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Jens Henrik Badsberg

2004-Mar-16 10:37 UTC

[R] Documentation on how to put classes and methods in packages with namespace?

Documentation on how to put classes and methods in packages with namespace?

 How should I define my classes and methods in "dynamicGraph"???

 (That is - Can some one point me to the documentation on
 how to put classes and methods in packages with a namespace? )

 Currently it is done by the code below.

 This gives problems, when a workspace with a "dynmaicGraph" is
restored:

 1. run:

     local({a <- CRAN.packages()
     install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a)})
     search()
     library(dynamicGraph)
     a <- DynamicGraph(1:10)
     search()
     ls(pos=3, all.names=TRUE)
     history()
     q(save="yes")

 2. run:

     search()
     ls()
     library(dynamicGraph)
     search()
     ls(pos=3, all.names=TRUE)
     b <- DynamicGraph(1:10)
     history()

 The classes and methods of dynamicGraph is not assigned, see the attached
"run2.txt",
 and compare with the list of the objects of dynamicGraph in
"run1.txt".

 I have experimented with the argument "where" to setClass, etc., see
the attached
 "onLoad.R".

 Regards,

 Jens Henrik Badsberg



".onAttach" <-
function (lib, pkg) 
{
    require(tcltk)
}
".onLoad" <-
function (lib, pkg) 
{
    .onLoad.dynamicGraph()
}
".onLoad.dynamicGraph" <-
function () 
{
    library(methods)
    setClass("GraphLatticeProto", representation(vertices =
"list",
        blocks = "list", blockTree = "list", graphs =
"list"))
    setClass("CanvasProto", representation(top = "tkwin",
canvas = "tkwin",
        tags = "list", id = "numeric", visibleVertices =
"numeric",
        graphEdges = "list", blockEdges = "list",
factorVertices = "list",
        factorEdges = "list"))
    setClass("NodeProto", representation(color =
"character",
        label = "character", label.position = "numeric"),
prototype(color = "black",
        label = "Label", label.position = c(0, 0, 0)))

    ### .... Many lines deleted ....

    if (!isGeneric("label")) {
        if (is.function("label")) 
            fun <- label
        else fun <- function(object) standardGeneric("label")
        setGeneric("label", fun)
    }
    setMethod("label", "NodeProto", function(object) object
at label)
    setGeneric("label<-", function(x, value)
standardGeneric("label<-"))
    setReplaceMethod("label", "NodeProto", function(x,
value) {
        x at label <- value
        x
    })

    ### .... Many lines deleted ....

}
 <<run1.txt>>  <<run2.txt>>  <<onLoad.R>> 
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Prof Brian Ripley

2004-Mar-16 11:37 UTC

head link

[R] Documentation on how to put classes and methods in packages with namespace?

See `Writing R Extensions' in 1.9.0 alpha and the stats4 package there as 
an example.  At this point you probably only want to check a package 
against 1.9.0 alpha, anyway.

On Tue, 16 Mar 2004, Jens Henrik Badsberg wrote:
> 
>  Documentation on how to put classes and methods in packages with
namespace?
> 
>  How should I define my classes and methods in "dynamicGraph"???
> 
>  (That is - Can some one point me to the documentation on
>  how to put classes and methods in packages with a namespace? )
[...]

-- 
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

Uwe Ligges

2004-Mar-16 12:51 UTC

head link

[R] Documentation on how to put classes and methods in packages with namespace?

Jens Henrik Badsberg wrote:
>  Documentation on how to put classes and methods in packages with
namespace?
> 
>  How should I define my classes and methods in "dynamicGraph"???

Jens Henrik,

without reading all the lines below, I'd like to point you to the 
"Writing R Extensions" manual of R-devel (1.9.0 alpha), which includes
some lines on handling S4 classes/methods in Namespaces.

