>>>> I just checked out bioperl-live from svn as follows
>>>> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk
>>>> bioperl-live
>>>> $ echo 'export
>>>> PERL5LIB="/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB"
>>>> #adds path of bioperl-live to PERL5LIB' >> ~/.profile
>>>>
>>>> I then restarted by shell and checked the version using
>>>> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>>>>
>>>> Which returned 1.006... I am sure this is the version of bioperl I had
>>>> previously installed and not the new one I just checked out. Is there
>>>> something else I need to do to tell my system to disregard the old bioperl
>>>> and instead use bioperl-live?
>>>>
>>>> I had installed BioPerl earlier using the GMOD GBrowse netinstaller 
>>>> although
>>>> I can't seem to locate where it was installed. Will this effect anything? 
>>>> If
>>>> so, how would I go about uninstalling it (I'm a little new to Linux)...
>>>>
>>>> By the way I am running Ubuntu Intrepid
>>>>
>>>> Thanks!
>>>> Lacey
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l 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
>>
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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