Re: [R-SIG-Mac] R installation issue
Sorry about that. I’m still on 12.6.2. > On 28 Jan 2023, at 10:38 pm, Prof Brian Ripley wrote: > > On 27/01/2023 22:48, Peter West wrote: >> Installation of R 4.2.2 on my M1 just succeeded. > > Yes, that has been very widely tested. We don't know what OS you or the OP > are running, though. > > Machines with M2 CPUs are very new (like 1-2 days old) and are presumably > running 13.1 or 13.2. > > I have just re-installed 4.2.2 on Macs running Ventura 13.2 with M1 Pro and > M1 Mac CPUs. If I had a failure my first step would be to look at the > Console logs (the Console App is under Applications/Utilities). And I would > make sure my OS was up-to-date (13.2 is also new this week). > >>> On 28 Jan 2023, at 3:29 am, Calboli Federico (LUKE) >>> wrote: >>> >>> What are your security settings? >>> >>> BW >>> >>> F >>> >>>> On 27. Jan 2023, at 17.49, Zhengyang Xiao wrote: >>>> >>>> Hi, Adrian: >>>> >>>> Thank you for helping. >>>> My computer has M2 chip. I don’t have other computers. >>>> >>>> Travis >>>> >>>> >>>> Get Outlook for iOS >>>> From: Adrian Dușa >>>> Sent: Friday, January 27, 2023 8:23:24 AM >>>> To: Zhengyang Xiao >>>> Cc: R list >>>> Subject: Re: [R-SIG-Mac] R installation issue Hello Travis, >>>> >>>> Just a quick suggestion, from the screenshot it can be seen the installer >>>> is intended for the ARM architecture of MacOS. >>>> Do you have an M1 Apple or an Intel Apply computer? There are different >>>> installers for these two architectures. >>>> >>>> Hope this helps, >>>> Adrian >>>> >>>> >>>> On Fri, 27 Jan 2023 at 15:20, Zhengyang Xiao wrote: >>>> Hi, officers, >>>> I can't install R as the installer always shows 'The installation failed' >>>> as shown in the picture below. I have tried several times and restarted my >>>> computer, but it didn't work. The window says I should contact the >>>> software manufacturer for help, so I am here to ask for help. I am in a >>>> hurry to install it because I need it to finish my school assignment for >>>> the R-related course at my university. If you need any extra information, >>>> please email me, and I will respond as soon as possible. >>>> >>>> I am looking forward to hearing from you. >>>> >>>> Thanks! >>>> >>>> Travis Xiao > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Emeritus Professor of Applied Statistics, University of Oxford > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R installation issue
Installation of R 4.2.2 on my M1 just succeeded. — Peter West p...@pbw.id.au “If a kingdom is divided against itself, that kingdom cannot stand. And if a house is divided against itself, that house will not be able to stand.” > On 28 Jan 2023, at 3:29 am, Calboli Federico (LUKE) > wrote: > > What are your security settings? > > BW > > F > >> On 27. Jan 2023, at 17.49, Zhengyang Xiao wrote: >> >> Hi, Adrian: >> >> Thank you for helping. >> My computer has M2 chip. I don’t have other computers. >> >> Travis >> >> >> Get Outlook for iOS >> From: Adrian Dușa >> Sent: Friday, January 27, 2023 8:23:24 AM >> To: Zhengyang Xiao >> Cc: R list >> Subject: Re: [R-SIG-Mac] R installation issue Hello Travis, >> >> Just a quick suggestion, from the screenshot it can be seen the installer is >> intended for the ARM architecture of MacOS. >> Do you have an M1 Apple or an Intel Apply computer? There are different >> installers for these two architectures. >> >> Hope this helps, >> Adrian >> >> >> On Fri, 27 Jan 2023 at 15:20, Zhengyang Xiao wrote: >> Hi, officers, >> I can't install R as the installer always shows 'The installation failed' as >> shown in the picture below. I have tried several times and restarted my >> computer, but it didn't work. The window says I should contact the software >> manufacturer for help, so I am here to ask for help. I am in