Uwe



>  (That is - Can some one point me to the documentation on
>  how to put classes and methods in packages with a namespace? )
> 
>  Currently it is done by the code below.
> 
>  This gives problems, when a workspace with a "dynmaicGraph" is
restored:
> 
>  1. run:
> 
>      local({a <- CRAN.packages()
>      install.packages(select.list(a[,1],,TRUE), .libPaths()[1],
available=a)})
>      search()
>      library(dynamicGraph)
>      a <- DynamicGraph(1:10)
>      search()
>      ls(pos=3, all.names=TRUE)
>      history()
>      q(save="yes")
> 
>  2. run:
> 
>      search()
>      ls()
>      library(dynamicGraph)
>      search()
>      ls(pos=3, all.names=TRUE)
>      b <- DynamicGraph(1:10)
>      history()
> 
>  The classes and methods of dynamicGraph is not assigned, see the attached
"run2.txt",
>  and compare with the list of the objects of dynamicGraph in
"run1.txt".
> 
>  I have experimented with the argument "where" to setClass, etc.,
see the attached
>  "onLoad.R".
> 
>  Regards,
> 
>  Jens Henrik Badsberg
> 
> 
> 
> ".onAttach" <-
> function (lib, pkg) 
> {
>     require(tcltk)
> }
> ".onLoad" <-
> function (lib, pkg) 
> {
>     .onLoad.dynamicGraph()
> }
> ".onLoad.dynamicGraph" <-
> function () 
> {
>     library(methods)
>     setClass("GraphLatticeProto", representation(vertices =
"list",
>         blocks = "list", blockTree = "list", graphs =
"list"))
>     setClass("CanvasProto", representation(top =
"tkwin", canvas = "tkwin",
>         tags = "list", id = "numeric", visibleVertices
= "numeric",
>         graphEdges = "list", blockEdges = "list",
factorVertices = "list",
>         factorEdges = "list"))
>     setClass("NodeProto", representation(color =
"character",
>         label = "character", label.position =
"numeric"), prototype(color = "black",
>         label = "Label", label.position = c(0, 0, 0)))
> 
>     ### .... Many lines deleted ....
> 
>     if (!isGeneric("label")) {
>         if (is.function("label")) 
>             fun <- label
>         else fun <- function(object) standardGeneric("label")
>         setGeneric("label", fun)
>     }
>     setMethod("label", "NodeProto", function(object)
object at label)
>     setGeneric("label<-", function(x, value)
standardGeneric("label<-"))
>     setReplaceMethod("label", "NodeProto", function(x,
value) {
>         x at label <- value
>         x
>     })
> 
>     ### .... Many lines deleted ....
> 
> }
>  <<run1.txt>>  <<run2.txt>> 
<<onLoad.R>>
> 
> 
> ------------------------------------------------------------------------
> 
> 
> 
> local({a <- CRAN.packages()
> install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a)})
> search()
> library(dynamicGraph)
> a <- DynamicGraph(1:10)
> search()
> ls(pos=3, all.names=TRUE)
> history()
> q(save="yes")
> 
> 
> 
> R : Copyright 2003, The R Foundation for Statistical Computing
> Version 1.8.1  (2003-11-21), ISBN 3-900051-00-3
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for a HTML browser interface to help.
> Type 'q()' to quit R.
> 
> 
>>local({a <- CRAN.packages()
> 
> + install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a)})
> trying URL `http://cran.r-project.org/bin/windows/contrib/1.8/PACKAGES'
> Content type `text/plain; charset=iso-8859-1' length 16234 bytes
> opened URL
> downloaded 15Kb
> 
> trying URL
`http://cran.r-project.org/bin/windows/contrib/1.8/dynamicGraph_0.1.5.9.9.8.8.zip'
> Content type `application/zip' length 347067 bytes
> opened URL
> downloaded 338Kb
> 
> package  dynamicGraph  successfully unpacked and MD5 sums checked
> 
> Delete downloaded files (y/N)? y
> 
> updating HTML package descriptions
> 
>>search()
> 
> [1] ".GlobalEnv"      "package:methods"
"package:ctest"   "package:mva"
> [5] "package:modreg"  "package:nls"    
"package:ts"      "Autoloads"
> [9] "package:base"   
> 
>>library(dynamicGraph)
> 
> Loading required package: tcltk 
> 
>>a <- DynamicGraph(1:10)
>>search()
> 
>  [1] ".GlobalEnv"           "package:tcltk"       
"package:dynamicGraph"
>  [4] "package:methods"      "package:ctest"       
"package:mva"
