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 >> > -- Hervé Pagès 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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
