Henrik Bengtsson wrote:
> [Cross-posting to BioC-devel to]
>
> Thank you for this.
>
>> The changes are internal but extensive. All packages that use S4
>> methods and classes need to be reinstalled from source to use the new
>> version.
>
> Is there an easy way to detect if a package is using S4 or not?
If you have your package source in various directories under a single
directory (which is how I usually work), then, from the directory above
the package directories, the comand:
grep "Depends:.*methods" */DESCRIPTION
will pick up the packages that declare a dependency on methods. There
may be cleaner techniques.
> If
> so, I could scan my already installed libraries and call
> install.packages() on its S4 subset of packages. The alternative is
> to do install.packages() an all libraries (sic!). Bioconductor: maybe
> biocLite() could have such an update mechanism built in internally?
>
> If I miss to reinstall one S4 package, what should I expect?
The typical symptom is a clutch of warning messages when you attach the
package. The warnings try to mention that the package may need
reinstallling, though sometimes the package name is misleading.
> I assume
> there will be an error, but I just want to confirm that there is no
> risk of getting weird "results" but still a running program?
>
> Reinstallation is also required for all package that comes as Windows
> binaries, correct?
Anything that uses S4 methods will have out-of-date objects for class
and method definitions.
John
>
> Best
>
> Henrik
>
> On 8/30/06, John Chambers <[EMAIL PROTECTED]> wrote:
>> A revision of r-devel 2.4.0 is being committed today with changes to
>> method and class management.
>>
>> The changes are internal but extensive. All packages that use S4
>> methods and classes need to be reinstalled from source to use the new
>> version.
>>
>> The main effects are to speed up method caching and dispatch, and to fix
>> some problems with selecting inherited methods. The new design is also
>> cleaner, so we can experiment more easily in the future with changes for
>> efficiency or semantics.
>>
>> The change will mostly be noticeable in attaching packages with many
>> methods. The CPU time for attaching package Matrix, for example, goes
>> down by about a factor of 7 compared to R 2.3.1, timed on a Mac G5.
>>
>> The other major change is that now _all_ inherited methods are examined
>> and one of the closest matches is chosen. The old selection took the
>> first candidate found, so the current version is better defined, and
>> will also let us experiment with various tuning & strategies.
>>
>> There is a draft paper describing method selection at
>> http://developer.r-project.org/howMethodsWork.pdf
>> (It's a document in progress, so go back in a few days for a revised
>> version.)
>>
>> If a package uses inheritance for method selection with multiple
>> arguments, there may well be changes in behavior. We found examples in
>> both methods itself and in Matrix that needed attention.
>>
>> John
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
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