Re: [R-SIG-Mac] Graphics in R, version 4.3.2, does not work well in MacOS

[Daniel Kelley]

For what it's worth, I also see the bug in the trial Sonoma identified as

macOS Version 14.4 Beta (23E5205c)

which was updated today.  I'm not sure how many beta versions they have 
released, but so far none has led to a fix.  My guess is that they are aware of 
the problem and working on it, because I've seen what seem to be similar 
problems with text (in the mail application for example) but they have lessened 
in the last two or so beta versions.

As others have noted, resizing fixes things.  I tend to just use x11() though, 
because it's also nice and fast for images and I use them a fair bit.

Many thanks to all of those who have worked so hard on R over the years.  It's 
a very pleasant system, and community.

Dan.

> On Feb 21, 2024, at 5:57 PM, Simon Urbanek  
> wrote:
> 
> CAUTION: The Sender of this email is not from within Dalhousie.
> 
> I can confirm that this is a bug specific to macOS Sonoma 14.3.1, even 
> earlier versions of Sonoma don't have that problem. Given the number of 
> previous bugs in Sonoma chances are Apple may fix in the in the next release, 
> but I'll see if we can do anything about it on our end in the meantime.
> 
> Cheers,
> Simon
> 
> 
>> On 19/02/2024, at 5:56 AM, María de los Ángeles Casares de Cal via R-SIG-Mac 
>>  wrote:
>> 
>> Thank you very much for your information, Michael.
>> 
>> I had not realize that by changing the size of the window where all the 
>> plots should be, everything appears.
>> The same thing happens to me too.
>> 
>> Regards,
>> Ángeles
>> 
>> 
>> sessionInfo()
>> R version 4.3.2 (2023-10-31)
>> Platform: aarch64-apple-darwin20 (64-bit)
>> Running under: macOS Sonoma 14.3.1
>> 
>> Matrix products: default
>> BLAS:   
>> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;
>>   LAPACK version 3.11.0
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> time zone: Europe/Madrid
>> tzcode source: internal
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_4.3.2
>> 
>> system_profiler SPHardwareDataType | grep Model
>>Model Name: MacBook Air
>>Model Identifier: Mac14,2
>>Model Number: Z161000GJY/A
>> 
>> 
>> 
>>> El 16 feb 2024, a las 14:10, Michael Grundler  
>>> escribió:
>>> 
>>> I am also observing the same behavior as María with the 4.3.2 Patched
>>> binary from mac.r-project.org running under Sonoma 14.3.1 on an m3
>>> mac. Using the default quartz() device and running the example line by
>>> line shows a blank device. If the device window is resized, however,
>>> the expected result appears. The example runs fine using x11(). The
>>> example also runs fine on both quartz() and x11() on my old x86
>>> running under Sonoma 14.2.1.
>>> 
 sessionInfo()
>>> R version 4.3.2 Patched (2024-02-13 r85905)
>>> Platform: aarch64-apple-darwin20 (64-bit)
>>> Running under: macOS Sonoma 14.3.1
>>> 
>>> Matrix products: default
>>> BLAS:   
>>> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;
>>> LAPACK version 3.11.0
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> time zone: America/New_York
>>> tzcode source: internal
>>> 
>>> attached base packages:
>>> [1] stats graphics  grDevices utils datasets  methods   base
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] compiler_4.3.2
>>> 
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>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> 
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Re: [R-SIG-Mac] Problems with R and Big Sur

[Daniel Kelley]

I can confirm the warning message on a 2020 macbook-pro-13-inch with Big Sur.

I do not know about slowdowns, because I seldom work in R.app, and when I do, 
it’s just for a few moments at a time.  I do not see the warning when I run R 
in a terminal, in vim, or in RStudio, which makes sense because the warning 
seems to be related to the GUI that R.app is employing.