a hurry to >> install it because I need it to finish my school assignment for the >> R-related course at my university. If you need any extra information, please >> email me, and I will respond as soon as possible. >> >> I am looking forward to hearing from you. >> >> Thanks! >> >> Travis Xiao >> >> >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> >> -- >> Adrian Dusa >> University of Bucharest >> Romanian Social Data Archive >> Soseaua Panduri nr. 90-92 >> 050663 Bucharest sector 5 >> Romania >> https://adriandusa.eu >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > -- > Federico Calboli > Tutkija > Genomiikka ja jalostus, Luonnonvarakeskus > +358295322656 > > > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R-gui slow since last update
Is everyone running the same version of Big Sur? — Peter West p...@ehealth.id.au “I am the vine; you are the branches.” > On 4 May 2021, at 1:06 am, ALPEROVYCH Yan wrote: > > Dear Peter, Simon, > > Since I am not that of an expert in programming, is there any way to trace > what happens 'under the hood' of the gui to see what exactly slows down the > rendering of output on my end? > > On the warnings, some more came today. How that happened and the text that > came out are below. > > Thank you for your help, > Yan > > I looked at the Preferences -> Editor (once the window popped up, I clicked > on the Editor with a mouse and the error came). > ... > 2021-05-03 16:50:36.184 R[73442:2450140] 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. > 2021-05-03 16:50:36.186 R[73442:2450140] 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. > … > > In another instance, hitting cmd-n (new native editor window) gave me this: > ... > 2021-05-03 16:59:03.469 R[73442:2450140] 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. > 2021-05-03 16:59:03.471 R[73442:2450140] 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. > 2021-05-03 16:59:22.225 R[73442:2450140] 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. > 2021-05-03 16:59:22.226 R[73442:2450140] 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. > … > > When in native editor, I hit cmd-w (popping the save file request) gave me > this: > ... > 2021-05-03 16:59:24.024 R[73442:2450140] 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. > ... > > > On May 2, 2021, at 11:03 AM, peter dalgaard > mailto:pda...@gmail.com>> wrote: > > 2019 MB Air here, Big Sur, 4.0.5 off CRAN. I don't see the issue either. (I > do see the "...warmup" thing, though.) > > - Peter D. > > On 1 May 2021, at 21:01 , ALPEROVYCH Yan > mailto:alperov...@em-lyon.com>> wrote: > > Thank you Simon, > > Regarding the "NS..." warnings, the following came just now when I closed the > plot window (after a ggplot) with a mouse. > > 2021-05-01 20:53:35.117 R[2344:57535] +[NSSavePanel _warmUp] attempted warmup > > Since they are usually random, I will log them for some time, and report back. > > Yan > > On May 1, 2021, at 7:00 AM, Simon Urbanek > mailto:simon.urba...@r-project.org><mailto:simon.urba...@r-project.org>> > wrote: > > Yan, > > Thank you for the report, comments inline. > > > On May 1, 2021, at 03:56, ALPEROVYCH Yan > mailto:alperov...@em-lyon.com><mailto:alperov...@em-lyon.com>> > wrote: > > Dear all, > > Beyond the occasional red warnings about the 'NSPop….' buttons, warmups, etc. > and similar issues reported elsewhere here I’ve noted the slowdown of R > console with more and more output. Here is what I do to reliably reproduced > it on my machine - MacBook Pro 2017 with Touch Bar (sessionInfo() is below). > > > There are no known issues in R 4.0.5 so if you see any please report them. > > > 1. Start fresh R-gui > > 2. Paste the following text in the editor. Note that lines are commented, > this is enough to show the problem. It obvisouly gets worse