From Rainer at krugs.de  Thu Oct  3 12:22:57 2013
From: Rainer at krugs.de (Rainer M Krug)
Date: Thu, 3 Oct 2013 12:22:57 +0200
Subject: [Rd] check warning  with .onLoad() and setClass()
Message-ID: <m2zjqqfybi.fsf@krugs.de>

Hi

I am writing a package in which I define a new class in the .onLoad()
hook:

,----
| .onLoad <- function(libname, pkgname) {
|     setClass(
|         "inDrak",
|         representation(
|             init = "SpatialGridDataFrame"
|             ),
|         contains = "simObj"
|         )
| }
`----

The class "simObj" is defined in the package, which is in the depends
section in the DESCRIPTION file:

,----
| Package: InDrak
| Type: Package
| Title: Alien spread management simulation model for the Drakensberg
| Version: 0.1-0
| Date: 2013-10-03_11-55
| Author: Rainer M. Krug
| Maintainer: Rainer M Krug <Rainer at krugs.de>
| Description: Simulate the spread of three Invasive Alien Plants under different
|     management and budget scenarios
| License: GPL-3
| LazyLoad: yes
| Depends:
|     RSQLite,
|     simecol
| Imports:
|     methods,
|     sp,
|     spgrass6,
|     DBI,
|     logger,
|     fireSim,
|     seedProd,
|     seedGerm,
|     seedDisp
| LinkingTo: Rcpp
| Collate:
|     'beginYear.R'
|     'clearAliens.R'
|     'competition.R'
|     'cumulativeDc.R'
|     'dcToIndLayer.R'
|     'dispProb2D.R'
|     'endYear.R'
|     'fireAliens.R'
|     'germEst.R'
|     'initfunc.R'
|     'layerIO.R'
|     'layerNames.R'
|     'main.R'
|     'newInDrak.R'
|     'onLoad.R'
|     'package.R'
|     'parameter.R'
|     'parmsAcacia.R'
|     'parmsBudget.R'
|     'parmsFire.R'
|     'parmsPinus.R'
|     'parmsRubus.R'
|     'resetOptions.R'
|     'seedDispersal.R'
|     'seedProduction.R'
|     'stats.R'
`----

If important, the NAMESPACE file is here:

,----
| export(depRateName)
| export(exportRaster)
| export(fireLayerName)
| export(ignitionRiskName)
| export(importAliens)
| export(importClearingHistory)
| export(importFireHistory)
| export(importIgnitionRisk)
| export(importSpecies)
| export(importVegetation)
| export(layerExists)
| export(layerName)
| export(newInDrak)
| export(parameter)
| export(parmsAcacia)
| export(parmsBudget)
| export(parmsFire)
| export(parmsPinus)
| export(parmsRubus)
| export(resetOptions)
| export(statDistName)
| export(suitName)
| import(DBI)
| import(fireSim)
| import(logger)
| import(methods)
| import(seedDisp)
| import(seedGerm)
| import(seedProd)
| import(sp)
| import(spgrass6)
`----

The package builds fine, it installs without problems and works as
expected, but when checking it, I get the following error:

,----
| $ R CMD check ./InDrak_0.1-0.tar.gz 
| * using log directory ?/Users/rainerkrug/Documents/Projects/R-Packages/inDrak/InDrak.Rcheck?
| * using R version 3.0.1 (2013-05-16)
| * using platform: x86_64-apple-darwin10.8.0 (64-bit)
| * using session charset: UTF-8
| * checking for file ?InDrak/DESCRIPTION? ... OK
| * checking extension type ... Package
| * this is package ?InDrak? version ?0.1-0?
| * checking package namespace information ... OK
| * checking package dependencies ... OK
| * checking if this is a source package ... OK
| * checking if there is a namespace ... OK
| * checking for executable files ... OK
| * checking for hidden files and directories ... OK
| * checking for portable file names ... OK
| * checking for sufficient/correct file permissions ... OK
| * checking whether package ?InDrak? can be installed ... OK
| * checking installed package size ... OK
| * checking package directory ... OK
| * checking DESCRIPTION meta-information ... OK
| * checking top-level files ... OK
| * checking for left-over files ... OK
| * checking index information ... OK
| * checking package subdirectories ... OK
| * checking R files for non-ASCII characters ... OK
| * checking R files for syntax errors ... OK
| * checking whether the package can be loaded ... OK
| * checking whether the package can be loaded with stated dependencies ... OK
| * checking whether the package can be unloaded cleanly ... OK
| * checking whether the namespace can be loaded with stated dependencies ... WARNING
| Error: .onLoad failed in loadNamespace() for ?InDrak?, details:
|   call: reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, 
|   error: no definition was found for superclass ?simObj? in the specification of class ?inDrak?
| Execution halted
| 
| A namespace must be able to be loaded with just the base namespace
| loaded: otherwise if the namespace gets loaded by a saved object, the
| session will be unable to start.
| 
| Probably some imports need to be declared in the NAMESPACE file.
| * checking whether the namespace can be unloaded cleanly ... WARNING
| Error: .onLoad failed in loadNamespace() for ?InDrak?, details:
|   call: reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, 
|   error: no definition was found for superclass ?simObj? in the specification of class ?inDrak?
| Execution halted
| * checking loading without being on the library search path ... OK
| * checking for unstated dependencies in R code ... OK
| * checking S3 generic/method consistency ... OK
| * checking replacement functions ... OK
| * checking foreign function calls ... OK
| * checking R code for possible problems ... NOTE
| .initfunc: no visible global function definition for
|   ?initialSeedProductionAliens?
| .initfunc: no visible global function definition for ?endYear?
| .main: no visible global function definition for ?beginYear?
| .main: no visible global function definition for ?fireAliens?
| .main: no visible global function definition for ?seedProductionAliens?
| .main: no visible global function definition for ?seedDispersalAliens?
| .main: no visible global function definition for ?germEstAliens?
| .main: no visible global function definition for ?endYear?
| * checking Rd files ... OK
| * checking Rd metadata ... OK
| * checking Rd cross-references ... OK
| * checking for missing documentation entries ... OK
| * checking for code/documentation mismatches ... OK
| * checking Rd \usage sections ... OK
| * checking Rd contents ... OK
| * checking for unstated dependencies in examples ... OK
| * checking examples ... NONE
| * checking PDF version of manual ... OK
| 
| WARNING: There were 2 warnings.
| NOTE: There was 1 note.
| See
|   ?/Users/rainerkrug/Documents/Projects/R-Packages/inDrak/InDrak.Rcheck/00check.log?
| for details.
`----

I am sure I am missing something simple here and I really think I
overlooked it in the "Writing R extensions"...

Thanks,

Rainer

-- 
Rainer M. Krug

email: RMKrug<at>gmail<dot>com
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 486 bytes
Desc: not available
URL: <https://stat.ethz.ch/pipermail/r-devel/attachments/20131003/18e7ac4e/attachment.bin>


[Rd] check warning with .onLoad() and setClass()
Rainer M Krug