[BioC] Using htmlpage

[James W. MacDonald]

Hi John,

john seers (IFR) wrote:
> Hello Bioconductor people
> 
> I am trying to use htmlpage (from the annotate package) so it can
> generate html links in addition to the types of links already provided. 
> 
>>From the documentation of htmlpage it says:
> 
> "Additional repositories can easily be added. See getQueryLink for more
> information."

Easily is in the eye of the beholder. It is actually quite easy, but you 
will need to add the functions to the source package and then 
build/install. As you have noted, the namespace prevents you from easily 
  modifying the package by dumping new functions in the workspace.

What repository are you trying to add? It might be easiest to just add 
the repository to the package itself, if it is something that others 
might want to use.

Best,

Jim


> 
> But it does not seem as straightforward as I hoped. Trying to modify the
> scripts hits difficulties with namespaces and local names. Can anyone
> tell me if there is a simpler way? 
> 
> I defined my own copy of getQueryLink but htmlpage still called the
> namespace version. This I could change using:
> 
> assignInNamespace("getQueryLink", getQueryLink, ns="annotate")
> 
> But then it did not work because getQueryLink could not see the original
> internal scripts such as getQuery4Affy. So I modified the script again
> to remove all the repositories I did not need. But I still needed the
> getQuery4Affy helper script so I had to redefine that and use
> assignInNamespace again.  
> 
> This seems too complicated. Have I missed an easier way? Any
> suggestions? 
> 
> 
> 
> 
> Regards
> 
> 
> John
> 
> 
> 
> ########################################################################
> ################################
> 
> 
>> sessionInfo()
> R version 2.8.1 (2008-12-22) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices datasets  utils     methods
> 
> [8] base     
> 
> other attached packages:
> [1] annotate_1.20.1     xtable_1.5-4        AnnotationDbi_1.4.2
> [4] Biobase_2.2.1       RWinEdt_1.8-0      
> 
> loaded via a namespace (and not attached):
> [1] DBI_0.2-4     RSQLite_0.7-1
> 
> 
> 
> 
> ---
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662