[Bioperl-l] A couple of CVS questions.

[Ewan Birney]

On Wed, 3 Jan 2001, Jason Stajich wrote:

> On Tue, 2 Jan 2001, Hilmar Lapp wrote:
> 
> > Peter Schattner wrote:
> > > 
> > > A couple of CVS questions.
> > > 
> > > 1. How can one access earlier releases of bioperl?  I haven't been able
> > > to find them on CVS or elsewhere.  Where should I be looking?
> > > 
> > 
> > You can checkout based on one of version, tag, or date. You very likely
> > don't want to checkout a release by version, as each file has a different
> > version. There is a tag for the 0.6.x release branch, and also for other
> > releases. If you want to checkout the whole development trunk in an earlier
> > version, the most sensible way is probably to go by date (option -D). For
> > individual modules you can go either way.
> > 
> > Do you have the manpages of cvs? They're actually poor compared to the
> > info-files cvs comes with. On a Unix box with info installed you should be
> > able to type 'info cvs'.
> > 
> > > 2. Some modules were moved to different directories within the CVS
> > > structure recently (eg Bio::Tools::Alignment::Clustalw.pm was moved to
> > > Bio::Tools::Run::Alignment::Clustalw.pm ).  Since then, I don't seem to
> > > be able to find the versions of the modules made prior to the date that
> > > the modules were moved.  Can someone tell me if these older versions are
> > > accessible and if so how to find them.
> > 
> > The files were moved without retaining the revision history (cvs is bad at
> > file moving and renaming; you have to mess with the repository in order to
> > have cvs history preserved in this case). The version at the former
> > location was deleted, so you can restore it at the former place only. The
> > file at the new location has lost all its revision information before the
> > move.
> 
> Many apologies, this was my stupidness for not moving the files the
> correct way.  I wish I had waited for Hilmar's email.... Learned my
> lesson though.... I didn't realize we could move the RCS files (itchy
> trigger finger) before I moved the src files.  If you look at the
> first date in Bio::Tools::Run::Alignment or Bio::Tools::StandAloneBlast
> you can see when the move occurred and then checkout with -D as some day
> or time before then.

It is, in my book, bad form to move the actual files. If you move files
then CVS checkouts on old versions screw up with sometimes disasterous
effects. 

The removal and cvs add is "The Right Way" tm in my book.



> 
> > 
> > Hope this helps.
> > 
> > 	Hilmar
> > -- 
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp@gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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