Re: [Rd] S4 and Namespaces problems {was "error message from lmer"}
Generic functions include a "package" slot. The concept is that only
one definition of the generic _for a particular package_ should exist.
For various reasons, there may be "copies" of that generic in multiple
places (from the way namespaces work, e.g.) but the model is that they
are really the same generic and dispatch the same methods.
Changes now partly in place should enforce this model for 2.6.0. To
each (non-generic) function in a package, there corresponds an implicit
generic version, either by default or by the owner of the package having
used a mechanism that's being added (function implicitGeneric() and
friends). The mechanism allows arguments to be excluded from method
dispatch or to prohibit a generic version entirely.
As Robert says, there can be other generic functions of the same name,
but they will have different package slots, and conceptually will be
unrelated to each other.
I think we are all looking for much the same solution. The proposed
mechanism is to ensure that all the methods defined for a function foo
from package A will be consistent, and use the same definition of the
generic. So far as is evident at this point, the mechanism can be
implemented with the implicit generic code, and probably some extra code
invoked when packages/namespaces are attached/loaded, to catch new
"copies" of a given generic.
Extra tinkering for functions in base (other than establishing implicit
generics) seems a different issue: The model for generics by package
doesn't need to single out functions in base.
John
Prof Brian Ripley wrote:
> On Wed, 18 Jul 2007, Robert Gentleman wrote:
>
>
>> Hi,
>>
>> Martin Maechler wrote:
>>
>>> Here is a reproducible example for the Bug that both Sebastian
>>> and Dale Barr found.
>>>
>>> As Brian mentioned in an another thread,
>>> the problem is in the interaction of Namespaces and S4 generics
>>> and which S4 generic should keep which methods.
>>>
>>> We know there are workarounds, but till now they seem either
>>> ugly or very much against the idea that conceptually there
>>> should be only one generic which may have methods defined in
>>> many different packages / namespaces.
>>>
>> There should *not* be one generic. Generics are no different than any
>> other function. Package A can have a generic named foo, and so can
>> package B. Other packages that want to add methods to a generic named
>> foo need to know which one they would like to add to. These generics
>> can be masked. If Package A is first on the search path then that is the
>> foo that is found first (and if Package B is first then that is the foo,
>> users that specifically want foo from B should use B::foo).
>>
>
> I do think base is a special case here, given its privileged position in
> the namespace hierarchy. I'd take Martin's position as rather that there
> should be only one generic derived by take-over from a function, at least
> for those in base.
>
> I believe that if you are allowed to make a function in base S4-generic
> (and it is not obvious that you should be in many cases), then the derived
> generic should conceptually be in base and thus always be found in place
> of that in base. Since base is not a normal environment or namespace,
> that is not straightforward to implement but it should be possible by
> (e.g.) C-level hacking and a environment to store such derived generics.
> Primitives are rather different, and we now have a fairly efficient way to
> allow designated primitives to have S4 methods.
>
> I believe the registration model for S3 methods is pretty much the right
> one: methods are set on the first 'foo' on the relevant search path, and
> that does not cause another 'foo' to be created elsewhere that may or may
> not precede the original in the relevant search path (since there are
> multiple search paths once namespaces enter the mix).
>
> The new implied generics model helps here: taking over a function in base
> unaltered (the same as the implied generic) could be a derived generic,
> and any alteration would create a new generic in your package. That
> protects code in other namespaces from your alterations.
>
>
>>> I would like us (R-core, mostly) to resolve this as quickly as
>>> possible.
>>>
>
> It seems tricky enough to need debate what we want for a while and aim for
> 2.6.0. But we have been discussing it on and off for at least two years.
>
> Brian
>
>
>>> -
>>>
>>> ### Do this in a fresh R session:
>>>
>>> summary # S3 generic
>>> find("summary") # base
>>>
>>> library(stats4)
>>> summary # S4 generic
>>> find("summary") # stats4 , base
>>>
>>> library(lme4)
>>> ## -> loads Matrix (and lattice)
>>> find("summary") # lme4, Matrix, stats4 , base --- 4 times ! ---
>>>
>> Have they all defined generics? If that is the case then there are 4.
