Gabriel Becker
2014-Mar-26 13:13 UTC
[Rd] Conflicting definitions for function redefined as S4 generics
Perhaps a patch to R such that generics don't clobber each-other's method tables if the signatures agree? I haven't dug deeply, but simply merging the method tables seems like it would be safe when there are no conflicts. That way this type of multiplicity would not be a problem, though it wouldn't help (as it shouldn't) if the two generics didn't agree on signature or both carried methods for the same class signature. ~G On Wed, Mar 26, 2014 at 4:38 AM, Michael Lawrence <lawrence.michael@gene.com> wrote:> The BiocGenerics package was designed to solve this issue within > Bioconductor. It wouldn't be the worst thing in the world to depend on the > simple BiocGenerics package for now, but ideally the base generics would be > defined higher up, perhaps in the methods package itself. Maybe someone > else has a more creative solution, but any sort of conditional/dynamic > approach would probably be too problematic in comparison. > > Michael > > > > On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer < > bodenhofer@bioinf.jku.at > > wrote: > > > [cross-posted to R-devel and bioc-devel] > > > > Hi, > > > > I am trying to implement a 'sort' method in one of the CRAN packages I am > > maintaining ('apcluster'). I started with using setMethod("sort", ...) in > > my package, which worked fine. Since many users of my package are from > the > > bioinformatics field, I want to ensure that my package works smoothly > with > > Bioconductor. The problem is that the BiocGenerics package also redefines > > 'sort' as an S4 generic. If I load BiocGenerics before my package, > > everything is fine. If I load BiocGeneric after I have loaded my package, > > my setMethod("sort", ...) is overridden by BiocGenerics and does not work > > anymore. A simple solution would be to import BiocGenerics in my package, > > but I do not want this, since many of this package's users are outside > the > > bioinformatics domain. Moreover, I am reluctant to include a dependency > to > > a Bioconductor package in a CRAN package. I thought that maybe I could > > protect my setMethod("sort", ...) from being overridden by BiocGeneric by > > sealed=TRUE, but that did not work either. Any ideas are gratefully > > appreciated! > > > > Thanks a lot, > > Ulrich > > > > > > ------------------------------------------------------------------------ > > *Dr. Ulrich Bodenhofer* > > Associate Professor > > Institute of Bioinformatics > > > > *Johannes Kepler University* > > Altenberger Str. 69 > > 4040 Linz, Austria > > > > Tel. +43 732 2468 4526 > > Fax +43 732 2468 4539 > > bodenhofer@bioinf.jku.at <mailto:bodenhofer@bioinf.jku.at> > > http://www.bioinf.jku.at/ <http://www.bioinf.jku.at> > > > > ______________________________________________ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML version deleted]]
Michael Lawrence
2014-Mar-26 13:44 UTC
[Rd] Conflicting definitions for function redefined as S4 generics
That might be worth thinking about generally, but it would still be nice to have the base generics pre-defined, so that people are not copy and pasting the definitions everywhere, hoping that they stay consistent. On Wed, Mar 26, 2014 at 6:13 AM, Gabriel Becker <gmbecker@ucdavis.edu>wrote:> Perhaps a patch to R such that generics don't clobber each-other's method > tables if the signatures agree? I haven't dug deeply, but simply merging > the method tables seems like it would be safe when there are no conflicts. > > That way this type of multiplicity would not be a problem, though it > wouldn't help (as it shouldn't) if the two generics didn't agree on > signature or both carried methods for the same class signature. > > ~G > > > On Wed, Mar 26, 2014 at 4:38 AM, Michael Lawrence < > lawrence.michael@gene.com> wrote: > >> The BiocGenerics package was designed to solve this issue within >> Bioconductor. It wouldn't be the worst thing in the world to depend on the >> simple BiocGenerics package for now, but ideally the base generics would >> be >> defined higher up, perhaps in the methods package itself. Maybe someone >> else has a more creative solution, but any sort of