Hi,
from the man page ?methods, I expected to be able to build pairs
(class,package) for a given S3 method, e.g., print, using
attr(methods(print), 'info').
However all the methods, except the ones defined in base or S4
methods, get the 'from' value "registered S3method for print",
instead
of the actual package name (see below for the first rows).
Is this normal behaviour? If so, is there a way to get what I want: a
character vector mapping class to package (ideally in loading order,
but this I can re-order from search()).
Thank you.
Bests,
Renaud
visible
from generic isS4
print.abbrev FALSE registered
S3method for print print FALSE
print.acf FALSE registered
S3method for print print FALSE
print.AES FALSE registered
S3method for print print FALSE
print.agnes FALSE registered
S3method for print print FALSE
print.anova FALSE registered
S3method for print print FALSE
print.Anova FALSE registered
S3method for print print FALSE
print.anova.loglm FALSE registered
S3method for print print FALSE
print,ANY-method TRUE
base print TRUE
print.aov FALSE registered
S3method for print print FALSE
On 07/07/2015 02:05 AM, Renaud Gaujoux wrote:> Hi, > > from the man page ?methods, I expected to be able to build pairs > (class,package) for a given S3 method, e.g., print, using > > attr(methods(print), 'info'). > > However all the methods, except the ones defined in base or S4 > methods, get the 'from' value "registered S3method for print", instead > of the actual package name (see below for the first rows). > > Is this normal behaviour? If so, is there a way to get what I want: a > character vector mapping class to package (ideally in loading order, > but this I can re-order from search()).It's the way it has always been, so normal in that sense. There could be two meanings of 'from' -- the namespace in which the generic to which the method belongs is defined, and the namespace in which the method is defined. I think the former is what you're interested in, but the latter likely what methods() might be modified return. For your use case, maybe something like .S3methodsInNamespace <- function(envir, pattern) { mtable <- get(".__S3MethodsTable__.", envir = asNamespace(envir)) methods <- ls(mtable, pattern = pattern) env <- vapply(methods, function(x) { environmentName(environment(get(x, mtable))) }, character(1)) setNames(names(env), unname(env)) } followed by nmspc = loadedNamespaces() lapply(setNames(nmspc, nmspc), .S3methodsInNamespace, "^plot.") which reveals the different meanings of 'from', e.g., > lapply(setNames(nmspc, nmspc), .S3methodsInNamespace, "^plot.")["graphics"] $graphics stats graphics stats "plot.acf" "plot.data.frame" "plot.decomposed.ts" graphics stats stats "plot.default" "plot.dendrogram" "plot.density" stats graphics graphics "plot.ecdf" "plot.factor" "plot.formula" graphics stats graphics "plot.function" "plot.hclust" "plot.histogram" stats stats stats "plot.HoltWinters" "plot.isoreg" "plot.lm" stats stats stats "plot.medpolish" "plot.mlm" "plot.ppr" stats stats stats "plot.prcomp" "plot.princomp" "plot.profile.nls" graphics stats stats "plot.raster" "plot.spec" "plot.stepfun" stats graphics stats "plot.stl" "plot.table" "plot.ts" stats stats "plot.tskernel" "plot.TukeyHSD" Also this is for loaded, rather than attached, namespaces. Martin Morgan> Thank you. > > Bests, > Renaud > > visible > from generic isS4 > print.abbrev FALSE registered > S3method for print print FALSE > print.acf FALSE registered > S3method for print print FALSE > print.AES FALSE registered > S3method for print print FALSE > print.agnes FALSE registered > S3method for print print FALSE > print.anova FALSE registered > S3method for print print FALSE > print.Anova FALSE registered > S3method for print print FALSE > print.anova.loglm FALSE registered > S3method for print print FALSE > print,ANY-method TRUE > base print TRUE > print.aov FALSE registered > S3method for print print FALSE > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
