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

[Uwe Ligges]

On 25.05.2015 18:59, Richard M. Heiberger wrote:
> I am still working on your suggestions.  While doing so I found a more
> general concern.
>
> I am now trapped in incompatible circular dependencies.  I don't know
> how to resolve them.
>
> The immediate specific is that ggplot2::layer and latticeExtra::layer
> are incompatible.
>
> Due to these dependencies I don't think I have control over which one
> has precedence.

You have: import selectively from these packages using importFrom() 
directives rather than simple import(). So you only import the layer 
version you actually need in your package (if any).
Try to get rid of Depends and solve all dependenciy issues via imports, 
i.e. NAMESPACE directives, where possible.


> I depend on lattice and latticeExtra and gridExtra.
> I import Hmisc and Rcmdr
>
> Hmisc Depends:  lattice and ggplot2
> Imports: latticeExtra,  gridExtra
>
> gridExtra suggests ggplot2 and lattice
>
> Rcmdr imports abind,
>      suggests e1071, Hmisc
>
> The message I am seeing with HH (which I cannot interpret by myself)
> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
> versionCheck = vI[[j]]) :
>    there is no package called 'abind'
> seems to be a consequence of importing Rcmdr.
> Since I do have this package the message is confusing at best.  Can
> you rephrase the message?

Perhaps a bug in another package? ANyway, can you give us the HH version 
that triggers these problems?


> Perhaps by listing which specific line in which file is triggering it.
>
> I also sometime get a similar complaint about e1071 which I don't use
> at all but is suggested by Rcmdr.

If a function in e1071 that needs it is called from a function in your 
package, you may need to suggest it as well.


> I also get a complaint about TeachingDemos, which I have but don't use
> in HH.  I haven't spotted
> where that dependency is coming from.  However I see that
> TeachingDemos suggests both lattice and ggplot2.

Don't know, again, I'd need the full package in order to say more.

Best,
Uwe


> Rich
>
> On Mon, May 25, 2015 at 3:44 AM, Uwe Ligges
> <ligges at statistik.tu-dortmund.de> wrote:
>> Two ideas:
>>
>> 1. Solve the first error at first:
>>
>> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
>> vI[[j]]) :
>>    there is no package called 'abind'
>> Error: package or namespace load failed for 'HH'
>> Execution halted
>>
>> Looks like you forgot to declare abind as an Imports in your DESCRIPTION
>> file?
>>
>>
>> 2. If you still get the other problems, please make a version of your
>> package available so that someone else can check and debug this.
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>>
>>
>> On 25.05.2015 05:01, Richard M. Heiberger wrote:
>>>
>>> The problem is still there.  I am working on both Windows and Macintosh.
>>>
>>> The packages I have check clean using R-3.1.2 on Windows.
>>> They "INSTALL --build" and "build" using 3.3.0-devl on Windows and 3.2.0
>>> on Mac,
>>>
>>> I downloaded R-devel for Windows this afternoon and updated to Rtools33.
>>> I have attached two R CMD check log files with this combination
>>> * using R Under development (unstable) (2015-05-22 r68399)
>>> * using platform: i386-w64-mingw32 (32-bit)
>>>
>>>
>>> The 3.1-15 is the version currently on CRAN.
>>> It complains it can't find Hmisc.  Hmisc is installed.
>>> The built package inside the Rcheck directory loads.
>>> Package check results on CRAN don't show this warning.
>>>
>>>
>>> The 3.1-17 is the version I am working on.
>>> It complains it can't find abind.  abind is installed.
>>> It gives 6 versions of this message.
>>> Error in validObject(.Object) :
>>>     invalid class "ObjectsWithPackage" object: superclass "atomicVector"
>>> not defined in the environment of the object's class
>>> I don't understand what is triggering them.
>>> The built package inside the Rcheck directory loads.
>>>
>>> On Sat, May 23, 2015 at 9:02 AM, Uwe Ligges
>>> <ligges at statistik.tu-dortmund.de> wrote:
>>>>
>>>> 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)
>>>>>
>>>>>
>>>>>
>>>>> ______________________________________________
>>>>> R-package-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>
>>>>
>>