if R has to > evaluate. > > # m[[ 1]] <- .f(update(fml, . ~ . -x1 + x2)) > # m[[ 2]] <- .f(update(fml, . ~ . -x1 + x2 + x3)) > # m[[ 3]] <- .f(update(fml, . ~ . -x1 + x2 + x4)) > # m[[ 4]] <- .f(update(fml, . ~ . -x1 + x2 + x5)) > # m[[ 5]] <- .f(update(fml, . ~ . -x1 + x2 + x6)) > # m[[ 6]] <- .f(update(fml, . ~ . -x1 + x2 + x7)) > # m[[ 7]] <- .f(update(fml, . ~ . -x1 + x2 + x8)) > # m[[ 8]] <- .f(update(fml, . ~ . -x1 + x2 + x9)) > # m[[ 9]] <- .f(update(fml, . ~ . -x1 + x2 + x10)) > # m[[10]] <- .f(update(fml, . ~ . -x1 + x2 + x11)) > > 3. Execute as block once - the output appears almost immediately. Execute the > second time - the slight delay is alread
[R-SIG-Mac] R CMD …
I see a lot of references to R CMD on the command line. Can I assume that the R in question is the R executable in Contents > MacOS within R.app? Peter — p...@ehealth.id.au “Those who are well have no need of a physician, but those who are sick.” ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] more rgl problems
I’ve enabled /opt/X11/libexec/launchd_startx for full disk access in Security & Privacy, but it hasn’t fixed the problem. > On 18 Feb 2021, at 10:06 pm, Peter West wrote: ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] more rgl problems
This is happening as a result of the Launch* startx and privileged_startx execution. The Operation not permitted stuff just scrolls on by. > On 18 Feb 2021, at 9:58 pm, Peter West wrote: > > Looks like an authorization problem. > > xclockk did not appear, so I had a look at system.log. > > Here’s a sample. > > --- > Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: waiting for X > server to begin accepting connections > Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: > /opt/X11/bin/xinit: giving up > Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: > /opt/X11/bin/xinit: unable to connect to X server: Operation timed out > Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: > /opt/X11/bin/xinit: /opt/X11/bin/xinit: server error > Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: > /opt/X11/bin/xinit: > Feb 18 21:51:40 Rosie org.macosforge.xquartz.startx[75167]: xauth: file > /Users/pbw/.serverauth.75168 does not exist > Feb 18 21:51:40 Rosie org.macosforge.xquartz.X11.stub[75265]: Xquartz: Unable > to locate waiting server: org.macosforge.xquartz.X11 > Feb 18 21:51:40 Rosie Xquartz[75272]: no path for address 0x7ffdffcec000 > Feb 18 21:51:40 Rosie org.macosforge.xquartz.X11.stub[75272]: Xquartz: > Starting X server: /Applications/Utilities/XQuartz.app/Contents/MacOS/X11 > --listenonly > Feb 18 21:51:40 Rosie org.macosforge.xquartz.privileged_startx[54309]: > /System/Library/Fonts/fonts.scale: fopen(w): Operation not permitted > Feb 18 21:51:40 Rosie org.macosforge.xquartz.privileged_startx[54309]: > /System/Library/Fonts/fonts.dir: fopen(w): Operation not permitted > Feb 18 21:51:40 Rosie org.macosforge.xquartz.privileged_startx[54309]: > /System/Library/Fonts/Supplemental/fonts.scale: fopen(w): Operation not > permitted > Feb 18 21:51:40 Rosie org.macosforge.xquartz.privileged_startx[54309]: > /System/Library/Fonts/Supplemental/fonts.dir: fopen(w): Operation not > permitted > Feb 18 21:51:42 Rosie org.macosforge.xquartz.startx[75167]: > > Feb 18 21:51:44 Rosie org.macosforge.xquartz.startx[75167]: waiting for X > server to begin accepting connections > Feb 18 21:52:04 --- last message repeated 9 times --- > Feb 18 21:52:04 Rosie org.macosforge.xquartz.X11.stub[75265]: Xquartz: > bootstrap_look_up(): Unknown service name > Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: waiting for X > server to begin accepting connections > Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: waiting for X > server to begin accepting connections giving up > Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: > /opt/X11/bin/xinit: unable to connect to X server: Connection refused > Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: > /opt/X11/bin/xinit: unable to connect to X server/opt/X11/bin/xinit: server > error > Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: > /opt/X11/bin/xinit: unable to connect to X server > Feb 18 21:52:06 Rosie org.macosforge.xquartz.privileged_startx[54309]: > /opt/X11/bin/font_cache: line 92: /System/Library/Fonts/fonts.list: Operation > not permitted > Feb 18 21:52:06 Rosie org.macosforge.xquartz.privileged_startx[54309]: > /opt/X11/bin/font_cache: line 92: > /System/Library/Fonts/Supplemental/fonts.list: Operation not permitted > Feb 18 21:52:06 Rosie org.macosforge.xquartz.startx[75566]: expr: syntax error > Feb 18 21:52:06 --- last message repeated 2 times --- > @ > Feb 18 21:52:30 --- last message repeated 7 times --- > Feb 18 21:52:30 Rosie org.macosforge.xquartz.X11.stub[75664]: Xquartz: > bootstrap_look_up(): Unknown service name > Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: waiting for X > server to begin accepting connections > Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: waiting for X > server to begin accepting connections giving up > Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: > /opt/X11/bin/xinit: unable to connect to X server: Connection refused > Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: waiting for X > server to begin accepting connections /opt/X11/bin/xinit: server error > Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: waiting for X > server to begin accepting connections > Feb 18 21:52:32 Rosie org.macosforge.xquartz.startx[75977]: expr: syntax error > Feb 18 21:52:32 --- last message repeated 2 times --- > Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]: > /opt/X11/bin/font_cache: line 92: /System/Library/Fonts/fonts.list: Operation > not permitted > Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]: > /
Re: [R-SIG-Mac] more rgl problems
org.macosforge.xquartz.privileged_startx[54309]:
/System/Library/Fonts/fonts.scale: fopen(w): Operation not permitted
Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]:
/System/Library/Fonts/fonts.dir: fopen(w): Operation not permitted
Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]:
/System/Library/Fonts/Supplemental/fonts.scale: fopen(w): Operation not
permitted
Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]:
/System/Library/Fonts/Supplemental/fonts.dir: fopen(w): Operation not permitted
Feb 18 21:52:34 Rosie org.macosforge.xquartz.startx[75977]:
Feb 18 21:52:36 Rosie org.macosforge.xquartz.startx[75977]: waiting for X
server to begin accepting
connections---
> On 18 Feb 2021, at 9:30 pm, Duncan Murdoch wrote:
>
> On 18/02/2021 6:14 a.m., Peter West wrote:
>> Yes, I went through that process. I have no org.xquartz.* files in /Library
>> Launch* now.
>
> If you run x11(), does it cause the same issue?
>
> What about not starting R at all, and just running some X11 app like xclock
> from the terminal?
>
> Duncan Murdoch
>
>>> On 18 Feb 2021, at 9:08 pm, Duncan Murdoch >> <mailto:murdoch.dun...@gmail.com>> wrote:
>>>
>>> On 17/02/2021 10:13 p.m., Peter West wrote:
>>>> And speaking of M1 Silicon:
>>>> My XQuartz version is 2.7.11.
>>>> Started R 4.0.4.
>>>> Stopped R 4.0.4
>>>> Started RStudio
>>>>> install.packages("rgl")
>>>> trying URL
>>>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz
>>>> <https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz>'
>>>> Content type 'application/x-gzip' length 6446159 bytes (6.1 MB)
>>>> ==
>>>> downloaded 6.1 MB
>>>> The downloaded binary packages are in
>>>> /var/folders/jf/mkyz74311796dl4mxx_7tcx8gn/T//RtmpflD1wL/downloaded_packages
>>>>> library(rgl)
>>>> RStudio hangs indefinitely.
>>>> My RStudio is at 1.4.1103.
