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

Tomas Kalibera tom@@@k@||ber@ @end|ng |rom gm@||@com
Thu Apr 25 16:50:53 CEST 2019

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,
> 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
> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
> /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

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