conditional/dynamic >> approach would probably be too problematic in comparison. >> >> Michael >> >> >> >> On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer < >> bodenhofer@bioinf.jku.at >> > wrote: >> >> > [cross-posted to R-devel and bioc-devel] >> > >> > Hi, >> > >> > I am trying to implement a 'sort' method in one of the CRAN packages I >> am >> > maintaining ('apcluster'). I started with using setMethod("sort", ...) >> in >> > my package, which worked fine. Since many users of my package are from >> the >> > bioinformatics field, I want to ensure that my package works smoothly >> with >> > Bioconductor. The problem is that the BiocGenerics package also >> redefines >> > 'sort' as an S4 generic. If I load BiocGenerics before my package, >> > everything is fine. If I load BiocGeneric after I have loaded my >> package, >> > my setMethod("sort", ...) is overridden by BiocGenerics and does not >> work >> > anymore. A simple solution would be to import BiocGenerics in my >> package, >> > but I do not want this, since many of this package's users are outside >> the >> > bioinformatics domain. Moreover, I am reluctant to include a dependency >> to >> > a Bioconductor package in a CRAN package. I thought that maybe I could >> > protect my setMethod("sort", ...) from being overridden by BiocGeneric >> by >> > sealed=TRUE, but that did not work either. Any ideas are gratefully >> > appreciated! >> > >> > Thanks a lot, >> > Ulrich >> > >> > >> > ------------------------------------------------------------------------ >> > *Dr. Ulrich Bodenhofer* >> > Associate Professor >> > Institute of Bioinformatics >> > >> > *Johannes Kepler University* >> > Altenberger Str. 69 >> > 4040 Linz, Austria >> > >> > Tel. +43 732 2468 4526 >> > Fax +43 732 2468 4539 >> > bodenhofer@bioinf.jku.at <mailto:bodenhofer@bioinf.jku.at> >> > http://www.bioinf.jku.at/ <http://www.bioinf.jku.at> >> > >> > ______________________________________________ >> > R-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-devel >> > >> >> [[alternative HTML version deleted]] >> >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > > -- > Gabriel Becker > Graduate Student > Statistics Department > University of California, Davis >[[alternative HTML version deleted]]
Duncan Murdoch
2014-Mar-26 13:48 UTC
[Rd] Conflicting definitions for function redefined as S4 generics
On 26/03/2014, 9:13 AM, Gabriel Becker wrote:> Perhaps a patch to R such that generics don't clobber each-other's method > tables if the signatures agree? I haven't dug deeply, but simply merging > the method tables seems like it would be safe when there are no conflicts. > > That way this type of multiplicity would not be a problem, though it > wouldn't help (as it shouldn't) if the two generics didn't agree on > signature or both carried methods for the same class signature.I don't think R should base the decision on the signature. There are two very different situations where this might come up. In one, package A and package B might both define a generic named foo() that happens to have the same signature, but with nothing in common. That should be allowed, and should behave the same as when they both create functions with the same name: it should be up to the user to specify which generic is being called. If R merged the two generics into one, there would be chaos. The other situation is more likely to apply to this case. It sounds as though both apcluster and BiocGenerics are creating a sort() generic by promoting the base package S3 generic into an S4 generic. Clearly they should not be creating separate generics, there's just one. I don't know if there's something wrong with the way apcluster or BiocGenerics are doing things, or something wrong with the way the methods package is creating the generic, but it sure looks like a bug somewhere. Duncan Murdoch> > ~G > > > On Wed, Mar 26, 2014 at 4:38 AM, Michael Lawrence <lawrence.michael at gene.com >> wrote: > >> The BiocGenerics package was designed to solve this issue within >> Bioconductor. It wouldn't be the worst thing in the world to depend on the >> simple BiocGenerics package for now, but ideally the base generics would be >> defined higher up, perhaps in