>>>
>>> That looks a lot like the issue Rich had last week (which I think is
>>> unrelated to the one posted today). Have you tried the solution I posted
>>> for that? Here's a copy:
>>>
>>>> This worked for me to apparently fix my system:
>>>> Start with a newly rebooted system.
>>>> Uninstall XQuartz by dragging it to the trash.
>>>> Look in /Library/LaunchAgents/ for filenames related to xquartz. I had
>>>> two: a five year old one called org.macosforge.xquartz.startx.plist, and
>>>> one from around the time I installed the XQuartz beta named
>>>> org.xquartz.startx.plist. I deleted the latter.
>>>> Look in /Library/LaunchDaemons/ for similar files. I deleted one with the
>>>> same name, i.e. org.xquartz.startx.plist, and left an older one.
>>>> Reboot the system again, and install XQuartz 2.7.11. Relogin, and things
>>>> seem fine.
>>>
>>> I suspect it would be sufficient to just delete the
>>> /Library/LaunchAgents/org.xquartz.startx.plist and
>>> /Library/LaunchDaemons/org.xquartz.startx.plist files and reboot, but I
>>> haven't tried that.
>>>
>>> Duncan Murdoch
>
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Re: [R-SIG-Mac] more rgl problems
Yes, I went through that process. I have no org.xquartz.* files in /Library
Launch* now.
> On 18 Feb 2021, at 9:08 pm, Duncan Murdoch wrote:
>
> On 17/02/2021 10:13 p.m., Peter West wrote:
>> And speaking of M1 Silicon:
>> My XQuartz version is 2.7.11.
>> Started R 4.0.4.
>> Stopped R 4.0.4
>> Started RStudio
>>> install.packages("rgl")
>> trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz'
>> Content type 'application/x-gzip' length 6446159 bytes (6.1 MB)
>> ==
>> downloaded 6.1 MB
>> The downloaded binary packages are in
>>
>> /var/folders/jf/mkyz74311796dl4mxx_7tcx8gn/T//RtmpflD1wL/downloaded_packages
>>> library(rgl)
>> RStudio hangs indefinitely.
>> My RStudio is at 1.4.1103.
>
> That looks a lot like the issue Rich had last week (which I think is
> unrelated to the one posted today). Have you tried the solution I posted for
> that? Here's a copy:
>
>> This worked for me to apparently fix my system:
>> Start with a newly rebooted system.
>> Uninstall XQuartz by dragging it to the trash.
>> Look in /Library/LaunchAgents/ for filenames related to xquartz. I had two:
>> a five year old one called org.macosforge.xquartz.startx.plist, and one
>> from around the time I installed the XQuartz beta named
>> org.xquartz.startx.plist. I deleted the latter.
>> Look in /Library/LaunchDaemons/ for similar files. I deleted one with the
>> same name, i.e. org.xquartz.startx.plist, and left an older one.
>> Reboot the system again, and install XQuartz 2.7.11. Relogin, and things
>> seem fine.
>
> I suspect it would be sufficient to just delete the
> /Library/LaunchAgents/org.xquartz.startx.plist and
> /Library/LaunchDaemons/org.xquartz.startx.plist files and reboot, but I
> haven't tried that.
>
> Duncan Murdoch
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Re: [R-SIG-Mac] more rgl problems
Ken,
I only used RStudio because it is easier to remove packages. I should have made
that clear.
The same thing happens with R.app; that is, library(rgl) hangs indefinitely.
Peter
—
p...@ehealth.id.au
“For what does it profit a man if he gains the whole world and loses or
forfeits himself?”
> On 18 Feb 2021, at 1:41 pm, Ken Beath wrote:
>
> RStudio have a page for reporting bugs at
> https://github.com/rstudio/rstudio/issues/
> <https://github.com/rstudio/rstudio/issues/> You may be the first M! bug.
