[Bioc-devel] include data from non self-sufficient .R files

Laurent Gatto laurent.gatto at gmail.com
Wed Oct 13 01:34:28 CEST 2010

Dear Vincent,

On 12 October 2010 18:13, Vincent Carey <stvjc at channing.harvard.edu> wrote:
> If I understand correctly, Laurent wants to avoid serializing S4
> objects (in data folder), probably because he may have to remember to
> update the serializations if the class definitions change, even if the
> serialized data is not affected by such definition changes.
> The SNPlocs.* packages address this concern -- while there could be
> nice advantages to having SNP metadata serialized as GRanges
> instances, the actual data is well-represented in a SQLite table and
> one uses a function to get a GRanges representation when desired.
> This avoids the problem of requiring reserialization of a potentially
> large object whenever the GRanges class definition changes.

Thank you for the SNPlocs.* hint. I am looking at it.

> I doubt there is a completely satisfactory solution to this problem.
> Especially when one S4 class extends another that has unstable
> definition, serialized S4 instances can become a bit problematic to
> maintain.  A number of bioc core packages illustrate how updateObject
> methods can be written to simplify aspects of maintenance.  The class
> versioning discipline defined in Biobase is also useful for
> maintenance, but I do not know how broadly it is used in contributed
> packages.

For the matter, some of the classes I am developing do contain
Biobase's Versioned and VersionedBiobase.

Best wishes,


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