the methods package itself. Maybe someone >> else has a more creative solution, but any sort of conditional/dynamic >> approach would probably be too problematic in comparison. >> >> Michael >> >> >> >> On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer < >> bodenhofer at bioinf.jku.at >>> wrote: >> >>> [cross-posted to R-devel and bioc-devel] >>> >>> Hi, >>> >>> I am trying to implement a 'sort' method in one of the CRAN packages I am >>> maintaining ('apcluster'). I started with using setMethod("sort", ...) in >>> my package, which worked fine. Since many users of my package are from >> the >>> bioinformatics field, I want to ensure that my package works smoothly >> with >>> Bioconductor. The problem is that the BiocGenerics package also redefines >>> 'sort' as an S4 generic. If I load BiocGenerics before my package, >>> everything is fine. If I load BiocGeneric after I have loaded my package, >>> my setMethod("sort", ...) is overridden by BiocGenerics and does not work >>> anymore. A simple solution would be to import BiocGenerics in my package, >>> but I do not want this, since many of this package's users are outside >> the >>> bioinformatics domain. Moreover, I am reluctant to include a dependency >> to >>> a Bioconductor package in a CRAN package. I thought that maybe I could >>> protect my setMethod("sort", ...) from being overridden by BiocGeneric by >>> sealed=TRUE, but that did not work either. Any ideas are gratefully >>> appreciated! >>> >>> Thanks a lot, >>> Ulrich >>> >>> >>> ------------------------------------------------------------------------ >>> *Dr. Ulrich Bodenhofer* >>> Associate Professor >>> Institute of Bioinformatics >>> >>> *Johannes Kepler University* >>> Altenberger Str. 69 >>> 4040 Linz, Austria >>> >>> Tel. +43 732 2468 4526 >>> Fax +43 732 2468 4539 >>> bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at> >>> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at> >>> >>> ______________________________________________ >>> R-devel at r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > >
Hervé Pagès
2014-Mar-26 17:54 UTC
Re: [Bioc-devel] Conflicting definitions for function redefined as S4 generics
Hi,
I agree. I can't think of an easy way to avoid this kind of clashes
between BioC and non-BioC S4 generics, other than by having things
like sort() already defined as an S4 generic in base R.
Note that, just having setMethod("sort", ...) in your package Ulrich,
and not putting a setGeneric() statement, is usually the right thing
to do. Because then there will be no clash as long as everybody else
does the same thing. That's because if several packages with a
setMethod("sort", ...) statement are loaded, an implicit S4 generic
is created when the 1st package is loaded, and then "sort" methods
are attached to it when subsequent packages are loaded.
Unfortunately, the implicit S4 generic one gets when doing this
doesn't always have an optimum signature. For example, for sort()
we get dispatch on 'x' *and* 'decreasing':
> sort
standardGeneric for "sort" defined from package "base"
function (x, decreasing = FALSE, ...)
standardGeneric("sort")
<environment: 0x230bf28>
Methods may be defined for arguments: x, decreasing
Use showMethods("sort") for currently available ones.
This is why in BiocGenerics we have:
setGeneric("sort", signature="x")
The downside of this is that now if you load BiocGenerics after your
package, a new S4 generic is created for sort(), which overrides the
implicit S4 generic that was created when your package was loaded.
Of course we wouldn't need to do this in BiocGenerics if the implicit
S4 generic for sort() had the correct signature, or if this setGeneric()
statement we have in BiocGenerics was somewhere in base R.
Another reason for explicitly promoting some base R functions into
S4 generics in BiocGenerics is to have a man page for the generic.
That gives us a place to document some aspects of the S4 generic that
are not covered by the base man page. That's why BiocGenerics has
things like:
setGeneric("nrow")
setGeneric("relist")
The signatures of these generics is the same as the signature of
the implicit generic! But these explicit generics can be exported
and documented.
