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:
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
This question is not related to Macs, but here is the answer anyway.
First up, anyone who uses R should understand what a factor is. Find an
introductory text on R and read the section on factors. Even better, read the
whole book. It seems that it has been decided that R will not automatically
Thank you. dragging the org.xquartz.startx.* to Trash and reinstalling 2.7.11
restored my system to sanity.
From: Duncan Murdoch
Sent: Saturday, February 13, 2021 8:42 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: Re: [External] Re: [R-SIG-Mac]
> On Feb 13, 2021, at 8:30 PM, Simon Urbanek
> wrote:
>
> Michael,
> Thanks, but please don't post 3rd party links that are just one-liners with
> extra advertising, especially when they have been already mentioned.
> Cheers,
> Simon
I think my link expanded some on the original answer
Michael,
Thanks, but please don't post 3rd party links that are just one-liners with
extra advertising, especially when they have been already mentioned.
Cheers,
Simon
> On Feb 14, 2021, at 15:00, Michael Hall wrote:
>
>
>
>> On Feb 13, 2021, at 5:41 PM, r-sig-mac-requ...@r-project.org
> On Feb 13, 2021, at 5:41 PM, r-sig-mac-requ...@r-project.org wrote:
>
> xcrun: error: invalid active developer path
> (/Library/Developer/CommandLineTools), missing xcrun at:
> /Library/Developer/CommandLineTools/usr/bin/xcrun
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
It is looking for:
missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
This is the entirety of
/Library/Developer/CommandLineTools/usr/share/
/Library/Developer/CommandLineTools/usr/share/man:
total used in directory 40 available 1.3 TiB
drwxr-xr-x 3 root wheel 96
Remove the directory where xcrun says it is supposed to live and re-install the
command line tools?
el
—
Sent from Dr Lisse’s iPhone
On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote:
> I reported on installing xcode tools in my email
> Sat 2/13/2021 3:59 PM
> It didn't help.
>
> I did
I reported on installing xcode tools in my email
Sat 2/13/2021 3:59 PM
It didn't help.
I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1.
From: Dr Eberhard W Lisse
Sent: Saturday, February 13, 2021 4:44 PM
To: Duncan Murdoch; R-SIG-Mac;
Well, my original report didn't give full information because R locked up too
early.
>From here I am following instructions and reporting back:
R version 4.0.4 RC (2021-02-12 r79998) -- "Lost Library Book"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform:
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. I was able to change that
with this command: msPdf$site[13]="MLH”. That seems to have
On 13/02/2021 5:43 p.m., Simon Urbanek wrote:
Duncan,
not really - this is why the XQuartz betas are such a disaster - they replace
libraries with incompatible versions (under same file name) - and even remove
some libraries, thus breaking anything that was compiled against either
version.
Duncan,
not really - this is why the XQuartz betas are such a disaster - they replace
libraries with incompatible versions (under same file name) - and even remove
some libraries, thus breaking anything that was compiled against either
version. If you downgrade, you have to re-compile anything
Richard,
thanks - finally a more complete output to go on. This is exactly the reminder
why it is so important to post the _full_output - the actual facts were
completely missing from your previous report.
Firstly, the xcrun output is just a warning which indicates that R can't find
out
On 13/02/2021 4:54 p.m., Simon Urbanek wrote:
As mentioned earlier, the issue is likely that your X11-auto-launch is not working. You
can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you would on any unix system or
start X11 with X11(":0")
[personally, I hate that auto-launch "feature"
another new session
> setwd('/Users/rmh/Rwd/')
> Sys.getenv("DISPLAY")
[1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0"
> unlink(Sys.getenv("DISPLAY"))
>Sys.setenv(DISPLAY=":0.0")
> X11()
xcrun: error: invalid active developer path
(/Library/Developer/CommandLineTools), missing
another fresh R session
> X11(":0")
xcrun: error: invalid active developer path
(/Library/Developer/CommandLineTools), missing xcrun at:
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
unable to start device X11
In
Thanks for your detailed descriptions! I can now reproduce this, and I
have an ugly workaround. I should be able to get a better workaround soon.
To reproduce:
Install the beta. (I did this when it was pushed to me.) It worked
fine for me.
Install the previous version, 2.7.11. Reboot
As mentioned earlier, the issue is likely that your X11-auto-launch is not
working. You can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you would
on any unix system or start X11 with X11(":0")
[personally, I hate that auto-launch "feature" since it tries to start XQuartz
even if you
space in a directory name?
put the file in ~/Desktop and see what happens then.