>  [7] "package:modreg"       "package:nls"         
"package:ts"
> [10] "Autoloads"            "package:base"        
> 
>>ls(pos=3, all.names=TRUE)
> 
>   [1] ".__C__BlockEdgeProto"                  
".__C__BlockProto"
>   [3] ".__C__CanvasProto"                     
".__C__ContinuousVertexProto"
>   [5] ".__C__defaultModelObjectProto"         
".__C__defaultTestObjectProto"
>   [7] ".__C__DiscreteGeneratorProto"          
".__C__DiscreteVertexProto"
>   [9] ".__C__EdgeProto"                       
".__C__FactorEdgeProto"
>  [11] ".__C__FactorVertexProto"               
".__C__GeneratorProto"
>  [13] ".__C__GraphLatticeProto"               
".__C__LinearGeneratorProto"
>  [15] ".__C__NodeProto"                       
".__C__OrdinalVertexProto"
>  [17] ".__C__QuadraticGeneratorProto"         
".__C__VertexEdgeProto"
>  [19] ".__C__VertexProto"                     
".__M__addToPopups:dynamicGraph"
>  [21] ".__M__ancestors:dynamicGraph"          
".__M__ancestors<-:dynamicGraph"
>  [23] ".__M__color:dynamicGraph"              
".__M__color<-:dynamicGraph"
>  [25] ".__M__Colors:dynamicGraph"             
".__M__Colors<-:dynamicGraph"
>  [27] ".__M__descendants:dynamicGraph"        
".__M__descendants<-:dynamicGraph"
>  [29] ".__M__draw:dynamicGraph"               
".__M__edgeLabel:dynamicGraph"
>  [31] ".__M__edgeLabel<-:dynamicGraph"        
".__M__edgeWidth:dynamicGraph"
>  [33] ".__M__edgeWidth<-:dynamicGraph"        
".__M__index:dynamicGraph"
>  [35] ".__M__index<-:dynamicGraph"            
".__M__Indices:dynamicGraph"
>  [37] ".__M__label:dynamicGraph"              
".__M__label<-:dynamicGraph"
>  [39] ".__M__labelOfEdge:dynamicGraph"        
".__M__labelOfEdge<-:dynamicGraph"
>  [41] ".__M__labelPosition:dynamicGraph"      
".__M__labelPosition<-:dynamicGraph"
>  [43] ".__M__LabelPositions:dynamicGraph"     
".__M__LabelPositions<-:dynamicGraph"
>  [45] ".__M__Labels:dynamicGraph"             
".__M__Labels<-:dynamicGraph"
>  [47] ".__M__name:dynamicGraph"               
".__M__name<-:dynamicGraph"
>  [49] ".__M__Names:dynamicGraph"              
".__M__Names<-:dynamicGraph"
>  [51] ".__M__NodeAncestors:dynamicGraph"      
".__M__NodeAncestors<-:dynamicGraph"
>  [53] ".__M__NodeDescendants:dynamicGraph"    
".__M__NodeDescendants<-:dynamicGraph"
>  [55] ".__M__nodeIndices:dynamicGraph"        
".__M__NodeIndices:dynamicGraph"
>  [57] ".__M__nodeIndices<-:dynamicGraph"      
".__M__nodeIndicesOfEdge:dynamicGraph"
>  [59] ".__M__nodeIndicesOfEdge<-:dynamicGraph"
".__M__NodeTypes:dynamicGraph"
>  [61] ".__M__nodeTypesOfEdge:dynamicGraph"    
".__M__oriented:dynamicGraph"
>  [63] ".__M__Oriented:dynamicGraph"           
".__M__oriented<-:dynamicGraph"
>  [65] ".__M__Oriented<-:dynamicGraph"         
".__M__position:dynamicGraph"
>  [67] ".__M__position<-:dynamicGraph"         
".__M__Positions:dynamicGraph"
>  [69] ".__M__Positions<-:dynamicGraph"        
".__M__Strata:dynamicGraph"
>  [71] ".__M__Strata<-:dynamicGraph"           
".__M__stratum:dynamicGraph"
>  [73] ".__M__stratum<-:dynamicGraph"          
".__M__visible:dynamicGraph"
>  [75] ".__M__Visible:dynamicGraph"            
".__M__visible<-:dynamicGraph"
>  [77] ".__M__Visible<-:dynamicGraph"          
".__M__width:dynamicGraph"
>  [79] ".__M__width<-:dynamicGraph"            
".__M__widthOfEdge:dynamicGraph"
>  [81] ".__M__widthOfEdge<-:dynamicGraph"      
".__M__Widths:dynamicGraph"
>  [83] ".__M__Widths<-:dynamicGraph"           
".onLoad.dynamicGraph"
>  [85] ".onLoad.dynamicGraphInterface"         
"addToPopups"
>  [87] "ancestors"                             
"ancestors<-"
>  [89] "blockTreeToList"                        "color"
>  [91] "color<-"                               
"Colors"
>  [93] "Colors<-"                              
"descendants"
>  [95] "descendants<-"                         
"draw"
>  [97] "DynamicGraph"                          
"dynamicGraphMain"
>  [99] "edgeLabel"                             
"edgeLabel<-"
> [101] "edgeWidth"                             
"edgeWidth<-"
> [103] "index"                                 