> On Dec 3, 2020, at 7:00 AM, Maria-Angeles Casares-de-Cal via R-SIG-Mac 
>  wrote:
> 
> CAUTION: The Sender of this email is not from within Dalhousie.
> 
> Thank you very much for the interest shown by everyone who has sent their 
> answers.
> 
> I think I have not explained well the issue. Now, there it goes (I hope 
> better explained!):
> 
> I have a 16-inch MacBook Pro (2019), I have installed the Big Sur 11.0.1 
> operating system, I have installed the R 4.0.3 and the R GUI 1.73.
> The R works fine, I think it is a problem with the R GUI.
> When I open a session in R, I get the following warning:
> 
> 2020-12-03 11: 34: 43.708 R [2479: 145386] Warning: Expected min height of 
> view: () to be less than or 
> equal to 30 but got a height of 32.00. This error will be logged once per 
> view in violation.
> 
> And from that moment, the management of the windows in R and the computer 
> slows down.
> Also, every time I open a new file in R (in the same session), the warning 
> appears again.
> 
> One of the messages I received on this mailing list said that it could be a 
> problem related to the TouchBar of the MacBook Pro.
> I have tested the same R and R GUI on a MacBook Air (Retina, 13-inch, 2020) 
> with Big Sur, and, indeed, that problem does not appear.
> 
> I know that in Terminal and RStudio there is no problem, but I would like to 
> solve this issue, since I prefer to work with R and the R GUI in a Mac, 
> instead of Terminal or RStudio.
> 
> Thank you very much for your attention.
> 
> Sincerely,
> María-Ángeles Casares-de-Cal
>[[alternative HTML version deleted]]
> 
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[R-SIG-Mac] R 4.0: many PCRE JIT compilation errors

[Daniel Kelley]

I am  trying to build the "oce" package, and I get many (tens of thousands) of 
warnings of form similar to

```R
Warning in gsub("\n \\.([^\n])", "\n  .\\1", gsub("\n[ \t]*\n", "\n .\n ",  :
  PCRE JIT compilation error
'no more memory'
```

I am working through the build/check/install in stages, and documenting things 
at

https://github.com/dankelley/oce/issues/1674

in case that's of any help to anyone else.  Perhaps my grep() and gsub() calls 
are poorly framed, but I've never seen this warning before, and I suspect the 
warnings (or some of them) may be coming from he "R CMD" stage itself, so my 
guess is that this is an indication of a problem with R-4.0/macos.

I wish to note my deep thanks to the team behind macos development for R.

PS. I'm glad to hear that there may be an upcoming macos equivalent to 
winbuilder, because I have had very uneven success with rhub (working one day, 
failing another, on identical code, etc).

Dan E. Kelley [he/him/his 314ppm]
Professor and Senator
Department of Oceanography
Dalhousie University
PO BOX 15000
Halifax, NS, Canada B3H 4R2
dan.kel...@dal.ca

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Re: [R-SIG-Mac] Macports installation problem

[Daniel Kelley]

This is an exact reposting from 2 weeks ago, and there have been over a dozen 
replies.

https://www.mail-archive.com/r-sig-mac@r-project.org/msg04526.html





On Oct 16, 2017, at 6:33 AM, John > 
wrote:

Hi,

  I tried to install Cairo graphics

https://www.cairographics.org/download/

  and I need to install Macports.

  I tried to install Macports on my Mac OS Sierra 10.12.6, and type "sudo
port install cairo", but it did not respond. I haven't seen any file name
or app called Macports, but one file called "port" which is located at

loca/bin/port"

  How should I do it?

  Thanks,

John
***

Last login: Sun Oct 15 02:52:49 on console
Johns-MacBook-Pro:~ john$ /opt/local/bin/port ; exit;
MacPorts 2.4.2
Entering shell mode... ("help" for help, "quit" to quit)
[Users/john] > sudo port install cairo
Error: Unrecognized action "port sudo"

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Re: [R-SIG-Mac] Macports installation problem

[Daniel Kelley]

John,

You could spin your wheels for a long time on this, because it seems that you 
lack some basic information, not related to R.  You best plan might be to drop 
consideration of R for a few weeks, to brush up on the basics. But, if just 
need to get R working for some particular one-off task, your should consider 
finding someone local you can help you in-person, in exchange for a coffee / 
beer / lunch.