Thank you for your reply Martin. Your code made me realize that S3 methods are added to the .__S3MethodsTable__. of the package that defines the generic, not to the ones defining the method itself. How does things work in the case of a method from one package B masking the one from another package A? I don't get any warning message and there seems to be only one entry in the relevant .__S3MethodsTable__. Aren't these tables updated when the masking package B is detached? On 7 July 2015 at 21:01, Martin Morgan <mtmorgan at fredhutch.org> wrote:> On 07/07/2015 02:05 AM, Renaud Gaujoux wrote: >> >> Hi, >> >> from the man page ?methods, I expected to be able to build pairs >> (class,package) for a given S3 method, e.g., print, using >> >> attr(methods(print), 'info'). >> >> However all the methods, except the ones defined in base or S4 >> methods, get the 'from' value "registered S3method for print", instead >> of the actual package name (see below for the first rows). >> >> Is this normal behaviour? If so, is there a way to get what I want: a >> character vector mapping class to package (ideally in loading order, >> but this I can re-order from search()). > > > It's the way it has always been, so normal in that sense. > > There could be two meanings of 'from' -- the namespace in which the generic > to which the method belongs is defined, and the namespace in which the > method is defined. I think the former is what you're interested in, but the > latter likely what methods() might be modified return. > > For your use case, maybe something like > > .S3methodsInNamespace <- function(envir, pattern) { > mtable <- get(".__S3MethodsTable__.", envir = asNamespace(envir)) > methods <- ls(mtable, pattern = pattern) > env <- vapply(methods, function(x) { > environmentName(environment(get(x, mtable))) > }, character(1)) > setNames(names(env), unname(env)) > } > > > followed by > > nmspc = loadedNamespaces() > lapply(setNames(nmspc, nmspc), .S3methodsInNamespace, "^plot.") > > which reveals the different meanings of 'from', e.g., > >> lapply(setNames(nmspc, nmspc), .S3methodsInNamespace, >> "^plot.")["graphics"] > $graphics > stats graphics stats > "plot.acf" "plot.data.frame" "plot.decomposed.ts" > graphics stats stats > "plot.default" "plot.dendrogram" "plot.density" > stats graphics graphics > "plot.ecdf" "plot.factor" "plot.formula" > graphics stats graphics > "plot.function" "plot.hclust" "plot.histogram" > stats stats stats > "plot.HoltWinters" "plot.isoreg" "plot.lm" > stats stats stats > "plot.medpolish" "plot.mlm" "plot.ppr" > stats stats stats > "plot.prcomp" "plot.princomp" "plot.profile.nls" > graphics stats stats > "plot.raster" "plot.spec" "plot.stepfun" > stats graphics stats > "plot.stl" "plot.table" "plot.ts" > stats stats > "plot.tskernel" "plot.TukeyHSD" > > Also this is for loaded, rather than attached, namespaces. > > Martin Morgan > >> Thank you. >> >> Bests, >> Renaud >> >> visible >> from generic isS4 >> print.abbrev FALSE registered >> S3method for print print FALSE >> print.acf FALSE registered >> S3method for print print FALSE >> print.AES FALSE registered >> S3method for print print FALSE >> print.agnes FALSE registered >> S3method for print print FALSE >> print.anova FALSE registered >> S3method for print print FALSE >> print.Anova FALSE registered >> S3method for print print FALSE >> print.anova.loglm FALSE registered >> S3method for print print FALSE >> print,ANY-method TRUE >> base print TRUE >> print.aov FALSE registered >> S3method for print print FALSE >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 >