>
> They haven’t progressed my fairly serious bug report about Windows (if you
> plot a graph and the screen hasn’t updated when you start parallel processing
> then R crashes) from 6 weeks ago, so I wouldn’t be anticipating much progress
> soon.
>
> Ken
>
>> On 18 Feb 2021, at 2:13 pm, Peter West > <mailto:p...@pbw.id.au>> wrote:
>>
>> And speaking of M1 Silicon:
>>
>> My XQuartz version is 2.7.11.
>>
>> Started R 4.0.4.
>> Stopped R 4.0.4
>> Started RStudio
>>
>>> install.packages("rgl")
>> trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz
>> <https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz>'
>> Content type 'application/x-gzip' length 6446159 bytes (6.1 MB)
>> ==
>> downloaded 6.1 MB
>>
>>
>> The downloaded binary packages are in
>>
>> /var/folders/jf/mkyz74311796dl4mxx_7tcx8gn/T//RtmpflD1wL/downloaded_packages
>>> library(rgl)
>>
>> RStudio hangs indefinitely.
>>
>> My RStudio is at 1.4.1103.
>>
>> Peter
>>
>> —
>> p...@ehealth.id.au <mailto:p...@ehealth.id.au>
>> “For what does it profit a man if he gains the whole world and loses or
>> forfeits himself?”
>>
>>> On 18 Feb 2021, at 10:36 am, Richard M. Heiberger wrote:
>>>
>>> This is repeatable when the lines are all pasted in at once.
>>> The example works if I allow some time delay between lines.
>>>
>>> This is might be a relative of the one from a few months ago.
>>> But this message is about invalid permissions.
>>> =
>>>
>>> R version 4.0.4 RC (2021-02-12 r79998) -- "Lost Library Book"
>>> Copyright (C) 2021 The R Foundation for Statistical Computing
>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>> Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>> setwd('/Users/rmh/Rwd/')
>>>> library(rgl)
>>>> x <- matrix(1:3, 1,3)
>>>> plot(1:10, col=7)
>>>> open3d()
>>> error: xp_attach_gl_context returned: 2
>>>
>>> *** caught segfault ***
>>> address 0x18, cause 'invalid permissions'
>>>
>>> Traceback:
>>> 1: rgl.open(useNULL)
>>> 2: open3d()
>>>
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>> Selection:
>>>
>>>
>>>
>>> MacBookAir with the M1 chip using the regular intel version of R from CRAN.
>>> Big Sur 11.2.1.
>>> The plot(1:10), col=7) ## went by default to the quartz() device.
>>>
>>>
>>> I repeated this about 5 times in ESS, and then once in Terminal.
>>>
>>> Let me know if you need more information.
>>>
>>>
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Re: [R-SIG-Mac] more rgl problems
And speaking of M1 Silicon:
My XQuartz version is 2.7.11.
Started R 4.0.4.
Stopped R 4.0.4
Started RStudio
> install.packages("rgl")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz'
Content type 'application/x-gzip' length 6446159 bytes (6.1 MB)
==
downloaded 6.1 MB
The downloaded binary packages are in
/var/folders/jf/mkyz74311796dl4mxx_7tcx8gn/T//RtmpflD1wL/downloaded_packages
> library(rgl)
RStudio hangs indefinitely.
My RStudio is at 1.4.1103.
Peter
—
p...@ehealth.id.au
“For what does it profit a man if he gains the whole world and loses or
forfeits himself?”
> On 18 Feb 2021, at 10:36 am, Richard M. Heiberger wrote:
>
> This is repeatable when the lines are all pasted in at once.
> The example works if I allow some time delay between lines.
>
> This is might be a relative of the one from a few months ago.
> But this message is about invalid permissions.
