[R-SIG-Mac] Homebrew

Rainer M Krug R@|ner @end|ng |rom krug@@de
Thu Apr 2 13:09:18 CEST 2020 


> On 2 Apr 2020, at 12:56, Hervé Pagès <hpages using 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.

Arguments against homebrew:

Not an official response, but in the past, homebrew was compiling everything on the local machine. This is not the case anymore, and the default installation in homebrew, installs a binary. 

All packages need to be installed from source. This takes time, but I had no problems with any of the packages I use.

Just some tidbits from previous discussions.

But I would like to also hear the official reason (no resources would be a good enough justification as well).

Arguments for homebrew: 

it is more Linux like, in the way that you have more control over the tools used. e.g. when still using the official R installation, I regularly used different versions of GDAL in R, GRASS, …, which can cause inconsistencies.

The installation is done without requiring root privileges, which is a big advantage (as I see it).



Cheers,

Rainer


> 
> 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
>> Switzerland
>> Office:	+41 (0)44 635 47 64
>> Cell:       	+41 (0)78 630 66 57
>> email:      Rainer.Krug using uzh.ch
>> 		Rainer using krugs.de
>> Skype:     RMkrug
>> PGP: 0x0F52F982
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> 
> -- 
> 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: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

--
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
Switzerland

Office:	+41 (0)44 635 47 64
Cell:       	+41 (0)78 630 66 57
email:      Rainer.Krug using uzh.ch
		Rainer using krugs.de
Skype:     RMkrug

PGP: 0x0F52F982




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