From tom@@@k@||ber@ @end|ng |rom gm@||@com  Thu Apr 25 16:50:53 2019
From: tom@@@k@||ber@ @end|ng |rom gm@||@com (Tomas Kalibera)
Date: Thu, 25 Apr 2019 16:50:53 +0200
Subject: [Rd] update.package() asking even when asked to not ask
In-Reply-To: <e1326c65-dedd-e4e6-d625-6f81931b5e84@fredhutch.org>
References: <e1326c65-dedd-e4e6-d625-6f81931b5e84@fredhutch.org>
Message-ID: <3ebf1285-7ec5-c4b8-8a9d-7cd4fc614494@gmail.com>

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.

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
>



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