> =
>
> R version 4.0.4 RC (2021-02-12 r79998) -- "Lost Library Book"
> Copyright (C) 2021 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin17.0 (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> setwd('/Users/rmh/Rwd/')
>> library(rgl)
>> x <- matrix(1:3, 1,3)
>> plot(1:10, col=7)
>> open3d()
> error: xp_attach_gl_context returned: 2
>
> *** caught segfault ***
> address 0x18, cause 'invalid permissions'
>
> Traceback:
> 1: rgl.open(useNULL)
> 2: open3d()
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
>
> MacBookAir with the M1 chip using the regular intel version of R from CRAN.
> Big Sur 11.2.1.
> The plot(1:10), col=7) ## went by default to the quartz() device.
>
>
> I repeated this about 5 times in ESS, and then once in Terminal.
>
> Let me know if you need more information.
>
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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Re: [R-SIG-Mac] I'm new to R in a Mac. How do I specify the path in read.table()?
David,
I thought I saw advice on this issue already that noted you could not use
backslashes in file paths on a Mac. Have you tried with
“/Users/DFP/Desktop/Monroe319Ecoli.txt”? Do you come from a Windows background?
Peter
—
p...@ehealth.id.au
“Why does this generation seek a sign? Truly, I say to you, no sign will be
given to this generation.”
> On 30 Jan 2021, at 6:25 am, Parkhurst, David F. wrote:
>
> I�ve tried for over an hour to figure this out with no luck. I�ve moved the
> text file (created from excel) to the desktop to simplify the path. If I
> click on the file and ask Get Info, it lists �Where� as iCloud Drive >
> Desktop. If I copy that to the clipboard and paste that into a read.table
> command in the R interface, it comes up as /Users/DFP/Desktop. But if I try
> read.table("\\Users\\DFP\\Desktop\\Monroe319Ecoli.txt"), I get No such file
> or directory. How can I get that file into a data frame?
[[alternative HTML version deleted]]
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Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC
Hi Duncan, When you say ‘fix,’ did that include running the compiled rgl successfully against your R installation? Peter — p...@ehealth.id.au Moved with pity, he stretched out his hand and touched him and said to him, “I will; be clean.” > On 14 Feb 2021, at 11:42 am, Duncan Murdoch wrote: > > This worked for me to apparently fix my system: > > Start with a newly rebooted system. > > Uninstall XQuartz by dragging it to the trash. > > Look in /Library/LaunchAgents/ for filenames related to xquartz. I had two: > a five year old one called org.macosforge.xquartz.startx.plist, and one from > around the time I installed the XQuartz beta named org.xquartz.startx.plist. > I deleted the latter. > > Look in /Library/LaunchDaemons/ for similar files. I deleted one with the > same name, i.e. org.xquartz.startx.plist, and left an older one. > > Reboot the system again, and install XQuartz 2.7.11. Relogin, and things > seem fine. > > Duncan Murdoch > [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Unable to change some members of a vector
Just incidentally, \xCA in MacRoman encoding is an NBSP – non-breaking space, which is the only one that looks sane. In Unicode, it’s Latin capital letter E with circumflex, as it is in ISO 8859-1. Peter — p...@ehealth.id.au Moved with pity, he stretched out his hand and touched him and said to him, “I will; be clean.” > On 14 Feb 2021, at 2:34 pm, Ken Beath wrote: … > There is an option in the read.table command of stringsAsFactors. You can set > it to FALSE to obtain character strings. You can also convert the factor to > character using as.character(). > … > Ken > >> On 14 Feb 2021, at 9:54 am, Parkhurst, David F. wrote: >> >> I have a problem I don’t know how to deal with. I’ve used read.table to >> create the data frame called msPdf. It contains three vectors: month, >> site, conc. Some of the site values look like this: MLH\xca. [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Optional Libraries, Frameworks and Applications for macOS
