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

Richard M. Heiberger rmh at temple.edu
Mon May 25 20:28:57 CEST 2015 

I posted three files to
http://astro.temple.edu/~rmh/HH-test/

HH_3.1-17.tar.gz  ## my development version of HH.

00check-HH-R-3.1.2.log ## it passes R-3.1.2 cleanly

00check-HH-r68399.log ## many messages that I don't understand.  Some
of them I believe are
reflections of the packages I depend or import or suggest.

Thanks
Rich


On Mon, May 25, 2015 at 1:30 PM, Uwe Ligges
<ligges at statistik.tu-dortmund.de> wrote:
>
>
> On 25.05.2015 19:28, Richard M. Heiberger wrote:
>>
>> I will send it.  what is the best way?  direct to you? posting it on my
>> website?
>
>
> Website so others can look at it as well?
>
> Best,
> Uwe
>
>
>>
>> On Mon, May 25, 2015 at 1:21 PM, Uwe Ligges
>> <ligges at statistik.tu-dortmund.de> wrote:
>>>
>>>
>>>
>>> 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
>>>>>>>>
>>>>>>>
>>>>>
>>>
>

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