[BioC] Biocinstall

[James W. MacDonald]

On 8/24/2011 12:38 PM, Dan Tenenbaum wrote:
> On Wed, Aug 24, 2011 at 6:42 AM, Vincent Carey
> <stvjc at channing.harvard.edu>  wrote:
>> set ask=F in the call?  an exclude pattern might be nice to have.
>
> Yes, setting ask=FALSE will not prompt at all.
>
> The y/n/c prompt comes from R's update.packages(), so we can't change it.

Right. But that isn't what I asked.

To me the issue is that new functionality has been added to biocLite(), 
where the default is to update packages. This is good, and is something 
that some people have been asking about for years (Hi HB).

However, the default is to just dump people into update.packages() with 
ask = TRUE. Which is fair enough. Some people would be off-put by having 
things updated against their wishes. So I see the point of setting ask = 
TRUE as the default.

However, to me it is simpler to just tell people that there are some 
packages that can be updated and ask them how they want to handle the 
situation. Please see the attached patch. If you want, I can just 
increment the version and commit.

Best,

Jim





>
> Dan
>
>>
>> On Wed, Aug 24, 2011 at 9:26 AM, James W. MacDonald
>> <jmacdon at med.umich.edu>wrote:
>>
>>> Hi,
>>>
>>> I like the new version of biocLite() where it asks if I want to update
>>> outdated package versions. However, if I have say 30 outdated packages,
>>> hitting 'y' 30 times is going to get annoying.
>>>
>>> Can it be changed to something like
>>>
>>> Available updates for 'affy' 'AnnotationDbi' 'Biostrings' etc
>>> Update all (y/N/c hit 'N' to choose by package)?
>>>
>>> And hitting N then sends the end user into the existing process?
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> Douglas Lab
>>> University of Michigan
>>> Department of Human Genetics
>>> 5912 Buhl
>>> 1241 E. Catherine St.
>>> Ann Arbor MI 48109-5618
>>> 734-615-7826
>>> ************************************************************
>>> Electronic Mail is not secure, may not be read every day, and should not be
>>> used for urgent or sensitive issues
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 
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