Dan Kelley






On Oct 18, 2017, at 11:39 PM, David Winsemius 
> wrote:


On Oct 18, 2017, at 6:09 PM, John > 
wrote:

Thanks, David and Rainer.

Where should I type them? On RStudio command line?

curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /

Those are Unix system functions, not R or RStudio functions. Do some reading 
regarding Unix bash and the MacOS Terminal.app

--
David.


I got this after typing in RStudio command line
curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
Error: unexpected symbol in "curl -O http"


J

2017-10-18 9:54 GMT-07:00 David Winsemius 
>:

On Oct 18, 2017, at 8:40 AM, Rainer Krug 
> wrote:



On 18 Oct 2017, at 17:17, David Winsemius 
> wrote:


On Oct 17, 2017, at 11:58 PM, Rainer Krug 
> wrote:

This is related to Macports and not to R - please post your question on their 
mailing list. If it would be about errors installing R, that would be different.


I think using MacPorts might actually be the "error" that needs correction. I 
would suggest an alternate strategy. Go to http://r.research.att.com/libs/ and 
get the appropriate version of cairo, probably the most recent one.

http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz

Scroll down to the bottom of that page and an appropriate modification of the 
two lines for unpacking to the root.

curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /


The Mac version of R does not do well with either MacPorts or homebrew 
installation of required system packages because those package managers put 
them in loaction that are not recognized by the static build that is the 
default.

Using homebrew (and as far as I know Macports as well) works without major 
problems. The problem start when you mix standard installations / homebrew / 
Macports. This results in problems.

The fact that the original poster had obviously not used MacPorts (and perhaps 
did not even know what it was) suggests that the appropriate reply should be to 
discourage him from using it and offer a strategy with greater likelihood of 
success in combination with the more typical installation method for the Mac R 
fork.


So: each of the approaches has it’s own pros and cons - it is only that 
homebrew and Macports are not officially supported by the R team.

One of the cons is that both homebrew and MacPorts requires a greater knowledge 
of the Unix under-pinnings of MacOS. If a poster is asking how to install 
MacPorts, it suggests that he don't already have such skills and perhaps 
doesn't even have the motivation to acquire them. (Your earlier response 
suggested that posting in R-SIG-Mac was the wrong way to do acquire such skills 
and I agree. Appears the poster has not yet developed the habit of reading 
supporting online documentation. He certainly did not do so regarding 
R-SIG-Mac. My opinion: A person who chooses not to read or heed online 
documentation should be actively discouraged from using either MacPorts of 
homebrew.)

Best;
David.



Cheers,

Rainer



--
David.

Cheers,

Rainer


On 18 Oct 2017, at 02:36, John > 
wrote:

Hi,

I tried to install Cairo graphics

https://www.cairographics.org/download/

and I need to install Macports.

I tried to install Macports on my Mac OS Sierra 10.12.6, and type "sudo
port install cairo", but it did not respond. I haven't seen any file name
or app called Macports, but one file called "port" which is located at

loca/bin/port"

How should I do it?

Thanks,

John
***

Last login: Sun Oct 15 02:52:49 on console
Johns-MacBook-Pro:~ john$ /opt/local/bin/port ; exit;
MacPorts 2.4.2
Entering shell mode... ("help" for help, "quit" to quit)
[Users/john] > sudo port install cairo
Error: Unrecognized action "port sudo"

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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57

Re: [R-SIG-Mac] rgdal problem with wintri projection (OSX, R-3.3.0, rgdal 1.1-9)

[Daniel Kelley]

This is fantastic — thanks, Simon and Roger! Users of the ‘oce’ package (which 
uses rgdal for map-projection calculations) will be very grateful.

Dan.

Dan E. Kelley, Professor  and Graduate Coordinator
Oceanography Department, Dalhousie University
PO BOX 15000
Halifax, NS B3H 4R2
phone:(902)494-1694 fax:(…)-3877 dan.kel...@dal.ca  
http://oceanography.dal.ca/person/Kelley_Dan.html



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