Back to the original issue: In the particular case of sort() though,
since base::sort() is an S3 generic, one possible workaround for you
is to define an S3 method for your objects.
Cheers,
H.
On 03/26/2014 06:44 AM, Michael Lawrence wrote:> That might be worth thinking about generally, but it would still be nice to
> have the base generics pre-defined, so that people are not copy and pasting
> the definitions everywhere, hoping that they stay consistent.
>
>
> On Wed, Mar 26, 2014 at 6:13 AM, Gabriel Becker
<gmbecker@ucdavis.edu>wrote:
>
>> Perhaps a patch to R such that generics don't clobber
each-other's method
>> tables if the signatures agree? I haven't dug deeply, but simply
merging
>> the method tables seems like it would be safe when there are no
conflicts.
>>
>> That way this type of multiplicity would not be a problem, though it
>> wouldn't help (as it shouldn't) if the two generics didn't
agree on
>> signature or both carried methods for the same class signature.
>>
>> ~G
>>
>>
>> On Wed, Mar 26, 2014 at 4:38 AM, Michael Lawrence <
>> lawrence.michael@gene.com> wrote:
>>
>>> The BiocGenerics package was designed to solve this issue within
>>> Bioconductor. It wouldn't be the worst thing in the world to
depend on the
>>> simple BiocGenerics package for now, but ideally the base generics
would
>>> be
>>> defined higher up, perhaps in the methods package itself. Maybe
someone
>>> else has a more creative solution, but any sort of
conditional/dynamic
>>> approach would probably be too problematic in comparison.
>>>
>>> Michael
>>>
>>>
>>>
>>> On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer <
>>> bodenhofer@bioinf.jku.at
>>>> wrote:
>>>
>>>> [cross-posted to R-devel and bioc-devel]
>>>>
>>>> Hi,
>>>>
>>>> I am trying to implement a 'sort' method in one of the
CRAN packages I
>>> am
>>>> maintaining ('apcluster'). I started with using
setMethod("sort", ...)
>>> in
>>>> my package, which worked fine. Since many users of my package
are from
>>> the
>>>> bioinformatics field, I want to ensure that my package works
smoothly
>>> with
>>>> Bioconductor. The problem is that the BiocGenerics package also
>>> redefines
>>>> 'sort' as an S4 generic. If I load BiocGenerics before
my package,
>>>> everything is fine. If I load BiocGeneric after I have loaded
my
>>> package,
>>>> my setMethod("sort", ...) is overridden by
BiocGenerics and does not
>>> work
>>>> anymore. A simple solution would be to import BiocGenerics in
my
>>> package,
>>>> but I do not want this, since many of this package's users
are outside
>>> the
>>>> bioinformatics domain. Moreover, I am reluctant to include a
dependency
>>> to
>>>> a Bioconductor package in a CRAN package. I thought that maybe
I could
>>>> protect my setMethod("sort", ...) from being
overridden by BiocGeneric
>>> by
>>>> sealed=TRUE, but that did not work either. Any ideas are
gratefully
>>>> appreciated!
