R devel - Apr 2019 - update.package() asking even when asked to not ask

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.

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

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
>

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