If it is a CSV make it moabsitechem.csv and see what that doesn.
el
—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 22:29 +0200, Parkhurst, David F. , wrote:
> I’m still having trouble with read.table, as follows
the Xcode Command line tools are missing. Install them and see what happens.
Did you recently upgrade MacOS?
el
—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
> That is next. Again a fresh session.
>
>
> > setwd('/Users/rmh/Rwd/')
> >
That is next. Again a fresh session.
> setwd('/Users/rmh/Rwd/')
> Sys.setenv(DISPLAY=":0.0")
> X11()
xcrun: error: invalid active developer path
(/Library/Developer/CommandLineTools), missing xcrun at:
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display,
Have you tried the change to DISPLAY, i.e.
Sys.setenv(DISPLAY=":0.0")
before running X11()?
Duncan Murdoch
On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
I tried this. It made no difference. Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new
I tried this. It made no difference. Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)
> X11()
xcrun: error: invalid active developer path
(/Library/Developer/CommandLineTools), missing xcrun at:
Thanks. I switched from years using PCs about a year ago when MS would no
longer support Windows 7. I have missed seeing extensions on files (probably
.txt for this one). It�s good to learn that I can change that.
From: Bryan Hanson
Date: Saturday, February 13, 2021 at 3:37 PM
To:
Try
list.files()
to see the names of the files in the current directory, and make certain you
are where you think you are, the file is there, has the name you think it has
etc. You may need to add the extension, presumably something like “.csv” to
your read.table call.
A possible point of
I’m still having trouble with read.table, as follows (and there IS a plain text
document called moabsitechem in this directory:
> getwd()
[1] "/Users/DFP/Documents/Documents - David’s iMac/ae/FriendsMonroe"
> read.table("moabsitechem")
Error in file(file, "rt") : cannot open the connection
In
Even better is to learn one of the many ways to start R in a working directory
of your choice, so you don't have to mix code and data from different projects
together in one directory just because that happens to be where your default R
icon sets it up.
Some ways:
a) Use Terminal and the cd
You can also point R to the directory where the file of interest is, rather
than moving the file to the directory where R is currently pointing.
setwd(“~/Desktop”)
Bryan
> On Feb 13, 2021, at 9:02 AM, Parkhurst, David F. wrote:
>
> Thank you. I thought I�d seen in some book that in a Mac,
Ah. That will simplify the process a lot!
From: Duncan Murdoch
Date: Saturday, February 13, 2021 at 10:52 AM
To: Parkhurst, David F. , r-sig-mac@r-project.org
Subject: Re: [R-SIG-Mac] How to find the path for a file to be read with
read.table() in a Mac
On 13/02/2021 10:42 a.m., Parkhurst,
Thank you. I thought I�d seen in some book that in a Mac, one had to specify
paths in the way I tried.
From: Duncan Murdoch
Date: Saturday, February 13, 2021 at 10:49 AM
To: Parkhurst, David F. , r-sig-mac@r-project.org
Subject: Re: [R-SIG-Mac] How to find the path for a file to be read with
On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:
I’ve several times to figure this out with no luck. I’ve moved a tab delimited 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
On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:
I’ve several times to figure this out with no luck. I’ve moved a tab delimited 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
I’ve several times to figure this out with no luck. I’ve moved a tab delimited
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
On 12/02/2021 11:12 p.m., Richard M. Heiberger wrote:
Using the intel R_4.0.4RC on the Mac M1.
Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the
8.0.3beta.
X11() now does not work at all.
X11()
xcrun: error: invalid active developer path
that has nothing to do with Xquartz but means you need to install the Command
line tools
sudo xcode-select —install
—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> Using the intel R_4.0.4RC on the Mac M1.
>
> Based on your recommendation I reinstalled
Thanks for testing and the reports!
Unfortunately, I cannot reproduce the touch-bar issue, because it doesn''t
appear when run in Xcode with touch-bar emulation and I don't have a Mac with
Big Sur and a touch-bar. Moreover, R is not providing custom touch-bar icons so
I can't even find out
The libraries are used to build the packages - they are all static, so the
package binaries will include them. It is not intended for users, but rather if
you were to compile packages on your own and wanted to replicate the CRAN setup.
Cheers,
Simon
> On Feb 13, 2021, at 7:33 PM, Peter West
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