> On 2 Apr 2020, at 12:56, Hervé Pagès <hpa...@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.dun...@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.k...@uzh.ch
>> rai...@krugs.de
>> Skype: RMkrug
>> PGP: 0x0F52F982
>> [[alternative HTML version deleted]]
>> _______________________________________________
>> R-SIG-Mac mailing list
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>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uDuycJflTWje5wqLzrbP7zBZojiWq6DmyxGuwakypr0&s=-Kazp7RDPhXbnKvMu3vyOfRSE7ZQBHDCH9Vy6MeGssA&e=
>
> --
> 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
--
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.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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