"index<-"
> [105] "Indices"                                "label"
> [107] "label<-"                               
"labelOfEdge"
> [109] "labelOfEdge<-"                         
"labelPosition"
> [111] "labelPosition<-"                       
"LabelPositions"
> [113] "LabelPositions<-"                      
"Labels"
> [115] "Labels<-"                              
"modalDialog"
> [117] "name"                                  
"name<-"
> [119] "Names"                                 
"Names<-"
> [121] "nameToVertexIndex"                     
"newBlock"
> [123] "newBlockEdge"                          
"newDefaultModelObject"
> [125] "newDefaultTestObject"                  
"newFactor"
> [127] "newFactorEdge"                         
"newVertex"
> [129] "newVertexEdge"                         
"NodeAncestors"
> [131] "NodeAncestors<-"                       
"NodeDescendants"
> [133] "NodeDescendants<-"                     
"nodeIndices"
> [135] "NodeIndices"                           
"nodeIndices<-"
> [137] "nodeIndicesOfEdge"                     
"nodeIndicesOfEdge<-"
> [139] "NodeTypes"                             
"nodeTypesOfEdge"
> [141] "oriented"                              
"Oriented"
> [143] "oriented<-"                            
"Oriented<-"
> [145] "position"                              
"position<-"
> [147] "Positions"                             
"Positions<-"
> [149] "returnBlockEdgeList"                   
"returnEdgeList"
> [151] "returnFactorEdgeList"                  
"returnFactorVerticesAndEdges"
> [153] "returnVertexList"                      
"setBlocks"
> [155] "setTreeBlocks"                          "Strata"
> [157] "Strata<-"                              
"stratum"
> [159] "stratum<-"                             
"validFactorClasses"
> [161] "validVertexClasses"                    
"visible"
> [163] "Visible"                               
"visible<-"
> [165] "Visible<-"                             
"width"
> [167] "width<-"                               
"widthOfEdge"
> [169] "widthOfEdge<-"                         
"Widths"
> [171] "Widths<-"                              
> 
>>history()
>>q(save="yes")
> 
> 
> 
> ------------------------------------------------------------------------
> 
> search()
> ls()
> library(dynamicGraph)
> search()
> ls(pos=3, all.names=TRUE)
> b <- DynamicGraph(1:10)
> history()
> 
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for a HTML browser interface to help.
> Type 'q()' to quit R.
> 
> [Previously saved workspace restored]
> 
> 
>>search()
> 
> [1] ".GlobalEnv"      "package:ctest"  
"package:mva"     "package:modreg"  "package:nls"
> [6] "package:ts"      "package:methods"
"Autoloads"       "package:base"
> 
>>ls()
> 
> [1] "a"
> 
>>library(dynamicGraph)
> 
> Loading required package: tcltk 
> 
>>search()
> 
>  [1] ".GlobalEnv"           "package:tcltk"       
"package:dynamicGraph"
>  [4] "package:ctest"        "package:mva"         
"package:modreg"
>  [7] "package:nls"          "package:ts"          
"package:methods"
> [10] "Autoloads"            "package:base"        
> 
>>ls(pos=3, all.names=TRUE)
> 
>  [1] ".onLoad.dynamicGraph"         
".onLoad.dynamicGraphInterface"
>  [3] "blockTreeToList"               "DynamicGraph"
>  [5] "dynamicGraphMain"              "modalDialog"
>  [7] "nameToVertexIndex"             "newBlock"
>  [9] "newBlockEdge"                 
"newDefaultModelObject"
> [11] "newDefaultTestObject"          "newFactor"
> [13] "newFactorEdge"                 "newVertex"
> [15] "newVertexEdge"                
"returnBlockEdgeList"
> [17] "returnEdgeList"               
"returnFactorEdgeList"
> [19] "returnFactorVerticesAndEdges"  "returnVertexList"
> [21] "setBlocks"                     "setTreeBlocks"
> [23] "validFactorClasses"           
"validVertexClasses"
> 
>>b <- DynamicGraph(1:10)
> 
> Error in getClass(superClass) : "NodeProto" is not a defined
class
> 
>>history()
>>q()
>>
>>
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>>
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