search for: matchsignature

...done R upgrades many times before; this is the first time I''ve had a problem. The full error message for lme4 can be seen at: http://www.ling.uni-potsdam.de/~vasishth/screen.txt One other unusual thing was that there were many warning messages during the Matrix install. ... Warning in matchSignature(signature, fdef, where) : in the method signature for function "coerce" no definition for class: "matrix.csr" Warning in matchSignature(signature, fdef, where) : in the method signature for function "coerce" no definition for class: "matrix.csr" Warning...

While trying to install a package, I received this error ** preparing package for lazy loading Error in matchSignature(signature, fdef, where) : more elements in the method signature (2) than in the generic signature (1) A more helpful variant is Error in matchSignature(signature, fdef, where) : more elements in the method signature (2) than in the generic signature (1) for function 'sort' which...

...package: chr [1:2] "" "" ..@ generic: atomic [1:1] bar .. ..- attr(*, "package")= chr ".GlobalEnv" This does not occur when the order of setMethod calls is reversed. The reason is that the package information added when methods/R/Methods.R:552 calls matchSignature are stripped (because matchSignature returns a vector with trailing 'ANY' classes removed) by the call to .matchSigLength at line 603. The context for this is the thread starting at https://stat.ethz.ch/pipermail/bioconductor/2012-August/047241.html where a complicated package dependen...

Hello R-Team, May you help me to post a 'S4-creating Package Problem'? Thanks already now for supporting. The problem sounds like: Hello R forum, while compiling my R-package these 'Warnings' occur: ... Warnung in matchSignature(signature, fdef, where) : in the method signature for function "plot" no definition for class: "prediction" Warnung in matchSignature(signature, fdef, where) : in the method signature for function "plot" no definition for class: "validation" ** help *...

...rm is a class defined in the marray package. After building and installing my package, I get the following warnings when I load my package (with library(maVis)): Warning messages: 1: In the method signature for function "plot", class "marrayRaw" has no current definition in: matchSignature(signature, fdef, where) 2: In the method signature for function "plot", class "marrayRaw" has no current definition in: matchSignature(signature, fdef, where) (but everything appears to work ok regardless). I have tried require(marray) both inside and outside of the .onLoad me...

...ric("foo")) setMethod("foo", "ANY", function(x) cat(x)) fails with Error in while (value[n] == "ANY") n <- n - 1 : missing value where logical needed It looks like the line while (value[n] == "ANY") n <- n - 1 in the source for matchSignature() should be while (n > 0 && value[n] == "ANY") n <- n - 1 FYI: I tried my suggested modification at it seems to work. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-devel mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FA...

With > R.version.string [1] "R version 2.15.0 alpha (2012-03-14 r58748)" trying to trace a method using the 'signature' argument fails rather than enabling the trace: > trace(initialize, signature="ANY") Error in matchSignature(signature, fdef, where) : trying to match a method signature of class ?signature?; expects a list or a character vector -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

...pt, but in version 1.9.0 I'm getting errors like: Error in inherits(x, "factor") : couldn't find function "winMenuNames" In addition: Warning message: In the method signature for function "contents", class "environment" has no current definition in: matchSignature(signature, fdef, where) Error in library(Biobase) : .First.lib failed Does anyone know if anything changed in version 1.9.0 that could explain these errors? Thanks Thon P.S. Below you find the script I use. %1 will contain the script that I try to run... ------------- @echo off copy %1 .Rp...

...as in library(Biobase) library(marrayClasses) is fine, but when Biobase is loaded via a require statement in marrayClasses' .First.Lib, I end up with: Warning message: In the method signature for function "coerce", class "exprSet" has no current definition in: matchSignature(signature, fdef, where) and based on the "band-aid" working above, suggests an initialization or evaluation timing problem. (and exprSet is defined in the Biobase package). best, -tony -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Heal...

...st.txt", sep = "\n") > x <- read.table("test.txt") > class(x$V1) [1] "factor" This is what we expect. > library(methods) > setAs('character', "AsIs", function(from) I(from)) Warning message: Class "AsIs"not defined in: matchSignature(fnames, signature, fdef) > This warning seems wrong to me, although I am not smart enough to follow the logic through the underlying code. It *seems* as if setAs does not consider `AsIs' to be an allowed class. However, the desired effect is achieved. > x <- read.table("test.tx...

Versions 0.9975-1 of the Matrix and lme4 packages will soon be available on CRAN for use with R version 2.4.0 or later. Purpose of the packages: The Matrix package provides S4 classes and methods for sparse and dense matrices. The lme4 package provides functions for fitting and assessing linear or generalized linear mixed effects models (also called multilevel models). Like the Matrix package,

Versions 0.9975-1 of the Matrix and lme4 packages will soon be available on CRAN for use with R version 2.4.0 or later. Purpose of the packages: The Matrix package provides S4 classes and methods for sparse and dense matrices. The lme4 package provides functions for fitting and assessing linear or generalized linear mixed effects models (also called multilevel models). Like the Matrix package,

...s(expr, envir, enclos) 7: setMethod("update", signature(statistic = "statisticInfo", newData = "numeric"), function(statistic, newData) { 8: isSealedMethod(f, signature, fdef, where = where) 9: getMethod(f, signature, optional = TRUE, where = where, fdef = fGen) 10: matchSignature(signature, f I don't understand this any help would be appreciated. Secondly, can anyone give any examples of where methods are used that makes sense besides just checking the class inputs? Thirdly, I've looked into passing by reference in R, and some options come up, but in general they...

...e file (as I read from the net). - What are the differences between "R CMD check" and "R CMD INSTALL" as far as the steps are involved. As a matter of fact: - R CMD check finds that everything is OK - R CMD INSTALL gives me a set of warnings of the following type: Warning in matchSignature(signature, fdef, where) : in the method signature for function "[<-" no definition for class: "db" I did not use the Collate option (that Martin suggested) as I am not sure of its syntax and where I should add these statements. The package works fine anyhow but I would li...

...ld do ?`foo,numeric-method` or ?`foo,numeric,ANY-method` to find the method has been a long-standing problem. H. On 3/21/19 21:29, Michael Lawrence wrote: If we started over, I'd try to avoid this sort of complexity, but "ANY" truncation has been happening since at least 2003. > matchSignature(c("numeric", "ANY"), foo) x "numeric" So I'm not sure we want to mess with it. Michael On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve <hpages at fredhutch.org<mailto:hpages at fredhutch.org>> wrote: Hi Michael, Thanks for looking into this. I...

Hi Michael, Thanks for looking into this. I suspect that truncation of ANY suffixes from method signatures is also the culprit behind the sudden breakage of aliases of the form \alias{foo,numeric-method} when a method without the ANY suffix in its signature gets added to the ecosystem. See my post about this to the Bioc-devel mailing list a couple of months ago:

...od("func","A",func1.A); showMethods("func") ##Function "func": ##obj = "A" func2.A <- function(obj,x){ print("A"); return(); } ## gives error ## setMethod("func",c("A","numeric"),func2.A); ##Error in matchSignature(signature, fdef) : ## Invalid names in signature: ## extending the signature setGeneric("func",function(obj,x,...){ res <- standardGeneric("func"); res at cal <- match.arg(); return(res); }); setMethod("func",c("A","numeric"),fun...

...the same output and attributes as varExp), but still I get the error message. Would it have anything to do with the warning I get when I create the coef.varExp2 and other functions: In the method signature for function "coef<-", class "varExp2" has no current definition in: matchSignature(signature, fdef, where) Any help would be greatly appreciated. Do I somehow need to tell nlme where to find my new functions? John

If we started over, I'd try to avoid this sort of complexity, but "ANY" truncation has been happening since at least 2003. > matchSignature(c("numeric", "ANY"), foo) x "numeric" So I'm not sure we want to mess with it. Michael On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve <hpages at fredhutch.org> wrote: > Hi Michael, > > Thanks for looking into this. I suspect that truncation...

...o JSONDebug.o JSONIterators.o JSONMemory.o JSONNode.o JSONNode_Mutex.o JSONPreparse.o JSONStream.o JSONValidator.o JSONWorker.o JSONWriter.o JSON_Base64.o JSON_parser.o RJSON.o internalJSONNode.o libjson.o rlibjson.o -L/usr/lib/R/lib -lR ** R ** inst ** preparing package for lazy loading Warning in matchSignature(signature, fdef, where) : in the method signature for function "isValidJSON" no definition for class: “AsIs” Warning in matchSignature(signature, fdef, where) : in the method signature for function "isValidJSON" no definition for class: “connection” Error in conformMethod(si...