Re: [R-pkg-devel] Any new developments on "apparent S3 method" issue?
On 03.05.2017 18:39, Lenth, Russell V wrote:
Package developers list:
I recently added an 'as.mcmc.list' method for objects in one of my packages.
Now, in doing an --as-cran check, I get this message:
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
as.mcmc.list
See section 'Registering S3 methods' in the 'Writing R Extensions' manual.
Apparently, the checking routines conclude that I should register an 'as.mcmc' method for class
"list" -- something that does not exist and is not needed. I did some searching, and
found an exchange on this issue from January 2015, in which a "nonS3Method()" construct
was proposed. That sure looks like what is needed, but it still doesn't exist. Is there a different
way to handle this that has been developed?
Further information -- this is related to the *coda* package, and my NAMESPACE
file contains this code:
if (requireNamespace("coda", quietly = TRUE)) {
importFrom(coda, as.mcmc, as.mcmc.list)
export(as.mcmc, as.mcmc.list)
S3method(as.mcmc, ref.grid)
S3method(as.mcmc.list, ref.grid)
}
This seems clear enough; and what's mysterious is that *coda* passes the CRAN
checks without this same NOTE.
Yes. coda had the name for a very long time and it was not reasonable to
fix this naming in felicity later on, hence there is a check exclusion
in R-devel/src/library/tools/R/utils.R for as.mcmc.list in package coda.
Best,
Uwe Ligges
As a possible workaround, I am considering:
-- providing and registering my own S3 method 'as.mcmc' for class "list" ---
in spite of my disinterest in providing this
-- not importing coda::as.mcmc.list and instead exporting my own generic that handles
objects of class "list" separately
Any suggestions?
Russ
Russell V. Lenth - Professor Emeritus
Department of Statistics and Actuarial Science
The University of Iowa - Iowa City, IA 52242 USA
Voice (319)335-0712 (Dept. office) - FAX (319)335-3017
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Re: [R-pkg-devel] Any new developments on "apparent S3 method" issue?
OK thanks -- this gives me a new perspective. I see this result:
> tools::nonS3methods("coda")
[1] "as.mcmc.list"
which indicates more about the mechanisms in place for this kind of situation.
So now it seems that if package 'pkg_B' simply imports and exports a function
'looks.like.S3.method' from package 'pkg_A', and 'looks.like.S3.method' is
already known via tools::nonS3methods("pkg_A") and thus has a check exclusion,
then 'pkg_B' should have the same check exclusion. I recognize that such a
check-exclusion-inheritance provision may not be very straightforward to
implement.
Russ
-Original Message-
From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: Thursday, May 4, 2017 3:06 AM
To: Lenth, Russell V ; r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Any new developments on "apparent S3 method" issue?
On 03.05.2017 18:39, Lenth, Russell V wrote:
> Package developers list:
>
> I recently added an 'as.mcmc.list' method for objects in one of my packages.
> Now, in doing an --as-cran check, I get this message:
>
> * checking S3 generic/method consistency ... NOTE Found the following
> apparent S3 methods exported but not registered:
> as.mcmc.list
> See section 'Registering S3 methods' in the 'Writing R Extensions' manual.
>
> Apparently, the checking routines conclude that I should register an
> 'as.mcmc' method for class "list" -- something that does not exist and is not
> needed. I did some searching, and found an exchange on this issue from
> January 2015, in which a "nonS3Method()" construct was proposed. That sure
> looks like what is needed, but it still doesn't exist. Is there a different
> way to handle this that has been developed?
>
> Further information -- this is related to the *coda* package, and my
> NAMESPACE file contains this code:
>
> if (requireNamespace("coda", quietly = TRUE)) {
> importFrom(coda, as.mcmc, as.mcmc.list)
> export(as.mcmc, as.mcmc.list)
> S3method(as.mcmc, ref.grid)
> S3method(as.mcmc.list, ref.grid)
> }
>
> This seems clear enough; and what's mysterious is that *coda* passes the CRAN
> checks without this same NOTE.
Yes. coda had the name for a very long time and it was not reasonable to fix
this naming in felicity later on, hence there is a check exclusion in
R-devel/src/library/tools/R/utils.R for as.mcmc.list in package coda.
Best,
Uwe Ligges
>
> As a possible workaround, I am considering:
>-- providing and registering my own S3 method 'as.mcmc' for class "list"
> --- in spite of my disinterest in providing this
> -- not importing coda::as.mcmc.list and instead exporting my own
> generic that handles objects of class "list" separately
>
> Any suggestions?
>
> Russ
>
> Russell V. Lenth - Professor Emeritus Department of Statistics and
> Actuarial Science The University of Iowa - Iowa City, IA 52242 USA
> Voice (319)335-0712 (Dept. office) - FAX (319)335-3017
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Any new developments on "apparent S3 method" issue?
On 04.05.2017 16:23, Lenth, Russell V wrote:
OK thanks -- this gives me a new perspective. I see this result:
> tools::nonS3methods("coda")
[1] "as.mcmc.list"
which indicates more about the mechanisms in place for this kind of situation. So now it
seems that if package 'pkg_B' simply imports and exports a function
'looks.like.S3.method' from package 'pkg_A', and 'looks.like.S3.method' is already known
via tools::nonS3methods("pkg_A") and thus has a check exclusion, then 'pkg_B'
should have the same check exclusion. I recognize that such a check-exclusion-inheritance
provision may not be very straightforward to implement.
Ideally, pkg_B avoids the infelicities that had been established with pkg A.
Best,
Uwe Ligges
Russ
-Original Message-
From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: Thursday, May 4, 2017 3:06 AM
To: Lenth, Russell V ; r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Any new developments on "apparent S3 method" issue?
On 03.05.2017 18:39, Lenth, Russell V wrote:
Package developers list:
I recently added an 'as.mcmc.list' method for objects in one of my packages.
Now, in doing an --as-cran check, I get this message:
* checking S3 generic/method consistency ... NOTE Found the following
apparent S3 methods exported but not registered:
as.mcmc.list
See section 'Registering S3 methods' in the 'Writing R Extensions' manual.
Apparently, the checking routines conclude that I should register an 'as.mcmc' method for class
"list" -- something that does not exist and is not needed. I did some searching, and
found an exchange on this issue from January 2015, in which a "nonS3Method()" construct
was proposed. That sure looks like what is needed, but it still doesn't exist. Is there a different
way to handle this that has been developed?
Further information -- this is related to the *coda* package, and my NAMESPACE
file contains this code:
if (requireNamespace("coda", quietly = TRUE)) {
importFrom(coda, as.mcmc, as.mcmc.list)
export(as.mcmc, as.mcmc.list)
S3method(as.mcmc, ref.grid)
S3method(as.mcmc.list, ref.grid)
}
This seems clear enough; and what's mysterious is that *coda* passes the CRAN
checks without this same NOTE.
Yes. coda had the name for a very long time and it was not reasonable to fix
this naming in felicity later on, hence there is a check exclusion in
R-devel/src/library/tools/R/utils.R for as.mcmc.list in package coda.
Best,
Uwe Ligges
As a possible workaround, I am considering:
-- providing and registering my own S3 method 'as.mcmc' for class "list" ---
in spite of my disinterest in providing this
-- not importing coda::as.mcmc.list and instead exporting my own
generic that handles objects of class "list" separately
Any suggestions?
Russ
Russell V. Lenth - Professor Emeritus Department of Statistics and
Actuarial Science The University of Iowa - Iowa City, IA 52242 USA
Voice (319)335-0712 (Dept. office) - FAX (319)335-3017
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
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https://stat.ethz.ch/mailman/listinfo/r-package-devel