Are the various libraries at different versions (e.g. geos-3.7.2 & geos-3.8.1) dependencies for different packages? I don’t suppose there’s a list of reverse package dependencies? Peter — p...@ehealth.id.au “What comes out of a person is what defiles him.” ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [External] Behaviour or Quartz windows
R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.0.3 tools_4.0.3 > On 10 Feb 2021, at 4:26 am, Prof Brian Ripley wrote: > > The quartz() device has nothing to so with XQuartz. Quartz is part of macOS: > https://en.wikipedia.org/wiki/Quartz_(graphics_layer) > > Using XQuartz betas is not supported: it is very unfortunate that they are > persuading users to install a beta version. > > You have not followed the posting guide and posted the sessionInfo(). We are > left to guess that you are using an Intel build of R under emulation, but > homebrew does have (a rather broken) arm64 build of R 4.0.3: we do not > support arm64 builds on R < 4.1.0. My understanding is that in the CRAN > release of R 4.0.3 only the X11() device and parts of Tk interact with > XQuartz, although other parts may in other builds. > > On 09/02/2021 17:33, Richard M. Heiberger wrote: >> Is R on M1 really talking to the REAL XQuartz? After I opened XQuartz from >> the spotlignt, it acknowledged the xterm window, but not the R graphics >> window. When I closed the XQuartz >> app, the R graphics window was still open and functioning. dev.cur() says >> "quartz". >> just checked on my older intel mac. same behavior. the Xquartz.app menu >> doesn't list >> the R graphics window, and the R graphics shows "...", not "XQuartz" in the >> menu bar. >> ____ >> From: R-SIG-Mac on behalf of Richard M. >> Heiberger >> Sent: Tuesday, February 9, 2021 11:56 AM >> To: Peter West; r-sig-mac@r-project.org >> Subject: Re: [R-SIG-Mac] [External] Behaviour or Quartz windows >> When I draw a 9x7 panel lattice it displays 12 panels, then sits there until >> I resize the window. then the rest appears. When I display another 9x7, it >> too sits at 12 panels. >> When I Cmd-left for the previous display, the current one vanishes entirely. >> When I send the command again, after it sits I resize the window. Now the >> full second display >> is visible. When I Cmd-left followed by Cmd-right, the second display is >> lost. >> I am using R version 4.0.3 (2020-10-10) on Silicon Mac Big Sur 11.1 from >> inside ESS. >> XQuartz doesn't report correctly. On the MenuBar it doesn't say "XQuartz". >> Instead it shows a >> small Apple Icon which has no information when clicked. When I search using >> the MenuBar Spotlight icon, it tells me Xquartz 2.8.0_beta1 and offers to >> update to beta3. Clicking on XQuartz.app in the Spotlight menu gives proper >> XQuartz information in the upper left corner >> of the MenuBar. >> Rich >> Get Outlook for iOS<https://aka.ms/o0ukef> >> >> From: R-SIG-Mac on behalf of Peter West >> >> Sent: Tuesday, February 9, 2021 10:35:59 AM >> To: r-sig-mac@r-project.org >> Subject: [External] [R-SIG-Mac] Behaviour or Quartz windows >> Hi, >> I�ll just confirm the odd behaviour of the Quartz window in Big Sur 11.2 R >> 4.0.3 GUI 1.73 on M1 silicon. I have installed the beta3 version of Quartz. >> In my case I have to CMD <- twice, then go forward to get the next to last >> plot. >> Are these Quartz windows constructed using native MacOS graphics or XQuartz? >> Peter >> � >> Peter West >> peter.b.w...@ehealth.id.au >> �that they might touch even the fringe of his garment. And as many as >> touched it were made well. >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> [[alternative HTML version deleted]] >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Emeritus Professor of Applied Statistics, University of Oxford ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Behaviour or Quartz windows
Hi, I’ll just confirm the odd behaviour of the Quartz window in Big Sur 11.2 R 4.0.3 GUI 1.73 on M1 silicon. I have installed the beta3 version of Quartz. In my case I have to CMD <- twice, then go forward to get the next to last plot. Are these Quartz windows constructed using native MacOS graphics or XQuartz? Peter — Peter West peter.b.w...@ehealth.id.au …that they might touch even the fringe of his garment. And as many as touched it were made well. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
