[Bioc-devel] BioC 2.5: "suspect" interpackage links

[cwon2 at fhcrc.org]

Hi, all,

As I have been fixing the missing links warnings for many packages in  
my spare time, I use the getRd function, listed below, to track the  
name of the Rd file in which as alias is documented. I only tested it  
on linux. Changes might be needed if used on other OS.

> getRd("pData")
     pakcages        Rd.file
1    Biobase      phenoData
2 simpleaffy PairComp-class

> getRd("ExpressionSet", "Biobase")
   pakcages             Rd.file
1  Biobase class.ExpressionSet



1) just simply do
index.search("ExpressionSet", file.path(.libPaths(), "Biobase")

2)
getRd <- function(alias, packages=NULL)
{
    ## example 1: getRd("ExpressionSet", "Biobase")
    ## example 2: getRd("pData")

    if (missing(alias)) stop("alias must be given")

    alias <- as.character(alias)
    lib.loc <- .libPaths()

    if (is.null(packages))
        packages <- .packages(all.available = TRUE, lib.loc = lib.loc)

    paths <- sapply(.find.package(packages, lib.loc),
                   function(p) index.search(alias, p, "AnIndex"))
    paths <- paths[paths != ""]

    return(data.frame(pakcages=basename(names(paths)),  
Rd.file=basename(paths)))
}

name of the Rd file in which an alias is
> documented is too private.
>>
>> I understand that I could fix the problem with   
>> \link[pkg:rdfilename]{bar}, but I believe that the specific naming   
>> of files in a developer's package directory is up to them.  I think  
>>  it is unreasonable to be expected to keep track of what everyone   
>> else chooses to name their files, considering that the file name is  
>>  completely arbitrary and doesn't have to bear any relation to the   
>> function name or help alias.  I'd prefer to remove the links than   
>> have to do that.
>>
>> Should I remove all links of this sort from my Bioconductor packages, or
>> wait for a better resolution?
>
> An excellent question.
>
> First, the links have always been broken, it is only now that they are
> being flagged as such.
>
> Second, the 'Suspect' links work in HTML, but not in other
> documentation forms, in particular PDF I think, so they are still
> broken for some users.
>
> Third, I really agree that the name of the Rd file in which an alias is
> documented is too private.
>
> I don't know what the likelihood of further change is in this, but will
> try to find out.
>
> My own strategy has been to update links as required to avoid the
> warning and to provide useful documentation, this has not proven too
> onerous. My recommendation would be to fix if that is your cup of tea,
> but to hold off on removing the links -- this sounds like it should
> really be a last resort.
>
> Martin
>
>> Regards
>> Gordon
>>
>> ---------- original message ----------------
>> [Bioc-devel] BioC 2.5: Broken interpackage man page links
>> Seth Falcon seth at userprimary.net
>> Fri Sep 4 20:46:56 CEST 2009
>>
>> * On 2009-09-04 at 09:37 -0700 Patrick Aboyoun wrote:
>>
>>> R-devel has recently begun surfacing long-time broken man   
>>> interpackage man page links such as \link[base]{mget} (corrected   
>>> link: \link[base:get]{mget} since mget is described in base's   
>>> get.Rd file). Up until this point, broken interpackage man page   
>>> links were not discovered through R CMD check. Now these broken   
>>> links are assigned WARNINGs.
>>
>> There is some discussion in the r-core group about this warning and
>> the behavior of \link[foo]{bar}.  The discussion has not concluded,
>> but there is a reasonable chance that the behavior of \link will at
>> least be enhanced to support the commonly used form of
>> \link[package]{topic} (rather than {filename} and that the warning
>> will not appear for these cases.
>>
>> + seth
>>
>
>
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
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