Thanks Kevin, this indeed clarifies a bit the S3 method registration universe. On 8 July 2015 at 15:48, Kevin Wright <kw.stat at gmail.com> wrote:> Not sure if this answers your question, but you can't unregister a method. See > > http://tolstoy.newcastle.edu.au/R/help/06/07/30791.html > > Kevin Wright > > > On Wed, Jul 8, 2015 at 5:09 AM, Renaud Gaujoux > <renaud at mancala.cbio.uct.ac.za> wrote: >> Thank you for your reply Martin. >> Your code made me realize that S3 methods are added to the >> .__S3MethodsTable__. of the package that defines the generic, not to >> the ones defining the method itself. >> How does things work in the case of a method from one package B >> masking the one from another package A? I don't get any warning >> message and there seems to be only one entry in the relevant >> .__S3MethodsTable__. >> Aren't these tables updated when the masking package B is detached? >> >> On 7 July 2015 at 21:01, Martin Morgan <mtmorgan at fredhutch.org> wrote: >>> On 07/07/2015 02:05 AM, Renaud Gaujoux wrote: >>>> >>>> Hi, >>>> >>>> from the man page ?methods, I expected to be able to build pairs >>>> (class,package) for a given S3 method, e.g., print, using >>>> >>>> attr(methods(print), 'info'). >>>> >>>> However all the methods, except the ones defined in base or S4 >>>> methods, get the 'from' value "registered S3method for print", instead >>>> of the actual package name (see below for the first rows). >>>> >>>> Is this normal behaviour? If so, is there a way to get what I want: a >>>> character vector mapping class to package (ideally in loading order, >>>> but this I can re-order from search()). >>> >>> >>> It's the way it has always been, so normal in that sense. >>> >>> There could be two meanings of 'from' -- the namespace in which the generic >>> to which the method belongs is defined, and the namespace in which the >>> method is defined. I think the former is what you're interested in, but the >>> latter likely what methods() might be modified return. >>> >>> For your use case, maybe something like >>> >>> .S3methodsInNamespace <- function(envir, pattern) { >>> mtable <- get(".__S3MethodsTable__.", envir = asNamespace(envir)) >>> methods <- ls(mtable, pattern = pattern) >>> env <- vapply(methods, function(x) { >>> environmentName(environment(get(x, mtable))) >>> }, character(1)) >>> setNames(names(env), unname(env)) >>> } >>> >>> >>> followed by >>> >>> nmspc = loadedNamespaces() >>> lapply(setNames(nmspc, nmspc), .S3methodsInNamespace, "^plot.") >>> >>> which reveals the different meanings of 'from', e.g., >>> >>>> lapply(setNames(nmspc, nmspc), .S3methodsInNamespace, >>>> "^plot.")["graphics"] >>> $graphics >>> stats graphics stats >>> "plot.acf" "plot.data.frame" "plot.decomposed.ts" >>> graphics stats stats >>> "plot.default" "plot.dendrogram" "plot.density" >>> stats graphics graphics >>> "plot.ecdf" "plot.factor" "plot.formula" >>> graphics stats graphics >>> "plot.function" "plot.hclust" "plot.histogram" >>> stats stats stats >>> "plot.HoltWinters" "plot.isoreg" "plot.lm" >>> stats stats stats >>> "plot.medpolish" "plot.mlm" "plot.ppr" >>> stats stats stats >>> "plot.prcomp" "plot.princomp" "plot.profile.nls" >>> graphics stats stats >>> "plot.raster" "plot.spec" "plot.stepfun" >>> stats graphics stats >>> "plot.stl" "plot.table" "plot.ts" >>> stats stats >>> "plot.tskernel" "plot.TukeyHSD" >>> >>> Also this is for loaded, rather than attached, namespaces. >>> >>> Martin Morgan >>> >>>> Thank you. >>>> >>>> Bests, >>>> Renaud >>>> >>>> visible >>>> from generic isS4 >>>> print.abbrev FALSE registered >>>> S3method for print print FALSE >>>> print.acf FALSE registered >>>> S3method for print print FALSE >>>> print.AES FALSE registered >>>> S3method for print print FALSE >>>> print.agnes FALSE registered >>>> S3method for print print FALSE >>>> print.anova FALSE registered >>>> S3method for print print FALSE >>>> print.Anova FALSE registered >>>> S3method for print print FALSE >>>> print.anova.loglm FALSE registered >>>> S3method for print print FALSE >>>> print,ANY-method TRUE >>>> base print TRUE >>>> print.aov FALSE registered >>>> S3method for print print FALSE >>>> >>>> ______________________________________________ >>>> R-devel at r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>> >>> >>> >>> -- >>> Computational Biology / Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. >>> PO Box 19024 Seattle, WA 98109 >>> >>> Location: Arnold Building M1 B861 >>> Phone: (206) 667-2793 >>> >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > > > > -- > Kevin Wright >