[BioC] Biocinstall

[Dan Tenenbaum]

Hi Jim,


On Wed, Aug 24, 2011 at 11:16 AM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
>
>
> 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.

I added a modified version of your patch. If ask==TRUE, your prompting
code is run, otherwise the value of ask is passed unchanged to
update.packages().

Also added some code to avoid calling readLines() from a
non-interactive session and in that case to behave as though the user
pressed "n", as update.packages() does.

This will auto-install starting tomorrow shortly after noon Seattle time.

Thanks for the suggestion.

Dan



>
> 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 outdated package versions. However, if I have say 30 outdated packages,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
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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