[R-pkg-devel] ERROR from R CMD check that I have never seen before

[Uwe Ligges]

Can you try a more recent version of R-devel with all relevant packages 
you depend on re-installed?

Looks like either a bug in that months old version of R-devel or an 
inconsistancy of installed packages and the version of the methods 
package or so.

Best,
Uwe Ligges



On 23.05.2015 05:29, Richard M. Heiberger wrote:
> followup.
>
> I backed up to R-3.1.2 and fixed the problems it found.
> Then I tried again with R-3.2.0 and I am still getting these messages
>
> Error in validObject(.Object) :
>    invalid class "ObjectsWithPackage" object: superclass "atomicVector"
> not defined in the environment of the object's class
> Calls: <Anonymous> ... metaNameUndo -> new -> initialize -> initialize
> -> validObject
> Execution halted
>
> On Fri, May 22, 2015 at 8:08 PM, Richard M. Heiberger <rmh at temple.edu> wrote:
>> I am updating the HH package and have series of messages that I don't recognize.
>>
>> bash-3.2$ R CMD check HH2
>> * using log directory '/Users/rmh/WindowsC/HOME/rmh/HH-R.package/HH2.Rcheck'
>> * using R Under development (unstable) (2015-02-12 r67812)
>> * using platform: x86_64-apple-darwin13.4.0 (64-bit)
>> * using session charset: ASCII
>> * checking for file 'HH2/DESCRIPTION' ... OK
>> * checking extension type ... Package
>> * this is package 'HH' version '3.1-17'
>> * 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 ... NOTE
>> Found the following hidden files and directories:
>>    .DS_Store
>>    inst/.DS_Store
>> These were most likely included in error. See section 'Package
>> structure' in the 'Writing R Extensions' manual.
>> * checking for portable file names ... OK
>> * checking for sufficient/correct file permissions ... OK
>> * checking whether package 'HH' 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 ... OK
>> * checking whether the namespace can be unloaded cleanly ... OK
>> * checking dependencies in R code ... NOTE
>> Error in validObject(.Object) :
>>    invalid class "ObjectsWithPackage" object: superclass "atomicVector"
>> not defined in the environment of the object's class
>> Execution halted
>>
>> I have two questions about it.
>> 1. What is it checking?  There are no words in the message that
>> indicate which of my
>> functions is being looked at.
>>
>> I am getting 6 of these.  They are all identically worded.  sometimes they are
>> NOTE ERROR WARNING
>>
>> Thanks
>> Rich
>>
>> 2. How can I run R CMD check, or its components, in a way that will stop and
>> let me investigate from the point?  I am looking for the equivalent of
>> the R option
>> option(error=recover)
>
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