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
Re: [R-SIG-Mac] Unable to change some members of a vector
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 add a factor level, which is probably a good idea. 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(). If Excel decides to put strange characters into your data file then that is Excel’s problem. I suggest looking at the file with a text editor. The free version of BBEdit will work fine. You can read Excel files directly using teh readxl package. 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. I was able to > change that with this command: msPdf$site[13]="MLH”. That seems to have been > allowed because some of the other sites are simply MLH. But the system won’t > let me make the same kind of change in another case: > msPdf$site[29]="MUH”. When I ask for that, I get > Warning message: > In `[<-.factor`(`*tmp*`, 29, value = c(5L, 2L, 1L, 11L, 5L, 12L, : > invalid factor level, NA generated >> #13 May MLH\xca 0.007 > Then if I enter msPdf$site[29], I get this response: > [1] > Levels: CrCr LMO MCE MCH MFSC MLE MLH MLH\xca MUE MUH\xca NFSC SFSC > > In other words, although other sites that were just plain MLH, there were not > other sites that were just plain MUH. > How can I fix this problem? I have no idea why excel added those \xca bits > to a few of the site values. > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ 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] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC
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] [External] Re: [External] Re: [External] Please test R 4.0.4 RC 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 On 13/02/2021 7:22 p.m., Richard M. Heiberger wrote: > 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 Feb 11 12:34 . >drwxr-xr-x 3 root wheel 96 Feb 11 12:34 .. >-rw-r--r-- 1 root wheel 20198 Jan 27 16:11 whatis > > So I will again try > sudo xcode-select --install > > It took a few minutes, and now from a new R session >> X11() > Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : >unable to start device X11 > In addition: Warning message: > In X11() : unable to open connection to X11 display '' >> Sys.getenv("DISPLAY") > [1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0" >> Sys.setenv(DISPLAY=":0.0") >> Sys.getenv("DISPLAY") > [1] ":0.0" >> X11() > Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : >unable to start device X11 > In addition: Warning message: > In X11() : unable to open connection to X11 display '' >> > > > > the xcrun is still not on the machine, and specifically not in > /Library/Developer/CommandLineTools/ > > From: Dr Eberhard W Lisse > Sent: Saturday, February 13, 2021 6:50 PM > To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger > Cc: e...@lisse.na > Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: > [External] Please test R 4.0.4 RC > > Remove the directory where xcrun says it is supposed to live and re-install > the command line tools? > > el > > — > Sent from Dr Lisse’s iPhone > On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote: > I reported on installing xcode tools in my email > Sat 2/13/2021 3:59 PM > It didn't help. > > I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1. > > > From: Dr Eberhard W Lisse > Sent: Saturday, February 13, 2021 4:44 PM > To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger > Cc: e...@lisse.na > Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] > Please test R 4.0.4 RC > > the Xcode Command line tools are missing. Install them and see what happens. > > Did you recently upgrade MacOS? > > el > > — > Sent from Dr Lisse’s iPhone > On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote: > That is next. Again a fresh session. > > > setwd('/Users/rmh/Rwd/') > Sys.setenv(DISPLAY=":0.0") > X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : > unable to start device X11 > In addition: Warning messages: > 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : > running command ''otool' -L > '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 > 2: In X11() : unable to open connection to X11 display '' > > > > and the R session is still alive. > > > This rasies for me a different question. Why should I want X11()? > > When X11 was working it was very slow, and didn't allow paging back through > previous images. > > In favor of X11, I think it uses the display space better. X11() has better > size and spacing for xlab, ylab, and main than quartz(). But that isn't a > strong enough > reason to use it while develkoping a graph. When I want it to look good, > I go directly to pdf() and get the spacing that I think looks better. > > > From: Duncan Murdoch > Sent: Saturday, February 13, 2021 4:05 PM > To: Richard M. Heiberger; R-SIG-Mac > Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R > 4.0.4 RC > > Have you tried the change to DISPLAY, i.e. > > Sys.setenv(DISPLAY=":0.0") > > before running X11()? > >
Re: [R-SIG-Mac] Please test R 4.0.4 RC
> 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 which it didn’t sound like worked. ‘ It included additionally… sudo xcode-select —reset and… If even that fails, go to the Apple developer download section and download Xcode manually. But I did just google it and have no personal experience with the error. Often though just google will find you someone else who has dealt with the issue. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Please test R 4.0.4 RC
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 wrote: >> >> xcrun: error: invalid active developer path >> (/Library/Developer/CommandLineTools), missing xcrun at: >> /Library/Developer/CommandLineTools/usr/bin/xcrun > > https://ma.ttias.be/mac-os-xcrun-error-invalid-active-developer-path-missing-xcrun/ > > > [[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 mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Please test R 4.0.4 RC
> 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 https://ma.ttias.be/mac-os-xcrun-error-invalid-active-developer-path-missing-xcrun/ [[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] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC
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 On 13/02/2021 7:22 p.m., Richard M. Heiberger wrote: 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 Feb 11 12:34 . drwxr-xr-x 3 root wheel 96 Feb 11 12:34 .. -rw-r--r-- 1 root wheel 20198 Jan 27 16:11 whatis So I will again try sudo xcode-select --install It took a few minutes, and now from a new R session X11() Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning message: In X11() : unable to open connection to X11 display '' Sys.getenv("DISPLAY") [1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0" Sys.setenv(DISPLAY=":0.0") Sys.getenv("DISPLAY") [1] ":0.0" X11() Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning message: In X11() : unable to open connection to X11 display '' the xcrun is still not on the machine, and specifically not in /Library/Developer/CommandLineTools/ From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 6:50 PM To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC Remove the directory where xcrun says it is supposed to live and re-install the command line tools? el — Sent from Dr Lisse’s iPhone On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote: I reported on installing xcode tools in my email Sat 2/13/2021 3:59 PM It didn't help. I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 4:44 PM To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC the Xcode Command line tools are missing. Install them and see what happens. Did you recently upgrade MacOS? el — Sent from Dr Lisse’s iPhone On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote: That is next. Again a fresh session. setwd('/Users/rmh/Rwd/') Sys.setenv(DISPLAY=":0.0") X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' and the R session is still alive. This rasies for me a different question. Why should I want X11()? When X11 was working it was very slow, and didn't allow paging back through previous images. In favor of X11, I think it uses the display space better. X11() has better size and spacing for xlab, ylab, and main than quartz(). But that isn't a strong enough reason to use it while develkoping a graph. When I want it to look good, I go directly to pdf() and get the spacing that I think looks better. From: Duncan Murdoch Sent: Saturday, February 13, 2021 4:05 PM To: Richard M. Heiberger; R-SIG-Mac Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC 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 *R* sessio n) X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta worked with intel R_4.0.3 on the Mac M1. From: Dr Eberhard
Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC
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 Feb 11 12:34 . drwxr-xr-x 3 root wheel 96 Feb 11 12:34 .. -rw-r--r-- 1 root wheel 20198 Jan 27 16:11 whatis So I will again try sudo xcode-select --install It took a few minutes, and now from a new R session > X11() Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning message: In X11() : unable to open connection to X11 display '' > Sys.getenv("DISPLAY") [1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0" > Sys.setenv(DISPLAY=":0.0") > Sys.getenv("DISPLAY") [1] ":0.0" > X11() Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning message: In X11() : unable to open connection to X11 display '' > the xcrun is still not on the machine, and specifically not in /Library/Developer/CommandLineTools/ From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 6:50 PM To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC Remove the directory where xcrun says it is supposed to live and re-install the command line tools? el — Sent from Dr Lisse’s iPhone On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote: I reported on installing xcode tools in my email Sat 2/13/2021 3:59 PM It didn't help. I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 4:44 PM To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC the Xcode Command line tools are missing. Install them and see what happens. Did you recently upgrade MacOS? el — Sent from Dr Lisse’s iPhone On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote: That is next. Again a fresh session. setwd('/Users/rmh/Rwd/') Sys.setenv(DISPLAY=":0.0") X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' and the R session is still alive. This rasies for me a different question. Why should I want X11()? When X11 was working it was very slow, and didn't allow paging back through previous images. In favor of X11, I think it uses the display space better. X11() has better size and spacing for xlab, ylab, and main than quartz(). But that isn't a strong enough reason to use it while develkoping a graph. When I want it to look good, I go directly to pdf() and get the spacing that I think looks better. From: Duncan Murdoch Sent: Saturday, February 13, 2021 4:05 PM To: Richard M. Heiberger; R-SIG-Mac Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC 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 *R* sessio n) X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta worked with intel R_4.0.3 on the Mac M1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 3:33 AM To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC 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 XQuartz 2.7.11 instead of the 8.0.3beta. X11() now does not work at all. X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at:
Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC
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 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; Richard M. Heiberger > Cc: e...@lisse.na > Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] > Please test R 4.0.4 RC > > 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/') > 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, d$width, d$height, d$pointsize, : > unable to start device X11 > In addition: Warning messages: > 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : > running command ''otool' -L > '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 > 2: In X11() : unable to open connection to X11 display '' > > > > and the R session is still alive. > > > This rasies for me a different question. Why should I want X11()? > > When X11 was working it was very slow, and didn't allow paging back through > previous images. > > In favor of X11, I think it uses the display space better. X11() has better > size and spacing for xlab, ylab, and main than quartz(). But that isn't a > strong enough > reason to use it while develkoping a graph. When I want it to look good, > I go directly to pdf() and get the spacing that I think looks better. > > > From: Duncan Murdoch > Sent: Saturday, February 13, 2021 4:05 PM > To: Richard M. Heiberger; R-SIG-Mac > Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R > 4.0.4 RC > > 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 *R* sessio n) > > X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > > > My prior was that the xcode call was irrelevant is that X11() using XQuart > 8.0.3beta > worked with intel R_4.0.3 on the Mac M1. > > > From: Dr Eberhard W Lisse > Sent: Saturday, February 13, 2021 3:33 AM > To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger > Cc: e...@lisse.na > Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC > > 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 XQuartz 2.7.11 instead of the > 8.0.3beta. > X11() now does not work at all. > > X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > C-c C-c C-c C-c > > Force-Killing XQuartz from the Activity Monitor doesn't help. > I have to Force-kill the R process. > > > From: R-SIG-Mac on behalf of Simon Urbanek > > Sent: Friday, February 12, 2021 6:50 PM > To: R-SIG-Mac > Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC > > Dear macOS useRs, > > please test the latest R 4.0.4 RC builds from > > https://mac.r-project.org/ > > especially if you are running macOS Big Sur. The known issues introduced by > Big Sur have been fixed, but I cannot replicate nor test the spurious > touchbar warning. > > Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - > they are betas for a reason (=unstable) and break things. > > Cheers, > Simon > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > 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] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC
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; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC 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/') 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, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' and the R session is still alive. This rasies for me a different question. Why should I want X11()? When X11 was working it was very slow, and didn't allow paging back through previous images. In favor of X11, I think it uses the display space better. X11() has better size and spacing for xlab, ylab, and main than quartz(). But that isn't a strong enough reason to use it while develkoping a graph. When I want it to look good, I go directly to pdf() and get the spacing that I think looks better. From: Duncan Murdoch Sent: Saturday, February 13, 2021 4:05 PM To: Richard M. Heiberger; R-SIG-Mac Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC 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 *R* sessio n) X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta worked with intel R_4.0.3 on the Mac M1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 3:33 AM To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC 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 XQuartz 2.7.11 instead of the 8.0.3beta. X11() now does not work at all. X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun C-c C-c C-c C-c Force-Killing XQuartz from the Activity Monitor doesn't help. I have to Force-kill the R process. From: R-SIG-Mac on behalf of Simon Urbanek Sent: Friday, February 12, 2021 6:50 PM To: R-SIG-Mac Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC Dear macOS useRs, please test the latest R 4.0.4 RC builds from https://mac.r-project.org/ especially if you are running macOS Big Sur. The known issues introduced by Big Sur have been fixed, but I cannot replicate nor test the spurious touchbar warning. Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - they are betas for a reason (=unstable) and break things. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ 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] Re: [External] Please test R 4.0.4 RC
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: 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/') > system("Applications/Xquartz") sh: Applications/Xquartz: No such file or directory Warning message: In system("Applications/Xquartz") : error in running command > system("/Applications/Xquartz") sh: /Applications/Xquartz: No such file or directory Warning message: In system("/Applications/Xquartz") : error in running command > system("/Applications/Utilities/Xquartz") sh: /Applications/Utilities/Xquartz: No such file or directory Warning message: In system("/Applications/Utilities/Xquartz") : error in running command > system("/Applications/Utilities/Xquartz.app") sh: /Applications/Utilities/Xquartz.app: is a directory > system("/Applications/Utilities/Xquartz.app/Contents/MacOS/X11") > 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, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' > system("/Applications/Utilities/Xquartz.app/Contents/MacOS/X11") > ## from the Cmd-Tab I opened Xquartz, and from its Applications I opened > xterm, and then ran an ls in xterm. it works. > X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' > Sys.getenv("DISPLAY") [1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0" > unlink(Sys.getenv("DISPLAY")) >Sys.setenv(DISPLAY=":0.0") > X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' > From: Simon Urbanek Sent: Saturday, February 13, 2021 5:35 PM To: Richard M. Heiberger Cc: Dr Eberhard W Lisse; R-SIG-Mac Subject: Re: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC Richard, thanks - finally a more complete output to go on. This is exactly the reminder why it is so important to post the _full_output - the actual facts were completely missing from your previous report. Firstly, the xcrun output is just a warning which indicates that R can't find out whether you have XQuartz installed or not. It also shows that your Xcode/command line tools are broken. That in itself is not a problem as long as you don't intend to compile packages - but probably you should look into it. But more importantly your XQuartz doesn't work - or at least is not running at the time you are trying to run X11() in R. Make sure you start XQuartz first (from Applications -> Utilities) and it works. If in doubt, you can wipe it (it lives in /opt/X11) and re-install. Either way, neither seems to be an R issue per se. Cheers, Simon ` > On Feb 14, 2021, at 11:00 AM, Richard M. Heiberger wrote: > > another fresh R session > >> X11(":0") > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : > unable to start device X11 > In addition: Warning messages: > 1: In
[R-SIG-Mac] Unable to change some members of a vector
I have a problem I don’t know how to deal with. I’ve used read.table to create the data frame called msPdf. It contains three vectors: month, site, conc. Some of the site values look like this: MLH\xca. I was able to change that with this command: msPdf$site[13]="MLH”. That seems to have been allowed because some of the other sites are simply MLH. But the system won’t let me make the same kind of change in another case: msPdf$site[29]="MUH”. When I ask for that, I get Warning message: In `[<-.factor`(`*tmp*`, 29, value = c(5L, 2L, 1L, 11L, 5L, 12L, : invalid factor level, NA generated > #13 May MLH\xca 0.007 Then if I enter msPdf$site[29], I get this response: [1] Levels: CrCr LMO MCE MCH MFSC MLE MLH MLH\xca MUE MUH\xca NFSC SFSC In other words, although other sites that were just plain MLH, there were not other sites that were just plain MUH. How can I fix this problem? I have no idea why excel added those \xca bits to a few of the site values. ___ 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] Re: [External] Please test R 4.0.4 RC
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. If you downgrade, you have to re-compile anything you compiled against the beta. That is probably one of the lesser evils since you can't expect anything to be forwards-compatible. In theory, you could detect the version using otool - that's what X11() is doing to find whether XQuartz is present, but it only works for users that have dev tools installed, so not a good idea in general. Okay, thanks. I already have a no-X11 workaround; I'll just change the error message if the dyn.load() fails. Duncan Cheers, Simon On Feb 14, 2021, at 11:32 AM, Duncan Murdoch wrote: 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" since it tries to start XQuartz even if you don't want it]. Thanks. Here's another datum: I did my last build of rgl with the beta XQuartz installed. I'm now back to 2.7.11 and I get this when I try to start rgl: library(rgl) Error in dyn.load(dynlib) : unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libX11.6.dylib Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so Reason: Incompatible library version: rgl.so requires version 11.0.0 or later, but libX11.6.dylib provides version 10.0.0 Error: package or namespace load failed for ‘rgl’: .onLoad failed in loadNamespace() for 'rgl', details: call: NULL error:Loading rgl's DLL failed. This build of rgl depends on XQuartz, which you can download from xquartz.org. So it appears they updated the version of libX11.6.dylib, and rgl is asking for the wrong one. Is there some way for me to request a particular version during my build, or at least detect that the wrong version is installed? Duncan Murdoch Cheers, Simon On Feb 14, 2021, at 9:50 AM, 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 *R* sessio n) X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta worked with intel R_4.0.3 on the Mac M1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 3:33 AM To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC 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 XQuartz 2.7.11 instead of the 8.0.3beta. X11() now does not work at all. X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun C-c C-c C-c C-c Force-Killing XQuartz from the Activity Monitor doesn't help. I have to Force-kill the R process. From: R-SIG-Mac on behalf of Simon Urbanek Sent: Friday, February 12, 2021 6:50 PM To: R-SIG-Mac Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC Dear macOS useRs, please test the latest R 4.0.4 RC builds from https://mac.r-project.org/ especially if you are running macOS Big Sur. The known issues introduced by Big Sur have been fixed, but I cannot replicate nor test the spurious touchbar warning. Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - they are betas for a reason (=unstable) and break things. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org
Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC
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 you compiled against the beta. That is probably one of the lesser evils since you can't expect anything to be forwards-compatible. In theory, you could detect the version using otool - that's what X11() is doing to find whether XQuartz is present, but it only works for users that have dev tools installed, so not a good idea in general. Cheers, Simon > On Feb 14, 2021, at 11:32 AM, Duncan Murdoch wrote: > > 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" since it tries to start >> XQuartz even if you don't want it]. > > Thanks. Here's another datum: I did my last build of rgl with the beta > XQuartz installed. I'm now back to 2.7.11 and I get this when I try to start > rgl: > > > library(rgl) > Error in dyn.load(dynlib) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so': > dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so, > 6): Library not loaded: /opt/X11/lib/libX11.6.dylib > Referenced from: > /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so > Reason: Incompatible library version: rgl.so requires version 11.0.0 or > later, but libX11.6.dylib provides version 10.0.0 > Error: package or namespace load failed for ‘rgl’: > .onLoad failed in loadNamespace() for 'rgl', details: > call: NULL > error: Loading rgl's DLL failed. > This build of rgl depends on XQuartz, which you can download from > xquartz.org. > > So it appears they updated the version of libX11.6.dylib, and rgl is asking > for the wrong one. > > Is there some way for me to request a particular version during my build, or > at least detect that the wrong version is installed? > > Duncan Murdoch > >> Cheers, >> Simon >>> On Feb 14, 2021, at 9:50 AM, 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 *R* sessio n) >>> X11() >>> xcrun: error: invalid active developer path >>> (/Library/Developer/CommandLineTools), missing xcrun at: >>> /Library/Developer/CommandLineTools/usr/bin/xcrun >>> >>> >>> My prior was that the xcode call was irrelevant is that X11() using XQuart >>> 8.0.3beta >>> worked with intel R_4.0.3 on the Mac M1. >>> >>> >>> From: Dr Eberhard W Lisse >>> Sent: Saturday, February 13, 2021 3:33 AM >>> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger >>> Cc: e...@lisse.na >>> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC >>> >>> 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 XQuartz 2.7.11 instead of the >>> 8.0.3beta. >>> X11() now does not work at all. >>> >>> X11() >>> xcrun: error: invalid active developer path >>> (/Library/Developer/CommandLineTools), missing xcrun at: >>> /Library/Developer/CommandLineTools/usr/bin/xcrun >>> C-c C-c C-c C-c >>> >>> Force-Killing XQuartz from the Activity Monitor doesn't help. >>> I have to Force-kill the R process. >>> >>> >>> From: R-SIG-Mac on behalf of Simon >>> Urbanek >>> Sent: Friday, February 12, 2021 6:50 PM >>> To: R-SIG-Mac >>> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC >>> >>> Dear macOS useRs, >>> >>> please test the latest R 4.0.4 RC builds from >>> >>> https://mac.r-project.org/ >>> >>> especially if you are running macOS Big Sur. The known issues introduced by >>> Big Sur have been fixed, but I cannot replicate nor test the spurious >>> touchbar warning. >>> >>> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - >>> they are betas for a reason (=unstable) and break things. >>> >>> Cheers, >>> Simon >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> ___ >>> 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] Re: [External] Please test R 4.0.4 RC
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 whether you have XQuartz installed or not. It also shows that your Xcode/command line tools are broken. That in itself is not a problem as long as you don't intend to compile packages - but probably you should look into it. But more importantly your XQuartz doesn't work - or at least is not running at the time you are trying to run X11() in R. Make sure you start XQuartz first (from Applications -> Utilities) and it works. If in doubt, you can wipe it (it lives in /opt/X11) and re-install. Either way, neither seems to be an R issue per se. Cheers, Simon ` > On Feb 14, 2021, at 11:00 AM, Richard M. Heiberger wrote: > > 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 addition: Warning messages: > 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : > running command ''otool' -L > '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 > 2: In X11(":0") : unable to open connection to X11 display ':0' >> > > > From: Simon Urbanek > Sent: Saturday, February 13, 2021 4:54 PM > To: Richard M. Heiberger > Cc: Dr Eberhard W Lisse; R-SIG-Mac > Subject: Re: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC > > 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 don't want it]. > > Cheers, > Simon > > >> On Feb 14, 2021, at 9:50 AM, 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 *R* sessio n) >> >>> X11() >> xcrun: error: invalid active developer path >> (/Library/Developer/CommandLineTools), missing xcrun at: >> /Library/Developer/CommandLineTools/usr/bin/xcrun >> >> >> My prior was that the xcode call was irrelevant is that X11() using XQuart >> 8.0.3beta >> worked with intel R_4.0.3 on the Mac M1. >> >> >> From: Dr Eberhard W Lisse >> Sent: Saturday, February 13, 2021 3:33 AM >> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger >> Cc: e...@lisse.na >> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC >> >> 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 XQuartz 2.7.11 instead of the >> 8.0.3beta. >> X11() now does not work at all. >> >> X11() >> xcrun: error: invalid active developer path >> (/Library/Developer/CommandLineTools), missing xcrun at: >> /Library/Developer/CommandLineTools/usr/bin/xcrun >> C-c C-c C-c C-c >> >> Force-Killing XQuartz from the Activity Monitor doesn't help. >> I have to Force-kill the R process. >> >> >> From: R-SIG-Mac on behalf of Simon Urbanek >> >> Sent: Friday, February 12, 2021 6:50 PM >> To: R-SIG-Mac >> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC >> >> Dear macOS useRs, >> >> please test the latest R 4.0.4 RC builds from >> >> https://mac.r-project.org/ >> >> especially if you are running macOS Big Sur. The known issues introduced by >> Big Sur have been fixed, but I cannot replicate nor test the spurious >> touchbar warning. >> >> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - >> they are betas for a reason (=unstable) and break things. >> >> Cheers, >> Simon >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > ___ 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] Re: [External] Please test R 4.0.4 RC
