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 <e...@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@lists.r-forge.r-project.org > | | > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > | -- > | Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com > | > | > | > | > -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
