[Bioc-devel] Antw: New 2.1.4 Annotation packages in R-devel branch

mcarlson at fhcrc.org mcarlson at fhcrc.org
Sat Apr 12 18:56:20 CEST 2008

Quoting Claudio Lottaz <Claudio.Lottaz at klinik.uni-regensburg.de>:

> Hi Marc, 
> Just a quick question, which is probably of interest to all package
> developers, who maintain software packages that rely on metadata packages:
> Should I also adapt the dependencies of my package to use packages, which
> will not be depricated? E.g., is it advisable to depend on GO.db or
> hgu133a.db rather than GO and hgu133a respectively?
> Claudio
> --
> ------------------------------------------------------
> Claudio Lottaz
> Computational Diagnostics
> Institute for Functional Genomics
> University of Regensburg
> D-93047 Regensburg (Germany)
> phone: +49 941 943 1584
> fax: +49 941 5020

Hi Claudio, I am posting this reply back to the thread so that everyone can
the answer.


You should be adapting your package dependencies to use the new packages.

Sorry that I did not make this more clear.  You definitely should be adapting
your package dependencies.  That is a lot of why we are taking so long to
deprecate the older packages.  We want to give you plenty of time to do that. 
Of course, in most cases, you should only have to change the package name that
you refer to in your depends field, and your library calls to end with a .db
extension.  So for example, "hgu95av2" becomes "hgu95av2.db".  In most cases,
what you get from the newer packages will be the same.  There are a few
exceptions such as the mappings that I mentioned which have been dropped from
GO.db.  But when such a thing has been done, we have tried to offer an
alternative way to get that same information.  But these GO fields that I been
mentioning are really an exceptional case.  In most cases, when there are
differences between the old and new packages, the newer packages are the ones
that have the additional information.  So upgrading should be easy for you.


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