From simon.urbanek at r-project.org  Thu Nov  6 23:41:39 2008
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Thu, 6 Nov 2008 17:41:39 -0500
Subject: [Rd] problem packaging S4 class that contains a slot of jobjRef
	class
In-Reply-To: <Pine.SUN.4.58.0811060643230.21426@eskimo.com>
References: <Pine.SUN.4.58.0811060643230.21426@eskimo.com>
Message-ID: <040372AE-A3E4-4AEE-80CF-9E46D7951C06@r-project.org>

Adrian,

my guess would be that you're trying to crate some Java objects at the  
top level of your package. That won't work, because R stores a  
serialized image of created objects for efficiency and hence the  
reference to any Java objects that you create will disappear as soon  
as you're done installing the package. When you try to load the  
package you'll end up with null references for all objects you have  
attempted to create that way. You have two options to avoid that:

1) create objects at load time - i.e. in the initialization function  
after you have called .jpackage. Only then is Java up and running so  
you can safely create Java objects

2) [not recommended] use .jcache to serialize objects you want to keep  
at the top level after creating them. They will be then lazily  
deserialized after the package has been loaded. However, this requires  
all such classes to implement Serializable interface on the Java side  
and is conceptually not clean, because you have to be careful when  
your cached serialization goes out of sync with the actual object (see  
details in the documentation of .jcache).

This is just my guess based on the symptoms since I think you actually  
failed to send us the part of code that triggers the problem.

Cheers,
Simon


On Nov 6, 2008, at 10:04 , Adrian Dragulescu wrote:

>
>
> Hello,
>
> I'm trying to package some source files that link R to a broker using
> a Java API and the rJava package.  I am successful doing the  
> connection
> and operate on it using my R code.  I would like to package the  
> files and
> release the package.
>
> I created some S4 classes to hold several Java objects.  I use WinXP  
> and R
> 2.7.1.  I've searched RSeek and the Wiki for help, but could not  
> find a
> solution.
>
> Here is my class definition:
> twsConnect <- function(...)
>  new("twsConnect", ...)
>
> setClass(
>  Class="twsConnect",
>  representation=representation(
>    clientId    = "integer",
>    host        = "character",
>    port        = "integer",
>    reference   = "jobjRef"),
>  prototype=prototype(
>    clientId    = as.integer(0),
>    host        = "",
>    port        = as.integer(7496),
>    reference   = .jnull())
> )
>
> setMethod("initialize", "twsConnect", function(
>  .Object, clientId = 0, host = "", port = 7496, ...)
>  {
>    # hook up to the TWS
>    ref <- .jnew("dev/AAD_Trader", as.integer(clientId), host,
>                 as.integer(port))
>
>    if (class(ref)[1] != "jobjRef")
>      stop("Could not connect.  Check your settings.")
>
>    .Object at clientId <- as.integer(clientId)
>    .Object at host <- as.character(host)
>    .Object at port <- as.integer(port)
>    .Object at reference <- ref
>
>    .Object
>  }
> )
>
>
> setMethod("show", "twsConnect",
>  function(object){
>    cat("Object of class \"", class(object), "\":\n", sep="")
>    lines <- NULL
>    for (s in slotNames(object)){
>      cont  <- slot(object, s)
>      if (is.character(cont))cont <- paste('"', cont, '"', sep="")
>      if (class(cont)=="jobjRef") cont <- "jobjRef"
>      lines <- paste(lines, paste(s, " = ", cont, "\n",
>                                  sep=""), sep="")
>    }
>    cat(lines)
>  }
> )
>
>
>
> I have other files too.  Here is the output from package creation:
> S:\All\Risk\Software\R\R-2.7.1\bin>Rcmd build --force --binary
> H:/user/R/Adrian/RIB/
> * checking for file 'H:/user/R/Adrian/RIB/DESCRIPTION' ... OK
> * preparing 'H:/user/R/Adrian/RIB':
> * checking DESCRIPTION meta-information ... OK
> * removing junk files
> * excluding invalid files from 'RIB'
> Subdirectory 'R' contains invalid file names:
>  .make.IB.package.R .utilities.R
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> WARNING: directory 'RIB/inst/doc' is empty
> * building binary distribution
> WARNING: some HTML links may not be found
> installing R.css in C:/DOCUME~1/e47187/LOCALS~1/Temp/Rinst238480883
>
> Using auto-selected zip options ''
>
> ---------- Making package RIB ------------
>  adding build stamp to DESCRIPTION
>  installing NAMESPACE file and metadata
>  installing R files
>  installing inst files
>  preparing package RIB for lazy loading
> Loading required package: rJava
> Warning: package 'rJava' was built under R version 2.7.2
> Loading required package: zoo
>
> Attaching package: 'zoo'
>
>
>        The following object(s) are masked from package:base :
>
>         as.Date.numeric
>
> Creating a new generic function for "summary" in "RIB"
>  installing man source files
>  installing indices
>  installing help
>>>> Building/Updating help pages for package 'RIB'
>     Formats: text html latex example chm
>  IBrokers-package                  text    html    latex   example chm
>  reqAccountUpdates                 text    html    latex   example chm
>  reqHistoricalData                 text    html    latex   example chm
>  twsConnect                        text    html    latex   example chm
> Note: removing empty section \details
> Note: removing empty section \details
>  twsContract                       text    html    latex   example chm
>  twsOrder                          text    html    latex   example chm
> hhc: not found
> CHM compile failed: HTML Help Workshop not installed?
>  adding MD5 sums
>
> packaged installation of package 'RIB' as RIB_0.1.0.zip
> * DONE (RIB)
>
> Not clean yet, but good for testing.
>
> So, from R:
>
>> require("RIB")
> Loading required package: RIB
> Loading required package: rJava
> Loading required package: zoo
>
> Attaching package: 'zoo'
>
>
>        The following object(s) are masked from package:base :
>
>         as.Date.numeric
>
> Warning message:
> package 'rJava' was built under R version 2.7.2
>> tws <- twsConnect()
>> tws
> Object of class "twsConnect":
> clientId = 0
> host = ""
> port = 7496
> reference = jobjRef
>> tws at reference
> [1] "Java-Object<null>"
> So I have no connection...
>
>> tws <- new("twsConnect", 1, "", 7496)
> Error in initialize(value, ...) :
>  cannot use object of class "numeric" in new():  class "twsConnect"  
> does
> not extend that class
>>
>
> but if I source the file:
>> source("H:/user/R/Adrian/RIB/R/twsConnect.R")
>> tws <- twsConnect()
>> tws
> Object of class "twsConnect":
> clientId = 0
> host = ""
> port = 7496
> reference = jobjRef
>>
>> tws at reference
> [1] "Java-Object{dev.AAD_Trader at 12558d6}"
>>
> Things work as I want, I have the connection.  What does source do,  
> that I
> miss when packaging?
>
> My NAMESPACE file is:
> exportPattern("^[^\\.]")
>
> exportClasses("twsConnect", "twsContract", "twsExecutionFilter",
>              "twsOrder")
>
> exportMethods("show")
>
> My .onLoad function contains ".jpackage(pkgname)".
>
> I tried to package just the class twsConnect without the slot  
> reference,
> and things worked out fine.  I tried to say that twsConnect contains
> "jobjRef" but did not have much success.
>
>
> Thanks a lot,
> Adrian Dragulescu
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



[Rd] problem packaging S4 class that contains a slot of jobjRef class
Simon Urbanek