Homebrew [was: from Mac to LInux?]

On 3/04/2020, at 10:01 PM, Rainer M Krug <Rainer at krugs.de> wrote:

Thanks a lot for your detailed response - it is very much appreciated.

On 2 Apr 2020, at 22:30, Simon Urbanek <simon.urbanek at r-project.org> wrote:

On 2/04/2020, at 9:15 PM, Patrick Schratz <patrick.schratz at gmail.com> wrote:

AFAIK most people on that list would vote hard against installing R via homebrew for several reasons - maybe there should be a section about this on the R dev / CRAN page to address this topic, @Simon? Otherwise this will come up again and again.

That main objection is that people are mixing Homebrew with CRAN and vice-versa which leads to many problems. You cannot use packages from CRAN when using Homebrew, period, and you have to be really careful if you want to mix Homebrew libraries (not anything R-related) with CRAN (it is doable if you know what you're doing).

This is definitely true (and I assume, you are referring to CRAN binary packages).

But I am wondering: I am always installing from the normal CRAN mirrors, and my R installation (homebrew) always installs from source. I never use `type = ?source?`in the installation for packages. 

My question: when would I install incompatible packages (I assume, you mean binary packages for Mac) from CRAN?

The fundamental issue is that package managers like Homebrew replace system libraries with their own (for new features/updates that the system libraries don't provide) which break anything that relies on the system library. Out of all the package managers Homebrew the only one that is trying to address the issue by trying to separate them, but even that has been diverging over time.

The second issue is that they are increasingly replacing toolchains (compilers) with their own builds, which makes everything incompatible in explosive ways (things just segfault). Making sure that a compiler toolchain is stable is actually non-trivial and many packager manager authors/maintainers have little experience with this. That used the be the primary reason to avoid them, because it was just normal that the released binaries were miscompiled and things would break all the time. Fortunately, I think that has gotten better over time.

If you stick only with Homebrew, then you're likely ok, but you're on your own and have to compile all packages form sources.

This is true, but I did not encounter big problems. And this is, why I thought loud in suggesting to setup a (non official!) homebrew tap to install the packages, similar to how it is in linux (Debian).

Majority of our time as CRAN maintainers for the binary releases is about providing dependent libraries for packages and making sure things "just work?.

And I think everybody really appreciates this and is VErY happy about it. This is essential work!

It is doable, just a lot of work, so by using Homebrew every user has to spend that time.

Doable: definitely. lot of work: in my experience not that much more.

Overall, I definitely agree, that the official distribution should stay the proper apple way. But there are circumstances, where these are delayed, or problems occur after macOS upgrades, which will delay the compilation of new ones (GRASS did not have Mac binaries for a long time due to this problem). 

So an alternative way of installing, community supported but approved, would be preferable. The r formula for homebrew has been installed in the last year more that 112.000 times (https://formulae.brew.sh/formula/r) so I think there is likely a rather large user base of R from homebrew. 

A first step in this direction, would be to either include homebrew in this list, or create a new R-sig-hoebrew list, which could become the home of these discussions.

(FWIW I use Hombrew myself for tools, but not in /usr/local (I'm using /opt/brew) and I only put it on the PATH for the tools that I need, never to compile anything "native" against it.)

Than you are completely in the cold and without support from homebrew? As far as I heard, in this case, everything is locally compiled and not using the binaries - correct?

Cheers, and thanks again for your very useful clarifications,

Rainer

Cheers,
Simon

Anyhow, this is also not relating to the initial topic of that thread and should probably discussed separately.
On 2. Apr 2020, 10:04 +0200, Rainer M Krug <Rainer at krugs.de>, 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

On 2 Apr 2020, at 02:37, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

On 01/04/2020 2:48 p.m., Carl Witthoft wrote:

If I should ask over at r-sig-debian instead of here, please tell me.
I don't wish to clog r-sig-mac with off-topic stuff.
I've been watching the massive headaches people are dealing with trying
to keep R fully compatible with each MacOS X upgrade, I'm wondering
whether replacing my iMac (2009) with a new Mac really makes sense from
an R - user point of view, as opposed to getting some inexpensive
desktop and installing Linux. I know I can run R and RStudio under
Linux, for example, but don't know what limitations, if any there are
when it comes to building packages from source, getting compatible
compilers, and so on.
What have some of you 'power R users' discovered when/if you tried to
build , or incorporate Bioconductor or other repository's packages under
Linux?

If your iMac is still working, try installing Ubuntu or some other Linux on it. I think at that age Apple is no longer providing upgrades, but I just put Ubuntu on a 2008 iMac, and it works well. (I needed to upgrade the memory, but that just cost $40 for 4 GB.)

So I got a $40 desktop, with a nice screen.

Duncan Murdoch

--
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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
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Office: +41 (0)44 635 47 64
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email: Rainer.Krug at uzh.ch
Rainer at krugs.de
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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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland

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

PGP: 0x0F52F982




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