>>>>
>>>> Thanks a lot,
>>>> Ulrich
>>>>
>>>>
>>>>
------------------------------------------------------------------------
>>>> *Dr. Ulrich Bodenhofer*
>>>> Associate Professor
>>>> Institute of Bioinformatics
>>>>
>>>> *Johannes Kepler University*
>>>> Altenberger Str. 69
>>>> 4040 Linz, Austria
>>>>
>>>> Tel. +43 732 2468 4526
>>>> Fax +43 732 2468 4539
>>>> bodenhofer@bioinf.jku.at
<mailto:bodenhofer@bioinf.jku.at>
>>>> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>
>>>>
>>>> ______________________________________________
>>>> R-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>
>>> ______________________________________________
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>>
>>
>> --
>> Gabriel Becker
>> Graduate Student
>> Statistics Department
>> University of California, Davis
>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
Ulrich Bodenhofer
2014-Mar-27 09:13 UTC
Re: Conflicting definitions for function redefined as S4 generics
I fully agree, Michael, that this would be a great thing to have! I have often wondered why R and the standard packages are still sticking so much to the old-style S3 flavor though S4 is part of standard R. I acknowledge that backward compatibility is important, but, as far as I got it, redefining a function or S3 generic as an S4 generic should not harm existing functionality (if done properly). If it turns out not to be a good option to do this in the base package, why not as part of the methods package? That will leave existing functionality of base unchanged and will provide a clean situation to all users/packages using S4. This should not create a compatibility problem on the Bioconductor side either, since Bioconductor releases are explicitly bound to specific R versions. Once again: I fully support this idea (not only for sort(), but also for a wide range of other functions), though, not being an R core team member, I do not really feel in the position to demand such a fundamental change. For the time being, it seems I have three options: 1) not supplying the sort() function yet (it is not yet in the release, but only in my internal devel version) 2) including a dependency to BiocGenerics 3) leaving the problem open, mentioning in the documentation that users who want to use apcluster in conjunction with Bioconductor should load BiocGenerics first As far as I got it, there seems to be no other clean way to get rid of the problem, right? Best regards, Ulrich On 03/26/2014 02:44 PM, Michael Lawrence wrote:> That might be worth thinking about generally, but it would still be > nice to have the base generics pre-defined, so that people are not > copy and pasting the definitions everywhere, hoping that they stay > consistent. > > > On Wed, Mar 26, 2014 at 6:13 AM, Gabriel Becker <gmbecker@ucdavis.edu > <mailto:gmbecker@ucdavis.edu>> wrote: > > Perhaps a patch to R such that generics don't clobber each-other's > method tables if the signatures agree? I haven't dug deeply, but > simply merging the method tables seems like it would be safe when > there are no conflicts. > > That way this type of multiplicity would not be a problem, though > it wouldn't help (as it shouldn't) if the two generics didn't > agree on signature or both carried methods for the same class > signature. > > ~G > > > On Wed, Mar 26, 2014 at 4:38 AM, Michael Lawrence > <lawrence.michael@gene.com <mailto:lawrence.michael@gene.com>> wrote: > > The BiocGenerics package was designed to solve this issue within > Bioconductor. It wouldn't be the worst thing in the world to > depend on the > simple BiocGenerics package for now, but ideally the base > generics would be > defined higher up, perhaps in the methods package itself. > Maybe someone > else has a more creative solution, but any sort of > conditional/dynamic > approach would probably be too problematic in comparison. > > Michael > > > > On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer > <bodenhofer@bioinf.jku.at <mailto:bodenhofer@bioinf.jku.at> > > wrote: > > > [cross-posted to R-devel and bioc-devel] > > > > Hi, > > > > I am trying to implement a 'sort' method in one of the CRAN > packages I am > > maintaining ('apcluster'). I started with using > setMethod("sort", ...) in > > my package, which worked fine. Since many users of my > package are from the > > bioinformatics field, I want to ensure that my package works > smoothly with > > Bioconductor. The problem is that the BiocGenerics package > also redefines > > 'sort' as an S4 generic. If I load BiocGenerics before my > package, > > everything is fine. If I load BiocGeneric after I have > loaded my package, > > my setMethod("sort", ...) is overridden by BiocGenerics and > does not work > > anymore. A simple solution would be to import BiocGenerics > in my package, > > but I do not want this, since many of this package's users > are outside the > > bioinformatics domain. Moreover, I am reluctant to include a > dependency to > > a Bioconductor package in a CRAN package. I thought that > maybe I could > > protect my setMethod("sort", ...) from being overridden by > BiocGeneric by > > sealed=TRUE, but that did not work either. Any ideas are > gratefully > > appreciated! > > > > Thanks a lot, > > Ulrich > > >
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