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" since it tries to start XQuartz even if you don't want it]. Thanks. Here's another datum: I did my last build of rgl with the beta XQuartz installed. I'm now back to 2.7.11 and I get this when I try to start rgl: > library(rgl) Error in dyn.load(dynlib) : unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libX11.6.dylib Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so Reason: Incompatible library version: rgl.so requires version 11.0.0 or later, but libX11.6.dylib provides version 10.0.0 Error: package or namespace load failed for ‘rgl’: .onLoad failed in loadNamespace() for 'rgl', details: call: NULL error:Loading rgl's DLL failed. This build of rgl depends on XQuartz, which you can download from xquartz.org. So it appears they updated the version of libX11.6.dylib, and rgl is asking for the wrong one. Is there some way for me to request a particular version during my build, or at least detect that the wrong version is installed? Duncan Murdoch Cheers, Simon On Feb 14, 2021, at 9:50 AM, 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 *R* sessio n) X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta worked with intel R_4.0.3 on the Mac M1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 3:33 AM To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC 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 XQuartz 2.7.11 instead of the 8.0.3beta. X11() now does not work at all. X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun C-c C-c C-c C-c Force-Killing XQuartz from the Activity Monitor doesn't help. I have to Force-kill the R process. From: R-SIG-Mac on behalf of Simon Urbanek Sent: Friday, February 12, 2021 6:50 PM To: R-SIG-Mac Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC Dear macOS useRs, please test the latest R 4.0.4 RC builds from https://mac.r-project.org/ especially if you are running macOS Big Sur. The known issues introduced by Big Sur have been fixed, but I cannot replicate nor test the spurious touchbar warning. Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - they are betas for a reason (=unstable) and break things. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ 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] Re: [External] Re: [External] Please test R 4.0.4 RC
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 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 addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' > Sys.getenv("DISPLAY") [1] ":0.0" > I didn't make any more changes to the Xquartz. I previously had the beta and replaced it with 2.7.11, so I just continued from there. From: Duncan Murdoch Sent: Saturday, February 13, 2021 4:55 PM To: Richard M. Heiberger; R-SIG-Mac Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC 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 the system. Now running x11() in R causes the spinning beach ball. The workaround: Start R. The DISPLAY environment variable will show the name something like [1] "/private/tmp/com.apple.launchd.RuLLnvteCn/org.xquartz:0" This is a socket, not a regular file. Delete this, and set DISPLAY to ":0.0": unlink(Sys.getenv("DISPLAY")) Sys.setenv(DISPLAY=":0.0") Now x11() is fine. This is only a workaround. The unlink() is permanent, but setting the environment variable only lasts for the length of the R session. You'll need to enter Sys.setenv(DISPLAY=":0.0") again in future sessions, and I would guess the socket will be recreated the next time you restart the system (or maybe on login). Duncan Murdoch On 13/02/2021 4:21 p.m., Richard M. Heiberger wrote: > 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$display, d$width, d$height, d$pointsize, : >unable to start device X11 > In addition: Warning messages: > 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : >running command ''otool' -L > '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 > 2: In X11() : unable to open connection to X11 display '' >> > > > and the R session is still alive. > > > This rasies for me a different question. Why should I want X11()? > > When X11 was working it was very slow, and didn't allow paging back through > previous images. > > In favor of X11, I think it uses the display space better. X11() has better > size and spacing for xlab, ylab, and main than quartz(). But that isn't a > strong enough > reason to use it while develkoping a graph. When I want it to look good, > I go directly to pdf() and get the spacing that I think looks better. > > > From: Duncan Murdoch > Sent: Saturday, February 13, 2021 4:05 PM > To: Richard M. Heiberger; R-SIG-Mac > Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R > 4.0.4 RC > > 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 *R* sessio n) >> >>> X11() >> xcrun: error: invalid active developer path >> (/Library/Developer/CommandLineTools), missing xcrun at: >> /Library/Developer/CommandLineTools/usr/bin/xcrun >> >> >> My prior was that the xcode call was irrelevant is that X11() using XQuart >> 8.0.3beta >> worked with intel R_4.0.3 on the Mac M1. >> >> >> From: Dr Eberhard W Lisse >> Sent: Saturday, February 13, 2021 3:33 AM >> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger >> Cc: e...@lisse.na >> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC >> >> 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 XQuartz 2.7.11 instead of the >> 8.0.3beta. >> X11() now does not work at all. >> >> X11() >> xcrun: error: invalid
Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC
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 addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11(":0") : unable to open connection to X11 display ':0' > From: Simon Urbanek Sent: Saturday, February 13, 2021 4:54 PM To: Richard M. Heiberger Cc: Dr Eberhard W Lisse; R-SIG-Mac Subject: Re: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC 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 don't want it]. Cheers, Simon > On Feb 14, 2021, at 9:50 AM, 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 *R* sessio n) > >> X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > > > My prior was that the xcode call was irrelevant is that X11() using XQuart > 8.0.3beta > worked with intel R_4.0.3 on the Mac M1. > > > From: Dr Eberhard W Lisse > Sent: Saturday, February 13, 2021 3:33 AM > To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger > Cc: e...@lisse.na > Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC > > 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 XQuartz 2.7.11 instead of the > 8.0.3beta. > X11() now does not work at all. > > X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > C-c C-c C-c C-c > > Force-Killing XQuartz from the Activity Monitor doesn't help. > I have to Force-kill the R process. > > > From: R-SIG-Mac on behalf of Simon Urbanek > > Sent: Friday, February 12, 2021 6:50 PM > To: R-SIG-Mac > Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC > > Dear macOS useRs, > > please test the latest R 4.0.4 RC builds from > > https://mac.r-project.org/ > > especially if you are running macOS Big Sur. The known issues introduced by > Big Sur have been fixed, but I cannot replicate nor test the spurious > touchbar warning. > > Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - > they are betas for a reason (=unstable) and break things. > > Cheers, > Simon > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ 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] Re: [External] Re: [External] Please test R 4.0.4 RC
