[Bioperl-l] No version numbers on bioperl pms.

[Philip MacMenamin]

I am aware that the overall version of BioPerl is 1.2.2. I dont think I am 
interested in this though. I want the version of the specific modules. I 
have looked at the Bio::DB::GFF perldoc, and all I see is $Id$. There is 
nothing to the left or right of this. 

When I grep through it therefore, I get this returned: 
# $Id$

This is not helpful. When I perldoc it, there is nothing either. 

When I look at the other pms not in BioPerl (say Fatal.pm), there is a 
version number (ie $VERSION = 1.02) that is used and needed by things such as 
Makemaker. Without $VERSION makemaker may fail to work, and probably give 
some not helpful message (unless you have the newest version). 

Now, if you are telling me that by virtue of the fact that this is bioPerl 
1.2.2 *all* pms contained within are implicitly 1.2.2 this is another story. 
And I would be happy. But, I dont know that this is the case.

All I want to know is what version of Bio::DB::GFF and Bio::Graphics is the 
latest. (I downloaded it using cpan, not from source)

Thanks, 
Philip. 
On Wednesday 30 July 2003 04:02 pm, you wrote:
> % perldoc -m Bio::DB::GFF | grep Id
>
> There are only explict versions when we do a release. 1.2.2 is the latest
> stable release.
>
> Did you download the code from CVS, a release from the website,
> from http://bioperl.org/SRC?
>
> On Wed, 30 Jul 2003, Philip MacMenamin wrote:
> > OK, most of them have $Id$ at the start. (Although Graphics.pm does not).
> > However, if it is there, what do you do with it? When I perldoc it, I see
> > no version number.
> >
> > To be honest, all I want to know is the versions of the Bio::DB::GFF
> > Bio::Graphics that would have been downloaded in the last few days. (ie I
> > assume the most recent version)
> >
> > Thanks.
> >
> > On Wednesday 30 July 2003 02:59 pm, you wrote:
> > > you can also look at the
> > > $Id$
> > > in almost every file which list the Revision of the particular instance
> > > of the code you have.
> > >
> > > -jason
> > >
> > > On Wed, 30 Jul 2003, Philip MacMenamin wrote:
> > > > Hi Jason,
> > > >
> > > > OK, thats fine. However, the overall version number is not what I
> > > > need.
> > > >
> > > > I would like to know what version of Bio::DB::GFF i have, and what
> > > > version of Bio::Graphics. Because at the moment I just guessed a
> > > > $VERSION number and hacked it into them, and hoped for the best. And,
> > > > although GMOD installs, it doesnt work properly. And, its probably
> > > > nothing to do with the version I guessed, but I really dont know.
> > > >
> > > > It just seems that it might be straight forward to do things the same
> > > > way as in the rest of perl (from what I can see of the rest of perl
> > > > anyway), to make things easier for people like me, OR, to put some
> > > > comment in the code at the point were the VERSION number usually is,
> > > > (like line 2 or somthing) saying this is version such and such, but
> > > > we dont use $VERSION numbers for reason X.
> > > >
> > > > So, if anyone knows the version number of Bio::DB::GF, and
> > > > Bio::Graphics that I downloaded in the last couple of days is, I
> > > > would be much obliged to them if they let me know (so I dont have to
> > > > just guess it).
> > > >
> > > > Thanks again,
> > > > Philip.
> > > >
> > > > On Wednesday 30 July 2003 01:05 pm, you wrote:
> > > > > We're aware.
> > > > >
> > > > > We've implemented a new system
> > > > > Bio::Root::Version
> > > > > which will now make the overall version number of package
> > > > > available.
> > > > >
> > > > > This is only for current CVS bioperl-live so will be in bioperl 1.4
> > > > >
> > > > > -jason
> > > > >
> > > > > On Wed, 30 Jul 2003, philip wrote:
> > > > > > Hi,
> > > > > >
> > > > > > I assume that you are aware that your BioPerl pms are not
> > > > > > versioned.
> > > > > >
> > > > > > This seems unusual to me, however I am no perl head.
> > > > > >
> > > > > > BUT, it can cause problems (which took me a LONG time to
> > > > > > understand, see previous comment about my lack of perl cool
> > > > > > points) when I was trying to set up GMOD. What was happening that
> > > > > > when Lincolns Makefile.PL was demanding such and such version of
> > > > > > GFF etc, makemaker was going off, and looking for such and such
> > > > > > version number, was getting nothing, and saying that I didnt have
> > > > > > GFF at all. The newest makemaker does not do this, it gives out
> > > > > > about not understanding the version number or something.
> > > > > >
> > > > > > But, I don't know, I have looked at some other ordinary pms and
> > > > > > they all seem to have VERSION numbers. So, I just thought that I
> > > > > > would post this up here.
> > > > > >
> > > > > > All the best,
> > > > > > Philip.
> > > > > >
> > > > > > _______________________________________________
> > > > > > Bioperl-l mailing list
> > > > > > Bioperl-l at portal.open-bio.org
> > > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Philip MacMenamin
Center for Comparative Functional Genomics
NYU Department of Biology
1009 Silver Building
100 Washington Square East
New York, NY 10003-6688
phone: +(212) 998-8823
email: pm66 at nyu.edu