[R-SIG-Mac] Outdated links to the Bioconductor repos in R.app

[Kasper Daniel Hansen]

On May 24, 2006, at 1:21 PM, Paul Roebuck wrote:

> On Wed, 24 May 2006 Herve Pages wrote:
>
>> Quoting Simon Urbanek <simon.urbanek at r-project.org>:
>>
>>> On May 23, 2006, at 10:31 PM, Herve Pages wrote:
>>>
>>> [SNIP]
>>>
>>>> but they should be (in this order):
>>>>
>>>>    http://bioconductor.org/packages/bioc
>>>>    http://bioconductor.org/packages/data/annotation
>>>>    http://bioconductor.org/packages/data/experiment
>>>>    http://bioconductor.org/packages/omegahat
>>>>    http://bioconductor.org/packages/lindsey
>>>>    http://cran.fhcrc.org
>>>>
>>>
>>> Should CRAN be really on that list?
>>
>> Well it depends what you are trying to achieve: if you want the GUI
>> to show the user the list of Bioconductor packages only, then you
>> don't need the 3 last repos.
>> But if you also want the user to be able to install from this list  
>> and
>> then to load the newly installed stuff, then you need 2 things:
>>
>>   1) provide a set of repos that is closed for the dependency  
>> relationship
>>
>>   2) provide the user with the option to have all the dependencies
>>      installed in addition to the packages s/he selected
>>
>> Since the GUI doesn't support 2), then I agree that we don't really
>> need the 3 last repos (omegahat, lindsey and CRAN)... But I'd rather
>> keep them anyway because:
>>
>>   - Some users might want to do things like:
>>       install.packages('pkg', repos=getOption("BioC.Repos"),  
>> dep=TRUE)
>>     The only way to guarantee that this will work for _any_  
>> Bioconductor
>>     package is to have all 5 repos returned by getOption 
>> ("BioC.Repos")
>
> Forgive, but if that's the case, why can't it be specified as such:
>
> whole.enchilda.repos <- c(getOption("BioC.Repos"),
>                          "http://bioconductor.org/packages/omegahat",
>                          "http://cran.fhcrc.org")  # getOption 
> ("repos")?
> install.packages('pkg', repos = whole.enchilda.repos, depend = TRUE)
>
>>   - Things are consistent with the biocLite() function that we  
>> provide
>>     for users of _all_ platforms
>>       http://bioconductor.org/docs/install-howto.html
>
> Since the above would be an internal change to the install
> script, the above would be even less effort.
>
>> The inconvenient of this is that we end up with the GUI
>> displaying a very long list... but this is not really a
>> problem because I don't think many users actually browse
>> the entire list: they'd rather use the search box instead.
>
> I don't. There may be others as well... I'd rather BioC
> packages be kept separate from CRAN packages in the
> listing...

I second that. While I am indifferent to what goes on under the hood,  
the Gui (as it stands right now) should only list Bioconductor  
packages when selecting either "Bioconductor (sources)" or  
"Bioconductor (binaries)".

/Kasper



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