[BioC] biocLite, ask=FALSE bug

[Dan Tenenbaum]

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

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
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