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