Homebrew

On 2 Apr 2020, at 12:56, Herv? Pag?s <hpages at fredhutch.org> wrote:

Just for a minute let's ignore the fact that installing R via Homebrew is not considered a good option by the competent authorities (which sounds like a good enough reason to stay away from it). I'm still wondering: what's the benefit vs installing the official CRAN binary? Just curious.

Thanks,
H.

On 4/2/20 03:43, Rainer M Krug wrote:

On 2 Apr 2020, at 12:17, Duncan Murdoch <murdoch.duncan at 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rkrug_install&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uDuycJflTWje5wqLzrbP7zBZojiWq6DmyxGuwakypr0&s=ZUWEqptXXn0kw7PX-ToEnYb7DtfXGUcOn5PzyQVfVG8&e=
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.

Cheers,
Rainer

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://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uDuycJflTWje5wqLzrbP7zBZojiWq6DmyxGuwakypr0&s=rnzs7MN3dX-WT08dEbSoFz0AVBgX-xNNlW9keQhr0jg&e= "
		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

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Orcid ID: 0000-0002-7490-0066
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University of Z?rich
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		Rainer at krugs.de
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-- 
Herv? Pag?s

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