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 the system. Now running x11() in R causes the spinning beach ball. The workaround: Start R. The DISPLAY environment variable will show the name something like [1] "/private/tmp/com.apple.launchd.RuLLnvteCn/org.xquartz:0" This is a socket, not a regular file. Delete this, and set DISPLAY to ":0.0": unlink(Sys.getenv("DISPLAY")) Sys.setenv(DISPLAY=":0.0") Now x11() is fine. This is only a workaround. The unlink() is permanent, but setting the environment variable only lasts for the length of the R session. You'll need to enter Sys.setenv(DISPLAY=":0.0") again in future sessions, and I would guess the socket will be recreated the next time you restart the system (or maybe on login). Duncan Murdoch On 13/02/2021 4:21 p.m., Richard M. Heiberger wrote: 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$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' and the R session is still alive. This rasies for me a different question. Why should I want X11()? When X11 was working it was very slow, and didn't allow paging back through previous images. In favor of X11, I think it uses the display space better. X11() has better size and spacing for xlab, ylab, and main than quartz(). But that isn't a strong enough reason to use it while develkoping a graph. When I want it to look good, I go directly to pdf() and get the spacing that I think looks better. From: Duncan Murdoch Sent: Saturday, February 13, 2021 4:05 PM To: Richard M. Heiberger; R-SIG-Mac Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC 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 *R* sessio n) X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta worked with intel R_4.0.3 on the Mac M1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 3:33 AM To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC 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 XQuartz 2.7.11 instead of the 8.0.3beta. X11() now does not work at all. X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun C-c C-c C-c C-c Force-Killing XQuartz from the Activity Monitor doesn't help. I have to Force-kill the R process. From: R-SIG-Mac on behalf of Simon Urbanek Sent: Friday, February 12, 2021 6:50 PM To: R-SIG-Mac Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC Dear macOS useRs, please test the latest R 4.0.4 RC builds from https://mac.r-project.org/ especially if you are running macOS Big Sur. The known issues introduced by Big Sur have been fixed, but I cannot replicate nor test the spurious touchbar warning. Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - they are betas for a reason (=unstable) and break things. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ 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] Re: [External] Please test R 4.0.4 RC
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 don't want it]. Cheers, Simon > On Feb 14, 2021, at 9:50 AM, 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 *R* sessio n) > >> X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > > > My prior was that the xcode call was irrelevant is that X11() using XQuart > 8.0.3beta > worked with intel R_4.0.3 on the Mac M1. > > > From: Dr Eberhard W Lisse > Sent: Saturday, February 13, 2021 3:33 AM > To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger > Cc: e...@lisse.na > Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC > > 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 XQuartz 2.7.11 instead of the > 8.0.3beta. > X11() now does not work at all. > > X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > C-c C-c C-c C-c > > Force-Killing XQuartz from the Activity Monitor doesn't help. > I have to Force-kill the R process. > > > From: R-SIG-Mac on behalf of Simon Urbanek > > Sent: Friday, February 12, 2021 6:50 PM > To: R-SIG-Mac > Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC > > Dear macOS useRs, > > please test the latest R 4.0.4 RC builds from > > https://mac.r-project.org/ > > especially if you are running macOS Big Sur. The known issues introduced by > Big Sur have been fixed, but I cannot replicate nor test the spurious > touchbar warning. > > Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - > they are betas for a reason (=unstable) and break things. > > Cheers, > Simon > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory"
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 (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 addition: Warning message: > In file(file, "rt") : > cannot open file 'moabsitechem': No such file or directory > > How can I fix this problem? > > ___ > 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] [External] Re: [External] Re: [External] Please test R 4.0.4 RC
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/') > > 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$display, d$width, d$height, d$pointsize, : > unable to start device X11 > In addition: Warning messages: > 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : > running command ''otool' -L > '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 > 2: In X11() : unable to open connection to X11 display '' > > > > > and the R session is still alive. > > > This rasies for me a different question. Why should I want X11()? > > When X11 was working it was very slow, and didn't allow paging back through > previous images. > > In favor of X11, I think it uses the display space better. X11() has better > size and spacing for xlab, ylab, and main than quartz(). But that isn't a > strong enough > reason to use it while develkoping a graph. When I want it to look good, > I go directly to pdf() and get the spacing that I think looks better. > > > From: Duncan Murdoch > Sent: Saturday, February 13, 2021 4:05 PM > To: Richard M. Heiberger; R-SIG-Mac > Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R > 4.0.4 RC > > 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 *R* sessio n) > > > > > X11() > > xcrun: error: invalid active developer path > > (/Library/Developer/CommandLineTools), missing xcrun at: > > /Library/Developer/CommandLineTools/usr/bin/xcrun > > > > > > My prior was that the xcode call was irrelevant is that X11() using XQuart > > 8.0.3beta > > worked with intel R_4.0.3 on the Mac M1. > > > > > > From: Dr Eberhard W Lisse > > Sent: Saturday, February 13, 2021 3:33 AM > > To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger > > Cc: e...@lisse.na > > Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC > > > > 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 XQuartz 2.7.11 instead of the > > 8.0.3beta. > > X11() now does not work at all. > > > > X11() > > xcrun: error: invalid active developer path > > (/Library/Developer/CommandLineTools), missing xcrun at: > > /Library/Developer/CommandLineTools/usr/bin/xcrun > > C-c C-c C-c C-c > > > > Force-Killing XQuartz from the Activity Monitor doesn't help. > > I have to Force-kill the R process. > > > > > > From: R-SIG-Mac on behalf of Simon > > Urbanek > > Sent: Friday, February 12, 2021 6:50 PM > > To: R-SIG-Mac > > Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC > > > > Dear macOS useRs, > > > > please test the latest R 4.0.4 RC builds from > > > > https://mac.r-project.org/ > > > > especially if you are running macOS Big Sur. The known issues introduced by > > Big Sur have been fixed, but I cannot replicate nor test the spurious > > touchbar warning. > > > > Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - > > they are betas for a reason (=unstable) and break things. > > > > Cheers, > > Simon > > > > ___ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > ___ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > ___ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > ___ > 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] [External] Re: [External] Re: [External] Please test R 4.0.4 RC
