[Rcpp-devel] Warning: Class "C++Object" is defin ed (with package slot ‘Rcpp’) but n o metadata object fo und

[Steffen Neumann]

Hi,

the likely culprit are XCMS and/or mzR. Alejandra has a function
that creates an xcmsSet(), which in turn uses mzR for I/O.

Here is Alejandra's rISA description:
https://github.com/ISA-tools/Risa/blob/devel/DESCRIPTION

and here are xcms and mzR (u:readonly, p:readonly):
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms/DESCRIPTION
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR/DESCRIPTION

I still haven't grasped the R import/export/depends/NAMESPACE/...
universe, so I am unfortunately of no help here :-(
So I wouldn't be surprised if xcms/mzR are the culprits there.

Yours,
Steffen


On Mon, 2012-07-30 at 08:14 -0500, Dirk Eddelbuettel wrote:
> Hi Alejandra,
> 
> On 30 July 2012 at 10:50, Alejandra Gonzalez-Beltran wrote:
> | Dear Dirk,
> | 
> | Thanks for your reply.
> | 
> | Given that our package does not use Rcpp directly and after reading
> | documentation/forums without finding a solution, it had seem to me that it was
> | a generic warning and that there was no need to provide a pointer to the public
> | repository with our code. 
> | 
> | After sending my message, I resolved the warning by adding Rcpp in the
> | 'Depends' section of the DESCRIPTION file.
> 
> While I am very glad that your problem is solved, I have to say that this
> makes little sense. If your package does not use Rcpp, it would have to
> depend on it. But if you don't use Rcpp, you can't trigger the bug you
> reported.  So may another package [ if you use one ] may be buggy and not
> depend on Rcpp.  Impossible to say though from your incomplete report.
> 
> Dirk
> 
> | 
> | Kind regards,
> | 
> | Alejandra
> | 
> | On 24 July 2012 14:48, Dirk Eddelbuettel <edd at debian.org> wrote:
> | 
> | 
> |     Hi Alejandra.
> | 
> |     On 24 July 2012 at 14:11, Alejandra Gonzalez-Beltran wrote:
> |     | Hi,
> |     |
> |     | When running R CMD INSTALL over our R package, I get the following
> |     warning:
> |     |
> |     | Warning: Class "C++Object" is defined (with package slot ‘Rcpp’) but
> |     no
> |     | metadata object found to revise subclass information---not exported?
> |      Making a
> |     | copy in package ‘.GlobalEnv’
> |     |
> |     | (full output below)
> |     |
> |     | I am not importing Rcpp directly.
> |     |
> |     | Could you please provide any pointers on how to fix this warning?
> | 
> |     No. And you need to understand why: without a reproducible example there is
> |     NOTHING we can do here but point you to
> | 
> |        the Rcpp-package vignette
> | 
> |        the Rcpp.package.skeleton() function and its help
> | 
> |        the sources of 73 existing CRAN packages using Rcpp
> | 
> |     to see how working packages are laid out.
> | 
> |     Regards,  Dirk
> | 
> |     | The output of sessionInfo() is included below.
> |     |
> |     | Thanks,
> |     |
> |     | Alejandra
> |     |
> |     |
> |     | oerc-dynamic-226:R-packages agbeltran$ R CMD INSTALL ISA2R
> |     | * installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/
> |     | Resources/library’
> |     | * installing *source* package ‘ISA2R’ ...
> |     | ** R
> |     | ** inst
> |     | ** preparing package for lazy loading
> |     | Warning: Class "C++Object" is defined (with package slot ‘Rcpp’) but
> |     no
> |     | metadata object found to revise subclass information---not exported?
> |      Making a
> |     | copy in package ‘.GlobalEnv’
> |     | ** help
> |     | *** installing help indices
> |     | ** building package indices
> |     | ** installing vignettes
> |     | ** testing if installed package can be loaded
> |     | *** arch - i386
> |     | During startup - Warning message:
> |     | Class "C++Object" is defined (with package slot ‘Rcpp’) but no
> |     metadata
> |     | object found to revise subclass information---not exported?  Making a
> |     copy in
> |     | package ‘.GlobalEnv’ 
> |     | *** arch - x86_64
> |     | During startup - Warning message:
> |     | Class "C++Object" is defined (with package slot ‘Rcpp’) but no
> |     metadata
> |     | object found to revise subclass information---not exported?  Making a
> |     copy in
> |     | package ‘.GlobalEnv’ 
> |     |
> |     | * DONE (ISA2R)
> |     |
> |     |
> |     | > sessionInfo()
> |     | R version 2.15.1 (2012-06-22)
> |     | Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> |     |
> |     | locale:
> |     | [1] C/en_US.UTF-8/C/C/C/C
> |     |
> |     | attached base packages:
> |     | [1] stats     graphics  grDevices utils     datasets  methods  
> |     base  
> |     |   
> |     |
> |     | other attached packages:
> |     | [1] ISA2R_1.0.7        Biobase_2.17.6     BiocGenerics_0.3.0
> |     |
> |     | loaded via a namespace (and not attached):
> |     | [1] Rcpp_0.9.13     codetools_0.2-8 mzR_1.3.8       tools_2.15.1  
> |     |  xcms_1.33.13   
> |     |
> |     | ----------------------------------------------------------------------
> |     | _______________________________________________
> |     | 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
> |     --
> |     Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
> | 
> | 
> | 
> | 
> 

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
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