Marie Pierre Sylvestre wrote:
Hello R users,
I am trying to make a my first package and I get an error that I can
understand. The package is build out of three files (one for functions, 1
for s4 classes and 1 for s4 methods).
Once I source them I run
package.skeleton( name=TDC )
within a R session and I get
Creating directories ...
Creating DESCRIPTION ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './TDC/Read-and-delete-me'.
Warning messages:
1: In dump(internalObjs, file = file.path(code_dir,
sprintf(%s-internal.R, :
deparse of an S4 object will not be source()able
2: In dump(internalObjs, file = file.path(code_dir,
sprintf(%s-internal.R, :
deparse of an S4 object will not be source()able
3: In dump(internalObjs, file = file.path(code_dir,
sprintf(%s-internal.R, :
deparse of an S4 object will not be source()able
4: In dump(internalObjs, file = file.path(code_dir,
sprintf(%s-internal.R, :
deparse may be incomplete
I keep going in spite of the warnings with
R CMD check --no-examples TDC
and I get
* checking for working pdflatex ... OK
* using log directory
'/home/mariepierre/Packages/PermAlgo/PermAlgo/PermAlgo2/TDC.Rcheck'
* using R version 2.7.1 (2008-06-23)
* using session charset: UTF-8
* checking for file 'TDC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TDC' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'TDC' can be installed ... ERROR
Installation failed.
The error file says:
* Installing *source* package 'TDC' ...
** R
** preparing package for lazy loading
Error in parse(n = -1, file = file) : unexpected '' at
102: `.__C__BindArgs` -
103:
Calls: Anonymous - code2LazyLoadDB - sys.source - parse
Execution halted
ERROR: lazy loading failed for package 'TDC'
** Removing
'/home/mariepierre/Packages/PermAlgo/PermAlgo/PermAlgo2/TDC.Rcheck/TDC'
The problem is with my classes and methods. The respective files contain:
setClass(BindArgs, signature( function ))
setClass(BindArgs2, signature( function ))
and
setMethod(initialize, BindArgs, function( .Object, f, ... )
callNextMethod( .Object, function( x ) f( x, ... ) ))
setMethod(initialize, BindArgs2, function( .Object, f, ...)
callNextMethod( .Object, function( x, y ) f( x, y, ... ) ))
Everything works well within a R session but I can build the package.
If I look at the internal R file that this created I get
`.__C__BindArgs` -
S4 object of class structure(classRepresentation, package = methods)
`.__C__BindArgs2` -
S4 object of class structure(classRepresentation, package = methods)
`.__M__initialize:methods` -
S4 object of class structure(MethodsList, package = methods)
`.__T__initialize:methods` -
environment
Well, let just say that I am new to classes so this confuses me greatly. I
have checked the documentation and tried a few things but I reached my
personal limits!
I am using R 2.7.1 on Linux Fedora 8.
Any comments on what is happening and/or help would be greatly appreciated.
The main point is that you should not rely on R putting sensible code in
the package source files, but rather stay in control yourself. What the
warnings are telling you is that you cannot deparse an S4 object in a
way that can be reparsed, so dump() doesn't work. What you get is
obj - S4 object..
and the syntax error from source() if you try using it. So what you need
to is to delete it and put in the appropriate class/methods definitions
from your original sources. It might help to look at an existing
S4-using package.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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