[R-SIG-Mac] Homebrew

Rainer M Krug R@|ner @end|ng |rom krug@@de
Thu Apr 2 12:43:31 CEST 2020

> On 2 Apr 2020, at 12:17, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
> On 02/04/2020 5:58 a.m., Dr Eberhard W Lisse wrote:
>> New thread :-)-O
>> I am wondering if I should not try to figure out how automate this.
>> Is there a way of (only) listing all user installed (additional)
>> packages, ie not the ones that come with R?

I had something similar in mind - here is my repo which collects ides (no code yet) https://github.com/rkrug/install

If you are interested, we could get this going.

If I understand correctly, this would be very useful in many cases.

> Look at the "Priority" column in installed.packages().  "base" is part of R, "recommended" is normally distributed with R. "recommended" packages can be updated after R is installed, "base" packages can't.

That is a good idea. We should take this forward.

> If you just copy all the packages to the new library that aren't already there, and run update.packages(checkBuilt = TRUE) R will re-install everything that was originally installed under an earlier version.



> Duncan Murdoch
>> I could then construct the below file automagically, and if I was
>> really bothered and bored find out how to make Homebrew pre/post
>> install scripts to automate this :-)-O
>> And, for the record, other than that, I can only recall one serious
>> issue, when the openblas library got lost recently which was however
>> fixed quite quickly.
>> greetings, el
>> On 02/04/2020 10:17, Dr Eberhard W Lisse wrote:
>>> I do same, including Rstudio (Cask).
>>> Once in a while after major updates I need to reinstall all my extra
>>> packages, so I have written me a little script along the lines of
>>> 	#!/usr/local/bin/Rscript
>>> 	local({
>>> 		r <- getOption("repos")
>>> 		r["CRAN"] <- "https://cloud.r-project.org/"
>>> 		options(repos = r)
>>> 	})
>>> 	install.packages(c(
>>> 		"RMariaDB", "rstudioapi"
>>> 	))
>>> made it 0755 and can run it from the command line. Put it in my
>>> handbook so I don't forget and never looked back.
>>> greetings, el
>>> On 02/04/2020 10:03 am, Rainer M Krug wrote:
>>>> I am using Homebrew on a Mac (two Macs - one at home, one at work)
>>>> instead of the official R package, and I did not have any problems
>>>> after upgrades - maybe I am lucky, maybe not as picky in defining
>>>> “problem”, but my suggestion would be to try R from homebrew to
>>>> install R.
>>>> OK - no support from here - I know.
>>>> And homebrew has also binary versions.  What is missing, is a hombrew
>>>> R package repository.  Maybe an idea to create one?
>>>> Cheers,
>>>> Rainer
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Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Orcid ID: 0000-0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
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