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

[Richard M. Heiberger]

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.

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 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.

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.

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
>>>>
>>>
>