From hp@ge@ @end|ng |rom |redhutch@org  Sat Apr 20 22:39:32 2019
From: hp@ge@ @end|ng |rom |redhutch@org (Pages, Herve)
Date: Sat, 20 Apr 2019 20:39:32 +0000
Subject: [Rd] update.package() asking even when asked to not ask
Message-ID: <e1326c65-dedd-e4e6-d625-6f81931b5e84@fredhutch.org>

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



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