[BioC] biocLite, ask=FALSE bug

[James W. MacDonald]

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.

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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-- 
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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