[BioC] biocLite, ask=FALSE bug

[Dan Tenenbaum]

On Thu, Dec 1, 2011 at 2:35 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Thu, Dec 1, 2011 at 2:32 PM, James W. MacDonald
> <jmacdon at med.umich.edu> wrote:
>> There used to be the canonical update method:
>>
>> biocLite("Biobase")
>> library(Biobase)
>> z <- biocReposList()
>> update.packages(repos = z, ask = FALSE)
>>
>> Which is the only context in which I remember biocLite() and ask = FALSE
>> being used in close enough proximity that one might 'misremember' (to quote
>> our esteemed ex-president) using biocLite() with that argument.
>>
>
> BTW, there's still a way to do that, as documented here:
>
> http://bioconductor.org/install/#update-bioconductor-packages

Actually, the more up-to-date and concise way to do it is:

biocLite(character(), ask=FALSE)

Dan


>
> Dan
>
>
>> Best,
>>
>> Jim
>>
>>
>>
>>
>> On 12/1/2011 3:14 PM, Dan Tenenbaum wrote:
>>>
>>> Hi Kasper,
>>>
>>> On Thu, Dec 1, 2011 at 11:41 AM, Kasper Daniel Hansen
>>> <kasperdanielhansen at gmail.com>  wrote:
>>>>
>>>> I just used biocLite in R-2.13 (.2 patched) with ask=FALSE and got an
>>>> error:
>>>>
>>>> Using R version 2.13.2, biocinstall version 2.8.4.
>>>> Installing Bioconductor version 2.8 packages:
>>>> [1] "fdrtool"
>>>> Please wait...
>>>>
>>>> Error in download.file(url, destfile, method, mode = "wb", ...) :
>>>>  unused argument(s) (ask = FALSE)
>>>> Warning in download.packages(pkgs, destdir = tmpd, available = available,
>>>>  :
>>>>  download of package 'fdrtool' failed
>>>>
>>>> Seems like the ... argument is passed to download.file.  Not sure if
>>>> this is a "bug" but biocLite used to accept ask=FALSE.
>>>
>>> Are you sure? I looked in older versions, and it doesn't seem like we
>>> ever has an "ask" argument. Incidentally, install.packages() doesn't
>>> either, and it passes its ... to download.file() which also doesn't
>>> have an "ask" argument.
>>>
>>>> Btw, it works
>>>> in 2.14, so it might not be worth fixing.
>>>>
>>> Dan
>>>
>>>
>>>> Kasper
>>>>
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>>>
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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
>>
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