[R-SIG-Mac] Homebrew

[Hervé Pagès]

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 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://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
>>>
>>
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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
> Office Y34-J-74
> Winterthurerstrasse 190
> 8075 Zürich
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> 
> Office:	+41 (0)44 635 47 64
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> 		Rainer using krugs.de
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> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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