Transitioning from Mac to LInux?

  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?


--
Carl Witthoft
carl at witthoft.com
resume: https://app.box.com/file/498153801347

 ?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?

On 2/04/2020, at 7:48 AM, Carl Witthoft <carl at witthoft.com> 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?


-- 
Carl Witthoft
carl at witthoft.com
resume: https://app.box.com/file/498153801347

Carl,

I would argue that you won't really gain anything - if you use R the Linux-way (build R from sources), it would be the same on macOS and Linux - and some people do that. So for R I don't think there is a difference. I'm using Linux for everything other than my desktop/laptop and the main reason I'm sticking with macOS at the edge is the availability of software for dealing with the rest of the world (MS Office, Adobe, Apple Mail etc.). If you don't need any of it, then you may be happy with Linux. The biggest issue there tends to be setting up your machine as the hardware support is far less streamlined than on macOS. Some of my friends are running Linux on Mac hardware - but you need the be real expert for that.

Cheers,
Simon

On 2/04/2020, at 7:48 AM, Carl Witthoft <carl at witthoft.com> 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?


--
Carl Witthoft
carl at witthoft.com
resume: https://app.box.com/file/498153801347

   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?

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

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
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




[[alternative HTML version deleted]]

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 10:15, 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.

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
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




[[alternative HTML version deleted]]

	[[alternative HTML version deleted]]

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://cloud.r-project.org/"
		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

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 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://cloud.r-project.org/"
		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

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?

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.

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.

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://cloud.r-project.org/"
		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

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

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




	[[alternative HTML version deleted]]

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
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
	[[alternative HTML version deleted]]

-- 
Herv? Pag?s

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 at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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.

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

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://github.com/rkrug/install

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

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.

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
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




[[alternative HTML version deleted]]

	[[alternative HTML version deleted]]

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).

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.

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

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

(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.)

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
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




[[alternative HTML version deleted]]

	[[alternative HTML version deleted]]

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
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




[[alternative HTML version deleted]]

	[[alternative HTML version deleted]]

--
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




	[[alternative HTML version deleted]]

On 3 Apr 2020, at 13:25, Simon Urbanek <simon.urbanek at r-project.org> wrote:

Rainer,

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?

Maybe you wouldn't but I have seen people do it.

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). 

I'm not sure what you refer to, but if there are issues, please let me know. If you don't report issues, they won't get fixed.

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 <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.

I'm not sure I'd like to go there. I would direct that to Homebrew as we have nothing to do with the formulae used there. However, that's not really my call.

Today another reason came up why I have an issue with Homebrew: people install compilers and similar tools and then use them instead of Xcode for everything outside of Homebrew. That is absolutely unsupported, because they have different runtime environments, so things break. Sometimes in subtle ways and things segfault at random points. The thing is, if people knew what they were doing, and Homebrew was only used by developers, it would be all fine - they'd know not to mix and match run-times. But most user don't.

(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?

No, binaries are used where it is safe. There may be a few bottles that don't like to be installed in a custom location. I have not seen issues with it.

To be honest I think putting homebrew in /usr/local was a bad mistake as that causes a lot of problems since all 3rd party software installs there, so you get very quickly to completely broken state. As with all those things, it's predicated on full control so if you don't use anything but Homebrew ever it's ok. But pretty much all native open source packages/installers install into /usr/local so the moment you use one thing in addition to Homebrew things start breaking.

Cheers,
Simon

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
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




[[alternative HTML version deleted]]

	[[alternative HTML version deleted]]

--
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




	[[alternative HTML version deleted]]