[Bioc-devel] Attention Bioconductor Maintainers

Robert Gentleman rgentlem at fhcrc.org
Sat May 21 03:17:24 CEST 2005

Hi Gordon,
    Do you have an alternative?
The problem, as I see it is the following:
   As R changes we track and use, and some times are the reason for, 
those changes. So packages and developers need to do that on the devel 
arm, it is going to morph into the next BioC release and be compatible 
with the next release of R. If they do not bump their version numbers 
quite substantially, then there are problems with version numbers 
between release BioC, which must allow bug fixes, and hence must allow 
version number increments, and those on the devel arm, which we hope 
will have version number changes because people are active and adding 
new features etc. I think it would be very confusing to start 
interlacing these - but we are very happy to see anything that 
developers want and that will help to provide for both a happier 
developer experience and a happier user experience.

  This seemed to be the easiest way to achieve that, but certainly not 
the only one - so please let us know what you think would work better. 
If we can agree soon then we can implement it before too much divergence.


Gordon K Smyth wrote:
> Hi Seth,
> I agree with you that the distinction between Bioc release and devel can be confusing and needs to
> be clarified, but I don't think that this is the way to do it.  The trouble with incrementing all
> the package numbers is that it breaks the basic principle that version numbers track changes in
> packages.  It implies to a user that the packages have been changed, when they have not.  A user
> will not be able to tell whether they should go to the trouble of converting to the devel version
> or not.  It could even be considered to be a bit dishonest to give the impression that all the
> packages have been updated and (by implication) improved when actually they haven't.
> Anyway, this isn't a request for special treatment.  I think whatever you do you should do to all
> the packages, and I'll work-around whatever.
> Gordon
> On Sat, May 21, 2005 9:53 am, Seth Falcon said:
>>Package version numbers have been "bumped".
>>In order to distinguish between the Bioconductor 1.6 release branch
>>and the devel version of Bioc packages, I have made the following
>>version number change to all packages included in the 1.6 release:
>>x.y.z  ==>  x.y+1.0
>>For example, Biobase was released at 1.5.12.  It's new devel version
>>is 1.6.0.  This way, patches on the release branch can continue to
>>increment the z number without any confusion with the devel version of
>>the package.
>>If you strongly object to this change in your package version number,
>>please contact me so that we can work out a compromise.
>>+ seth
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