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

[Lincoln Stein]

Sort of a problem here.  I originally had version numbers in all my modules, 
but they were removed from the live branch when we went to the overall 
BioPerl versioning system.  However, before the 1.2 release, I moved many of 
my modules from "live" into branch-1-2.  This meant that the modules went 
into bioperl 1.2.X without any versions at all.

Lincoln


On Wednesday 30 July 2003 04:15 pm, Philip MacMenamin wrote:
> 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

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)