>>
>> We did discuss, and I hope to make pro
Re: [Rd] S4 and Namespaces problems {was "error message from lmer"}
On Wed, 18 Jul 2007, Robert Gentleman wrote:
> Hi,
>
> Martin Maechler wrote:
>> Here is a reproducible example for the Bug that both Sebastian
>> and Dale Barr found.
>>
>> As Brian mentioned in an another thread,
>> the problem is in the interaction of Namespaces and S4 generics
>> and which S4 generic should keep which methods.
>>
>> We know there are workarounds, but till now they seem either
>> ugly or very much against the idea that conceptually there
>> should be only one generic which may have methods defined in
>> many different packages / namespaces.
>
> There should *not* be one generic. Generics are no different than any
> other function. Package A can have a generic named foo, and so can
> package B. Other packages that want to add methods to a generic named
> foo need to know which one they would like to add to. These generics
> can be masked. If Package A is first on the search path then that is the
> foo that is found first (and if Package B is first then that is the foo,
> users that specifically want foo from B should use B::foo).
I do think base is a special case here, given its privileged position in
the namespace hierarchy. I'd take Martin's position as rather that there
should be only one generic derived by take-over from a function, at least
for those in base.
I believe that if you are allowed to make a function in base S4-generic
(and it is not obvious that you should be in many cases), then the derived
generic should conceptually be in base and thus always be found in place
of that in base. Since base is not a normal environment or namespace,
that is not straightforward to implement but it should be possible by
(e.g.) C-level hacking and a environment to store such derived generics.
Primitives are rather different, and we now have a fairly efficient way to
allow designated primitives to have S4 methods.
I believe the registration model for S3 methods is pretty much the right
one: methods are set on the first 'foo' on the relevant search path, and
that does not cause another 'foo' to be created elsewhere that may or may
not precede the original in the relevant search path (since there are
multiple search paths once namespaces enter the mix).
The new implied generics model helps here: taking over a function in base
unaltered (the same as the implied generic) could be a derived generic,
and any alteration would create a new generic in your package. That
protects code in other namespaces from your alterations.
>> I would like us (R-core, mostly) to resolve this as quickly as
>> possible.
It seems tricky enough to need debate what we want for a while and aim for
2.6.0. But we have been discussing it on and off for at least two years.
Brian
>>
>> -
>>
>> ### Do this in a fresh R session:
>>
>> summary # S3 generic
>> find("summary") # base
>>
>> library(stats4)
>> summary # S4 generic
>> find("summary") # stats4 , base
>>
>> library(lme4)
>> ## -> loads Matrix (and lattice)
>> find("summary") # lme4, Matrix, stats4 , base --- 4 times ! ---
>
> Have they all defined generics? If that is the case then there are 4.
>
> We did discuss, and I hope to make progress on the following
> proposal. For functions in base that have an S4 method defined for them
> (and hence we need a generic function), that we create a new package
> that lives slightly above base (and potentially other recommended
> packages) where these generics will live. Developers can then rely on
> finding the generic there, and using it - if their intention is to
> extend the base generic. Note that they may want to have their own
> generic with the same name as the one from base, and that is fine, it
> will mask the one in base.
>
> best wishes
>Robert
>>
>> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
>> ## -->
>> ## Error in lmer(Reaction ~ Days + (Days | Subject), sleepstudy) :
>> ## cannot get a slot ("Dim") from an object of type "NULL"
>>
>> -
>> Martin Maechler
>>
>>
>>> "BDR" == Prof Brian Ripley <[EMAIL PROTECTED]>
>>> on Thu, 28 Jun 2007 06:08:45 +0100 (BST) writes:
>>
>> BDR> See the thread starting
>> BDR> https://stat.ethz.ch/pipermail/r-devel/2007-June/046157.html
>> BDR> https://stat.ethz.ch/pipermail/r-devel/2007-June/046160.html
>>
>> BDR> I can't reproduce this without knowing what is in your
>> BDR> startup files: it should work with --vanilla, so please
>> BDR> try that and try to eliminate whatever is in your
>> BDR> .Rprofile etc that is causing the problem.
>>
>> BDR> Incidentally, using rcompletion is counterproductive in
>> BDR> R 2.5.1 RC: the base functionality using rcompgen is a
>> BDR> more sophisticated version.