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$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning messages: 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1 2: In X11() : unable to open connection to X11 display '' > and the R session is still alive. This rasies for me a different question. Why should I want X11()? When X11 was working it was very slow, and didn't allow paging back through previous images. In favor of X11, I think it uses the display space better. X11() has better size and spacing for xlab, ylab, and main than quartz(). But that isn't a strong enough reason to use it while develkoping a graph. When I want it to look good, I go directly to pdf() and get the spacing that I think looks better. From: Duncan Murdoch Sent: Saturday, February 13, 2021 4:05 PM To: Richard M. Heiberger; R-SIG-Mac Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC 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 *R* sessio n) > >> X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > > > My prior was that the xcode call was irrelevant is that X11() using XQuart > 8.0.3beta > worked with intel R_4.0.3 on the Mac M1. > > > From: Dr Eberhard W Lisse > Sent: Saturday, February 13, 2021 3:33 AM > To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger > Cc: e...@lisse.na > Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC > > 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 XQuartz 2.7.11 instead of the > 8.0.3beta. > X11() now does not work at all. > > X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > C-c C-c C-c C-c > > Force-Killing XQuartz from the Activity Monitor doesn't help. > I have to Force-kill the R process. > > > From: R-SIG-Mac on behalf of Simon Urbanek > > Sent: Friday, February 12, 2021 6:50 PM > To: R-SIG-Mac > Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC > > Dear macOS useRs, > > please test the latest R 4.0.4 RC builds from > > https://mac.r-project.org/ > > especially if you are running macOS Big Sur. The known issues introduced by > Big Sur have been fixed, but I cannot replicate nor test the spurious > touchbar warning. > > Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - > they are betas for a reason (=unstable) and break things. > > Cheers, > Simon > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ 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] Re: [External] Please test R 4.0.4 RC
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 *R* sessio n) X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta worked with intel R_4.0.3 on the Mac M1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 3:33 AM To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC 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 XQuartz 2.7.11 instead of the 8.0.3beta. X11() now does not work at all. X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun C-c C-c C-c C-c Force-Killing XQuartz from the Activity Monitor doesn't help. I have to Force-kill the R process. From: R-SIG-Mac on behalf of Simon Urbanek Sent: Friday, February 12, 2021 6:50 PM To: R-SIG-Mac Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC Dear macOS useRs, please test the latest R 4.0.4 RC builds from https://mac.r-project.org/ especially if you are running macOS Big Sur. The known issues introduced by Big Sur have been fixed, but I cannot replicate nor test the spurious touchbar warning. Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - they are betas for a reason (=unstable) and break things. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ 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] Re: [External] Please test R 4.0.4 RC
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: /Library/Developer/CommandLineTools/usr/bin/xcrun My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta worked with intel R_4.0.3 on the Mac M1. From: Dr Eberhard W Lisse Sent: Saturday, February 13, 2021 3:33 AM To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger Cc: e...@lisse.na Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC 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 XQuartz 2.7.11 instead of the 8.0.3beta. X11() now does not work at all. X11() xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun C-c C-c C-c C-c Force-Killing XQuartz from the Activity Monitor doesn't help. I have to Force-kill the R process. From: R-SIG-Mac on behalf of Simon Urbanek Sent: Friday, February 12, 2021 6:50 PM To: R-SIG-Mac Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC Dear macOS useRs, please test the latest R 4.0.4 RC builds from https://mac.r-project.org/ especially if you are running macOS Big Sur. The known issues introduced by Big Sur have been fixed, but I cannot replicate nor test the spurious touchbar warning. Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - they are betas for a reason (=unstable) and break things. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory"
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: Parkhurst, David F. Cc: r-sig-mac@r-project.org Subject: Re: [R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory" 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 confusion is that you may have your Mac set to not display file extensions, and life is generally easier in my opinion if those extensions are turned on. Plenty of advice on the internet as to how to turn this on for all files. Bryan > On Feb 13, 2021, at 1:29 PM, Parkhurst, David F. wrote: > > 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 addition: Warning message: > In file(file, "rt") : > cannot open file 'moabsitechem': No such file or directory > > How can I fix this problem? > > ___ > 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] Problem with read.table in my Mac. "No such file or directory"
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 confusion is that you may have your Mac set to not display file extensions, and life is generally easier in my opinion if those extensions are turned on. Plenty of advice on the internet as to how to turn this on for all files. Bryan > On Feb 13, 2021, at 1:29 PM, Parkhurst, David F. wrote: > > 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 addition: Warning message: > In file(file, "rt") : > cannot open file 'moabsitechem': No such file or directory > > How can I fix this problem? > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory"
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 addition: Warning message: In file(file, "rt") : cannot open file 'moabsitechem': No such file or directory How can I fix this problem? ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac
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 command before invoking R. b) Create a .RData file with nothing in it in the desired directory. Double-click that to automatically set the working directory there in R. c) Use RStudio, which lets you create an Rproj file that serves the same purpose as the .RData file but doesn't risk injecting broken code or old data into your working environment. On February 13, 2021 8:02:54 AM PST, "Parkhurst, David F." wrote: >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, 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 copy that to the clipboard and paste that >into a read.table command in the R console, it comes up as >/Users/DFP/Desktop. But if I try >read.table("\\Users\\DFP\\Desktop\\moabsitechem"), >I get No such file or directory. How can I get that file into a data >frame? >> >> Is there some place in my Mac that I can put the file so I could >enter just the file name, and not the whole path? > >Sorry, forget to answer your actual question: > >You can use getwd() to find the working directory. If you put the file >there, you won't need to specify the path. > >Duncan Murdoch > > [[alternative HTML version deleted]] -- Sent from my phone. Please excuse my brevity. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac
