From hp@ge@ @end|ng |rom |redhutch@org  Thu Apr 25 21:23:52 2019
From: hp@ge@ @end|ng |rom |redhutch@org (Pages, Herve)
Date: Thu, 25 Apr 2019 19:23:52 +0000
Subject: [Rd] update.package() asking even when asked to not ask
In-Reply-To: <3ebf1285-7ec5-c4b8-8a9d-7cd4fc614494@gmail.com>
References: <e1326c65-dedd-e4e6-d625-6f81931b5e84@fredhutch.org>
 <3ebf1285-7ec5-c4b8-8a9d-7cd4fc614494@gmail.com>
Message-ID: <d5e29a2f-72dc-cadb-53b4-ce50d8286d49@fredhutch.org>

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
>>
>
-- 
Herv? Pag?s

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 at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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