>>
>> BDR> On Wed, 27 Jun 2007, Sebastian P. Luque wrote:
>>
>>>> Hi,
>>>>
>>>> I've begun to use the lme4 package
Re: [Rd] S4 and Namespaces problems {was "error message from lmer"}
Hi,
Martin Maechler wrote:
> Here is a reproducible example for the Bug that both Sebastian
> and Dale Barr found.
>
> As Brian mentioned in an another thread,
> the problem is in the interaction of Namespaces and S4 generics
> and which S4 generic should keep which methods.
>
> We know there are workarounds, but till now they seem either
> ugly or very much against the idea that conceptually there
> should be only one generic which may have methods defined in
> many different packages / namespaces.
There should *not* be one generic. Generics are no different than any
other function. Package A can have a generic named foo, and so can
package B. Other packages that want to add methods to a generic named
foo need to know which one they would like to add to. These generics
can be masked. If Package A is first on the search path then that is the
foo that is found first (and if Package B is first then that is the foo,
users that specifically want foo from B should use B::foo).
>
> I would like us (R-core, mostly) to resolve this as quickly as
> possible.
>
> -
>
> ### Do this in a fresh R session:
>
> summary # S3 generic
> find("summary") # base
>
> library(stats4)
> summary # S4 generic
> find("summary") # stats4 , base
>
> library(lme4)
> ## -> loads Matrix (and lattice)
> find("summary") # lme4, Matrix, stats4 , base --- 4 times ! ---
Have they all defined generics? If that is the case then there are 4.
We did discuss, and I hope to make progress on the following
proposal. For functions in base that have an S4 method defined for them
(and hence we need a generic function), that we create a new package
that lives slightly above base (and potentially other recommended
packages) where these generics will live. Developers can then rely on
finding the generic there, and using it - if their intention is to
extend the base generic. Note that they may want to have their own
generic with the same name as the one from base, and that is fine, it
will mask the one in base.
best wishes
Robert
>
> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> ## -->
> ## Error in lmer(Reaction ~ Days + (Days | Subject), sleepstudy) :
> ##cannot get a slot ("Dim") from an object of type "NULL"
>
> -
> Martin Maechler
>
>
>> "BDR" == Prof Brian Ripley <[EMAIL PROTECTED]>
>> on Thu, 28 Jun 2007 06:08:45 +0100 (BST) writes:
>
> BDR> See the thread starting
> BDR> https://stat.ethz.ch/pipermail/r-devel/2007-June/046157.html
> BDR> https://stat.ethz.ch/pipermail/r-devel/2007-June/046160.html
>
> BDR> I can't reproduce this without knowing what is in your
> BDR> startup files: it should work with --vanilla, so please
> BDR> try that and try to eliminate whatever is in your
> BDR> .Rprofile etc that is causing the problem.
>
> BDR> Incidentally, using rcompletion is counterproductive in
> BDR> R 2.5.1 RC: the base functionality using rcompgen is a
> BDR> more sophisticated version.
>
> BDR> On Wed, 27 Jun 2007, Sebastian P. Luque wrote:
>
> >> Hi,
> >>
> >> I've begun to use the lme4 package, rather than nlme, for more
> flexibility
> >> during modelling, and running the examples in lmer I receive this error
> >> message:
> >>
> >> ---<---cut here---start-->---
> R> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
> >> Error in printMer(object) : no slot of name "status" for this object
> of class "table"
> >>
> R> sessionInfo()
> >> R version 2.5.1 RC (2007-06-25 r42057)
> >> x86_64-pc-linux-gnu
> >>
> >> locale:
> >>
> LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] "stats4""stats" "graphics" "grDevices" "utils"
> "datasets"
> >> [7] "methods" "base"
> >>
> >> other attached packages:
> >> lme4 Matrix rcompletionrcompgen latticediveMove
> >> "0.99875-2" "0.99875-2" "0.1-2""0.1-13" "0.15-11" "0.7-9"
> >> reshape
> >> "0.7.4"
> >> ---<---cut here---end>---
> >>
> >> Since this is happening in a fresh session, and with code from examples
> >> help file, this looks like a potential bug. Any thoughts?
> >>
> >>
> >> Cheers,
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Re