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, 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 > read.table() in a Mac > 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 copy that to the clipboard and paste that into a >> read.table command in the R console, it comes up as /Users/DFP/Desktop. But >> if I try >> read.table("\\Users\\DFP\\Desktop\\moabsitechem"), >> I get No such file or directory. How can I get that file into a data frame? >> >> Is there some place in my Mac that I can put the file so I could enter just >> the file name, and not the whole path? > > It doesn't make sense to use backslashes in the path: macOS will see > those as part of the name, not as path separators. Just use > read.table("/Users/DFP/Desktop/moabsitechm") if that's the filename. > > 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() 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, 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 copy that to the clipboard and paste that into a read.table > command in the R console, it comes up as /Users/DFP/Desktop. But if I try > read.table("\\Users\\DFP\\Desktop\\moabsitechem"), > I get No such file or directory. How can I get that file into a data frame? > > Is there some place in my Mac that I can put the file so I could enter just > the file name, and not the whole path? Sorry, forget to answer your actual question: You can use getwd() to find the working directory. If you put the file there, you won't need to specify the path. 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] How to find the path for a file to be read with read.table() in a Mac
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 read.table() in a Mac 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 copy that to the clipboard and paste that into a read.table > command in the R console, it comes up as /Users/DFP/Desktop. But if I try > read.table("\\Users\\DFP\\Desktop\\moabsitechem"), > I get No such file or directory. How can I get that file into a data frame? > > Is there some place in my Mac that I can put the file so I could enter just > the file name, and not the whole path? It doesn't make sense to use backslashes in the path: macOS will see those as part of the name, not as path separators. Just use read.table("/Users/DFP/Desktop/moabsitechm") if that's the filename. 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] 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, 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 copy that to the clipboard and paste that into a read.table command in the R console, it comes up as /Users/DFP/Desktop. But if I try read.table("\\Users\\DFP\\Desktop\\moabsitechem"), I get No such file or directory. How can I get that file into a data frame? Is there some place in my Mac that I can put the file so I could enter just the file name, and not the whole path? Sorry, forget to answer your actual question: You can use getwd() to find the working directory. If you put the file there, you won't need to specify the path. Duncan Murdoch ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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, 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 copy that to the clipboard and paste that into a read.table command in the R console, it comes up as /Users/DFP/Desktop. But if I try read.table("\\Users\\DFP\\Desktop\\moabsitechem"), I get No such file or directory. How can I get that file into a data frame? Is there some place in my Mac that I can put the file so I could enter just the file name, and not the whole path? It doesn't make sense to use backslashes in the path: macOS will see those as part of the name, not as path separators. Just use read.table("/Users/DFP/Desktop/moabsitechm") if that's the filename. Duncan Murdoch ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac
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 read.table command in the R console, it comes up as /Users/DFP/Desktop. But if I try read.table("\\Users\\DFP\\Desktop\\moabsitechem"), I get No such file or directory. How can I get that file into a data frame? Is there some place in my Mac that I can put the file so I could enter just the file name, and not the whole path? ___ 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] Please test R 4.0.4 RC
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 (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun C-c C-c C-c C-c Force-Killing XQuartz from the Activity Monitor doesn't help. I have to Force-kill the R process. I've received reports about this related to rgl. Some unconfirmed reports suggest that setting Sys.setenv(DISPLAY=":0.0") fixes it. Others say that didn't work. I'm still running the beta, and haven't seen any issues. Maybe I'll try going back to 2.7.11 to see if I can trigger things. Duncan Murdoch ___ 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] Please test R 4.0.4 RC
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 XQuartz 2.7.11 instead of the > 8.0.3beta. > X11() now does not work at all. > > > X11() > xcrun: error: invalid active developer path > (/Library/Developer/CommandLineTools), missing xcrun at: > /Library/Developer/CommandLineTools/usr/bin/xcrun > C-c C-c C-c C-c > > Force-Killing XQuartz from the Activity Monitor doesn't help. > I have to Force-kill the R process. > > > From: R-SIG-Mac on behalf of Simon Urbanek > > Sent: Friday, February 12, 2021 6:50 PM > To: R-SIG-Mac > Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC > > Dear macOS useRs, > > please test the latest R 4.0.4 RC builds from > > https://mac.r-project.org/ > > especially if you are running macOS Big Sur. The known issues introduced by > Big Sur have been fixed, but I cannot replicate nor test the spurious > touchbar warning. > > Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - > they are betas for a reason (=unstable) and break things. > > Cheers, > Simon > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > 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] Please test R 4.0.4 RC
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 which element it is complaining about. If anyone has any leads, let me know. If we ever find a work-arournd, it should be possible to do in the GUI alone so possibly after the release (unlike the Quartz bug which needed changes in core R). Other projects have seen the same issue so it's likely a macOS bug, but the fix that worked for others (re-compile with Xcode 12) did not work for us (the last build was using the latests Xcode 12.4). Cheers, Simon > On Feb 13, 2021, at 3:05 PM, John Fox wrote: > > Dear Simon, > > I'm still seeing the warning on a MacBook Pro with a touchbar running Big Sur: > > --- snip > > 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. > > [R.app GUI 1.74 (7929) x86_64-apple-darwin17.0] > > [History restored from /Users/johnfox/.Rapp.history] > > 2021-02-12 21:00:21.163 R[19677:11057750] 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. > > > sessionInfo() > R version 4.0.4 RC (2021-02-12 r79998) > 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_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] compiler_4.0.4 > > --- snip > > I hope this helps, > John > > John Fox, Professor Emeritus > McMaster University > Hamilton, Ontario, Canada > web: https://socialsciences.mcmaster.ca/jfox/ > > On 2021-02-12 6:50 p.m., Simon Urbanek wrote: >> Dear macOS useRs, >> please test the latest R 4.0.4 RC builds from >> https://mac.r-project.org/ >> especially if you are running macOS Big Sur. The known issues introduced by >> Big Sur have been fixed, but I cannot replicate nor test the spurious >> touchbar warning. >> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - >> they are betas for a reason (=unstable) and break things. >> Cheers, >> Simon >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Optional Libraries, Frameworks and Applications for macOS
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 wrote: > > 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac