From ripley at stats.ox.ac.uk  Fri Jan 30 12:56:54 2009
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 30 Jan 2009 11:56:54 +0000 (GMT)
Subject: [Rd] Methods not loaded in R-Devel vs 2.8.1
In-Reply-To: <B89F0CE41D45644A97CCC93DF548C1C3176BFC45@GBHENXMB02.corp.amvescap.net>
References: <B89F0CE41D45644A97CCC93DF548C1C3176BFBEF@GBHENXMB02.corp.amvescap.net>
	<B89F0CE41D45644A97CCC93DF548C1C3176BFC45@GBHENXMB02.corp.amvescap.net>
Message-ID: <alpine.OSX.1.00.0901301152390.2881@tystie.local>

I don't believe this is Rgui vs Rterm either.  More likely it is in 
the startup files for the two sessions, e.g. the library search paths.

Try using --vanilla.

On Fri, 30 Jan 2009, Pfaff, Bernhard Dr. wrote:

> Sorry for bothering the list one more time. When I run the code with RGui.exe the methods are shown in both versions of R and everything is fine. However, there is a difference whence the showMethods("residuals") is invoked via Rterm.exe. Here, neither under 2.8.1 nor R-Devel are the methods reported for "GoGARCH" and "Goestml". I have the following in my .emacs:
>
> (setq inferior-R-program-name "Q:/Shared/Applications/R/R-2.8.1/bin/Rterm.exe")
> (setq inferior-R-args "--internet2")
> (setq ess-ask-for-ess-directory nil)
>
> and the result is the same:
>
>> library(gogarch)
> Loading required package: fGarch
> Loading required package: timeDate
> Loading required package: timeSeries
> Loading required package: fBasics
> Loading required package: MASS
> Warning message:
> package 'gogarch' was built under R version 2.9.0
>> showMethods("residuals")
> Function: residuals (package stats)
> object="ANY"
> object="fGARCH"
>
>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats     graphics  datasets  utils     grDevices methods   base
>
> other attached packages:
> [1] gogarch_0.2-9     fGarch_280.75     fBasics_280.74    MASS_7.2-44
> [5] timeSeries_290.79 timeDate_290.81   fortunes_1.3-6
>
> loaded via a namespace (and not attached):
> [1] grid_2.8.1      lattice_0.17-17 nlme_3.1-89     urca_1.2-2
> [5] vars_1.4-4
>> getMethod("residuals", "GoGARCH")
> Error in getMethod("residuals", "GoGARCH") :
>  No method found for function "residuals" and signature GoGARCH
>>
>
> So now my question is rather about the difference between RGui.exe 
> and Rterm.exe with respect to the method map.
>
> Best,
> Bernhard
>
>
>
> Dr. Bernhard Pfaff
> Director
> Invesco Quantitative Strategies International
>
> Invesco Asset Management Deutschland GmbH
> Bleichstrasse 60-62
> D-60313 Frankfurt am Main
>
> Tel: +49 (0)69 29807 230
> Fax: +49 (0)69 29807 178
> www.institutional.invesco.com
> Email: bernhard_pfaff at fra.invesco.com
>
> Gesch?ftsf?hrer: Karl Georg Bayer, Bernhard Langer, Dr. Jens Langewand, Alexander Lehmann, Christian Puschmann
> Handelsregister: Frankfurt am Main, HRB 28469
> Sitz der Gesellschaft: Frankfurt am Main
>
>
>> -----Urspr?ngliche Nachricht-----
>> Von: r-devel-bounces at r-project.org
>> [mailto:r-devel-bounces at r-project.org] Im Auftrag von Pfaff,
>> Bernhard Dr.
>> Gesendet: Freitag, 30. Januar 2009 12:13
>> An: r-devel at r-project.org
>> Betreff: [Rd] Methods not loaded in R-Devel vs 2.8.1
>>
>> Dear list-member,
>>
>> I am currently developing a package with S4 classes. The
>> NAMESPACE and DESCRIPTION is printed below. Within this
>> package I have set a method "residuals" for two classes. In
>> version 2.8.1 these two are reported whereas in R-Devel
>> (2009-01-28 r47766). What have I missed? What has changed and
>> how can I rectify the issue? Your help and pointers are welcome.
>>
>>
>> For 2.8.1:
>> **********
>>
>>> library(gogarch)
>> Loading required package: fGarch
>> Loading required package: timeDate
>> Loading required package: timeSeries
>> Loading required package: fBasics
>> Loading required package: MASS
>> Warning message:
>> package 'gogarch' was built under R version 2.9.0
>>> showMethods("residuals")
>> Function: residuals (package stats)
>> object="ANY"
>> object="fGARCH"
>> object="Goestml"
>> object="GoGARCH"
>>
>>> getMethod("residuals", "GoGARCH")
>> Method Definition:
>>
>> function (object, ...)
>> {
>>    .local <- function (object, standardize = FALSE)
>>    {
>>        m <- ncol(object at X)
>>        n <- nrow(object at X)
>>        resl <- lapply(object at models, residuals, standardize =
>> standardize)
>>        resm <- matrix(c(unlist(resl)), ncol = m, nrow = n)
>>        ynames <- paste("y", 1:2, sep = "")
>>        colnames(resm) <- ynames
>>        rownames(resm) <- rownames(object at X)
>>        return(resm)
>>    }
>>    .local(object, ...)
>> }
>> <environment: namespace:gogarch>
>>
>> Signatures:
>>        object
>> target  "GoGARCH"
>> defined "GoGARCH"
>>> sessionInfo()
>> R version 2.8.1 (2008-12-22)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_
>> MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>>
>> attached base packages:
>> [1] stats     graphics  datasets  utils     grDevices methods
>> base
>>
>> other attached packages:
>> [1] gogarch_0.2-8     fGarch_280.75     fBasics_280.74
>> MASS_7.2-44
>> [5] timeSeries_290.79 timeDate_290.81   fortunes_1.3-6
>>>
>>
>>
>> For R-Devel:
>> ************
>>> library(gogarch)
>> Loading required package: fGarch
>> Loading required package: timeDate
>> Loading required package: timeSeries
>> Loading required package: fBasics
>> Loading required package: MASS
>>> showMethods("residuals")
>> Function: residuals (package stats)
>> object="ANY"
>> object="fGARCH"
>>
>>> getMethod("residuals", "GoGARCH")
>> Error in getMethod("residuals", "GoGARCH") :
>>  No method found for function "residuals" and signature GoGARCH
>>> sessionInfo()
>> R version 2.9.0 Under development (unstable) (2009-01-28 r47766)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_
>> MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices datasets  utils     methods
>> base
>>
>> other attached packages:
>> [1] gogarch_0.2-8     fGarch_280.75     fBasics_280.74
>> MASS_7.2-44
>> [5] timeSeries_290.79 timeDate_290.81   fortunes_1.3-6
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.9.0      lattice_0.17-17 nlme_3.1-89     urca_1.2-2
>> [5] vars_1.4-4
>>>
>>
>>
>> DESCRIPTION:
>> ************
>> Package: gogarch
>> Version: 0.2-8
>> Type: Package
>> Title: Generalized Orthogonal GARCH (GO-GARCH) models
>> Date: 2009-01-30
>> Author: Bernhard Pfaff
>> Maintainer: Bernhard Pfaff <bernhard at pfaffikus.de>
>> Depends: R (>= 2.7.0), stats, methods, fGarch
>> Suggests: vars
>> Description: Implementation of the GO-GARCH model class.
>> License: GPL (>= 2)
>> LazyLoad: yes
>> LazyLoad: yes
>>
>> NAMESPACE:
>> **********
>> ## Import packages
>> import(methods)
>>
>> ## Import functions
>> importFrom(stats, coef, logLik, residuals)
>>
>> ## Classes
>> exportClasses(Goestml, GoGARCH, Goinit, Orthom)
>>
>> ## Methods
>> exportMethods(angles, cvar, ccor, ccov, coef, converged,
>> goest, logLik, M, print, show, t, residuals)
>>
>> ## Functions
>> export(gogarch, goinit, gollh, gotheta, Rd2, UprodR, unvech,
>> validOrthomObject, validGoinitObject)
>>
>>
>>
>> Dr. Bernhard Pfaff
>> Director
>> Invesco Quantitative Strategies International
>>
>> Invesco Asset Management Deutschland GmbH
>> Bleichstrasse 60-62
>> D-60313 Frankfurt am Main
>>
>> Tel: +49 (0)69 29807 230
>> Fax: +49 (0)69 29807 178
>> www.institutional.invesco.com
>> Email: bernhard_pfaff at fra.invesco.com
>>
>> Gesch?ftsf?hrer: Karl Georg Bayer, Bernhard Langer, Dr. Jens
>> Langewand, Alexander Lehmann, Christian Puschmann
>> Handelsregister: Frankfurt am Main, HRB 28469
>> Sitz der Gesellschaft: Frankfurt am Main
>>
>> *****************************************************************
>> Confidentiality Note: The information contained in this
>> ...{{dropped:10}}
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


[Rd] Methods not loaded in R-Devel vs 2.8.1
Prof Brian Ripley