[Rcpp-devel] Error: .onLoad failed in loadNamespace()

Laurent Gatto lg390 at cam.ac.uk
Tue May 31 21:37:41 CEST 2011 

On 31 May 2011 20:11, Romain Francois <romain at r-enthusiasts.com> wrote:
> I'm using the same versions and I don't get the problem.
>
> getClass is in methods, and Rcpp does have
>
> import(methods)
>
> in its NAMESPACE file.
>
> Maybe this means that the client package also needs it. not sure.

Yes, I am confused here...
Never mind. I will report back if I come up with helpful data, but in
the mean time, thank you for looking at it.

Best wishes,

Laurent

> Le 31/05/11 19:55, Laurent Gatto a écrit :
>>
>> Dear Romain,
>>
>> On 31 May 2011 13:34, Romain Francois<romain at r-enthusiasts.com>  wrote:
>>>
>>> Works fine for me. Laurent, can you try with the current svn version of
>>> Rcpp.
>>>
>>> svn checkout svn://svn.r-forge.r-project.org/svnroot/rcpp
>>> cd rcpp/pkg
>>> R CMD INSTALL Rcpp
>>> Rscript -e "require(Rcpp); Rcpp.package.skeleton(module=TRUE)"
>>> R CMD check anRpackage
>>
>> Warning still there, although possibly with a hint:
>>
>> * checking whether the name space can be loaded with stated
>> dependencies ... WARNING
>> Error: .onLoad failed in loadNamespace() for ‘anRpackage’, details:
>>   call: value[[3L]](cond)
>>   error: failed to load module yada from package anRpackage
>> could not find function "getClass"
>> 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.
>>
>> I also updated R-devel; session information is:
>>
>> R version 2.14.0 Under development (unstable) (2011-05-30 r56024)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>>  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>>  [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8
>>  [7] LC_PAPER=C                LC_NAME=C
>>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] methods   stats     graphics  grDevices utils     datasets  base
>>
>> other attached packages:
>> [1] Rcpp_0.9.4.2
>>
>>
>> Note that I observed this warning while working on a 'real' package.
>> In the hope to track its origin down and provide a reproducible
>> example, I realised that the warning also came up with the standard
>> Rcpp.package.skeleton output, which ended up in this thread. However,
>> to my surprise (and embarrassment), I do not have the warning in the
>> original package any more (whether with Rcpp 0.9.4.2 or 0.9.4.1). I
>> tried to revert some of the changes I did (moving Rcpp from Depends to
>> Imports for instance, removing the import(Rcpp) statement in the
>> NAMESPACE file,...) but without any success.
>>
>> Not sure I am of any help here...
>>
>> Best wishes,
>>
>> Laurent
>>
>>
>>> Romain
>>>
>>> Le 30/05/11 21:58, Romain Francois a écrit :
>>>>
>>>> Le 28/05/11 04:04, Dirk Eddelbuettel a écrit :
>>>>>
>>>>> Hi Laurent,
>>>>>
>>>>> On 27 May 2011 at 17:17, Laurent Gatto wrote:
>>>>> | Dear all,
>>>>> |
>>>>> | A basic packages with Rcpp modules produces the warning described
>>>>> | below, that I would ideally, with your help, get rid of.
>>>>> |
>>>>> | Rscript -e "require(Rcpp); Rcpp.package.skeleton(module=FALSE)"
>>>>> | R CMD check anRpackage
>>>>> |
>>>>> | produces obvious warnings related to badly formatted documentation
>>>>> and
>>>>> | license. However
>>>>> |
>>>>> | Rscript -e "require(Rcpp); Rcpp.package.skeleton(module=TRUE)"
>>>>> | R CMD check anRpackage
>>>>> |
>>>>> | produces this additional warning that puzzles me:
>>>>> |
>>>>> | [ ...checker output... ]
>>>>> | * checking whether the name space can be loaded with stated
>>>>> | dependencies ... WARNING
>>>>> | Error: .onLoad failed in loadNamespace() for ‘anRpackage’, details:
>>>>> | call: value[[3L]](cond)
>>>>> | error: failed to load module yada from package anRpackage
>>>>> | 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.
>>>>> | [ ...checker output...]
>>>>> |
>>>>> | I suspect this may be related to the yada module not being exposed
>>>>> and
>>>>> | thus not available when the package is loaded. Any further
>>>>> explanation
>>>>> | or hints would however be warmly appreciated.
>>>>>
>>>>> I think you are pretty close. As I recall, this 'warning' has been a
>>>>> bit of a
>>>>> wart that won't quite go away. I just checked again what we do in the
>>>>> unit
>>>>> tests in file runit.Module.client.package.R: we build a package (ie
>>>>> create a
>>>>> tar.gz) and then install from it. That also triggers the warning, but
>>>>> passes
>>>>> it.
>>>>>
>>>>> Romain may have more details about how this is related to module
>>>>> initialization and startup.
>>>>>
>>>>> Dirk
>>>>
>>>> I'll have a go at installing a fresher R-devel and see what the next
>>>> move is. My guess is that R checks are tighter now.
>>>>
>>>>> |
>>>>> | sessionInfo() is appended below.
>>>>> |
>>>>> | Thank you very much in advance.
>>>>> |
>>>>> | Best wishes,
>>>>> |
>>>>> | Laurent
>>>>> |
>>>>> |
>>>>> |>  sessionInfo()
>>>>> | R version 2.14.0 Under development (unstable) (2011-05-04 r55760)
>>>>> | Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>> |
>>>>> | locale:
>>>>> | [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
>>>>> | [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
>>>>> | [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
>>>>> | [7] LC_PAPER=en_GB.utf8 LC_NAME=C
>>>>> | [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>> | [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>>>>> |
>>>>> | attached base packages:
>>>>> | [1] stats graphics grDevices utils datasets methods base
>>>>> |
>>>>> | other attached packages:
>>>>> | [1] Rcpp_0.9.4.1
>>>>
>>>>
>>>
>>>
>>> --
>>> Romain Francois
>>> Professional R Enthusiast
>>> +33(0) 6 28 91 30 30
>>> http://romainfrancois.blog.free.fr
>>> http://romain-francois.com
>>> |- http://bit.ly/hdKhCy : Rcpp article in JSS
>>> |- http://bit.ly/elZJRJ : Montpellier Comedie Club - Avril 2011
>>> `- http://bit.ly/fhqbRC : Rcpp workshop in Chicago on April 28th
>>>
>>>
>>> _______________________________________________
>>> Rcpp-devel mailing list
>>> Rcpp-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>>
>>
>
>
> --
> Romain Francois
> Professional R Enthusiast
> +33(0) 6 28 91 30 30
> http://romainfrancois.blog.free.fr
> http://romain-francois.com
> |- http://bit.ly/hdKhCy : Rcpp article in JSS
> |- http://bit.ly/elZJRJ : Montpellier Comedie Club - Avril 2011
> `- http://bit.ly/fhqbRC : Rcpp workshop in Chicago on April 28th
>
>
>



-- 
Laurent Gatto
Cambridge Centre For Proteomics
http://www.bio.cam.ac.uk/proteomics

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