[BioC] Rgraphviz redefines "head" function

[Herve Pages]

Hi Marco,

Thanks for reporting this! Since head/tail are already generics defined in the "utils"
package, they should not be redefined in Rgraphviz. Only methods for "AgEdge" objects
should go there.
I've just fixed this in Rgraphviz 1.14.1 (release) and Rgraphviz 1.15.5 (devel). These
new versions should become available via biocLite() in about 26 hours for the former
and 14 hours for the latter.

Cheers,
H.

marco zucchelli wrote:
> Dear all,
> 
>  seems weird but looks like Rgraphviz redefines the function head() ??
> I use fedora 5.
> 
> Regards
> 
> Marco
> 
> #########################################
>> head(gene.list)
>   chromosome_name start_position end_position entrezgene haplotype  length
> 1               1          58954        59871      79501         1 1060001
> 2               1         357522       358460      26683         1 1060001
> 3               1         357522       358460      81399         1 1060001
> 4               1         357522       358460     729759         1 1060001
> 5               1         610959       611897      26683         1 1060001
> 6               1         610959       611897      81399         1 1060001
>> library(Rgraphviz)
> Loading required package: graph
> Loading required package: geneplotter
> Loading required package: annotate
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> 
> Attaching package: 'annotate'
> 
> 
>         The following object(s) are masked from package:biomaRt :
> 
>          getGO
> 
> Loading required package: lattice
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
> 
> Attaching package: 'Rgraphviz'
> 
> 
>         The following object(s) are masked from package:annotate :
> 
>          toFile
> 
>> head(gene.list)
> Error in function (classes, fdef, mtable)  :
>         unable to find an inherited method for function "head", for
> signature "data.frame"
>> head
> standardGeneric for "head" defined from package "Rgraphviz"
> 
> function (x, ...)
> standardGeneric("head")
> <environment: 0x3189f70>
> Methods may be defined for arguments: x
> 
> 
> sessionInfo()
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "datasets"  "utils"
> [7] "methods"   "base"
> 
> other attached packages:
>          matlab       Rgraphviz     geneplotter         lattice
> annotate
>         "0.8-1"        "1.14.0"        "1.14.0"        "0.15-4"        "
> 1.14.1"
>         Biobase           graph humanLLMappings         biomaRt
> RCurl
>        "1.14.0"        "1.14.2"        "1.16.0"        "1.10.0"         "
> 0.8-0"
>             XML
>         "1.9-0"
> 
> 	[[alternative HTML version deleted]]
> 
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