[Rd] update.package() asking even when asked to not ask

[Pages, Herve]

On 4/25/19 07:50, Tomas Kalibera wrote:

> On 4/20/19 10:39 PM, Pages, Herve wrote:
>> Hi,
>>
>> I was trying to update packages today on one of our MacOS servers, and
>> got this:
>>
>>     > update.packages(ask=FALSE)
>>
>>       There is a binary version available but the source version is 
>> later:
>>           binary source needs_compilation
>>     gsl 1.9-10.3  2.1-6              TRUE
>>
>>     Do you want to install from sources the package which needs
>> compilation? (Yes/no/cancel)
>>
>> So it looks like 'ask=FALSE' only turns off one type of question. What
>> is not immediately obvious is that in order to also turn off the type of
>> question asked above one needs to set 'type' either to
>> "mac.binary.el-capitan" or "source" (by default 'type' is set to "both"
>> on Mac).
>>
>> Some clarification in the man page about the scope of 'ask=FALSE' would
>> be welcome, with possibly some hint about how to turn off all questions.
>
> From reading the documentation I think this behavior is intentional 
> and as documented. See "Binary packages" section in ?install.packages. 
> In particular there is option "install.packages.compile.from.source". 
> ?update.packages points to this option via "See Also:" 
> ‘install.packages’, "The options listed for ‘install.packages’ under 
> ‘options’.". The documentation for "ask" does not seem to suggest that 
> this would control all options asked by update.packages(), but I've 
> added a sentence to make that explicit.

Thanks Tomas. This small addition to the description of the 'ask' 
argument helps a lot and the pointer to 
'install.packages.compile.from.source' is very useful.

Cheers,

H.


>
> Best
> Tomas
>
>
>> Thanks,
>>
>> H.
>>
>>   > sessionInfo()
>> R version 3.6.0 beta (2019-04-16 r76403)
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> Running under: OS X El Capitan 10.11.6
>>
>> Matrix products: default
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib 
>>
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib 
>>
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.0 tools_3.6.0
>>
>
-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
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