[GenABEL-dev] Fwd: Problems in NAMESPACE files

[Yurii S. Aulchenko]

something to check with latest version of R-devel...

Begin forwarded message:

> From: Duncan Murdoch <murdoch.duncan at gmail.com>
> Date: November 29, 2010 1:44:18 AM GMT+01:00
> Subject: Problems in NAMESPACE files
>
> To various maintainers of CRAN and Bioconductor packages:
>
> Yesterday a bug in R NAMESPACE processing was discovered that  
> affects one of your packages.  (The full list of packages that are  
> known to be affected is shown below.)  The bug was that typos in  
> NAMESPACE files were not reported; those lines were just ignored.   
> As a package writer, you would not have been told that one or more  
> of the lines in your package NAMESPACE was ignored, you would just  
> see strange behaviour.
>
> As of today, the patched version of R 2.12.0 will give a warning  
> when it detects one of these errors, and R-devel (to become R 2.13.0  
> next spring) treats them as errors.  They are generally easy to  
> fix:  just find the error, and correct your NAMESPACE file to follow  
> the instructions in the Writing R Extensions manual.
>
> Most of the errors are simple typos in the spelling of directives.   
> For example, since R is case-sensitive, small differences (e.g.  
> "S3Method") will not be recognized.  Here is the list of correctly  
> spelled directives that will be recognized in a NAMESPACE file:
>
> "export"             "exportPattern"      "exportClassPattern"
> "exportClass"        "exportClasses"      "exportMethods"
> "import"             "importFrom"         "importClassFrom"
> "importClassesFrom"  "importMethodsFrom"  "useDynLib"
> "S3method"
>
> A few other directives that look like R code will be recognized  
> (e.g. conditional directives using "if"), but general R code is not  
> allowed in the NAMESPACE file.
>
> Brian Ripley ran checks today, and here is the list of packages that  
> he detected to have problems:
>
> CRAN:
> BLCOP, Cprob, EMC, EMCC, EffectiveDose, EquiNorm, FD, FGN, FitAR,
> FitARMA, G1DBN, GenABEL, IDPmisc, ISA, MSBVAR, MuMIn, PermuteNGS,
> RSeqMeth, SDMTools, SGP, SLC, SMC, VIM, bestglm, clValid,
> compositions, denstrip, distributions, extremevalues, formula.tools,
> gWidgetsWWW, ghyp, intamapInteractive, lordif, ltsa, metacor, muscor,
> mvtBinaryEP, obsSens, orth, orthogonalsplinebasis, pARcc,
> qualityTools, robCompositions, rwm, scout, sdcMicro, sdcTable,
> sigma2tools, simecol, sp, tensorA, tradeCost, trio
>
> BioC:
> GGtools, GLAD, LVSmiRNA, MassArray, RMAPPER, biocDatasets, dualKS,
> edgeR, geneRecommender, limma, mBPCR, marray, timecourse
>
> If you have any questions about how to fix your NAMESPACE file, I'd  
> be happy to help.
>
> Duncan Murdoch

-----------------------------------------------------------
Yurii Aulchenko
Erasmus MC Rotterdam
Department of Epidemiology, Ee 2200
Postbus 2040, 3000 CA Rotterdam
The Netherlands

phone: +31107043486
fax: +31107044657