Re: [R-SIG-Mac] Yosemite and R
Update on my issue: Upon reinstalling Xquartz, as suggested, all of my previous issues went away. -Ben -- Benjamin Y. Clark, PhD Assistant Professor of Public Administration (Levin College) Assistant Professor of Public Health (CEOMPH) Cleveland State University Executive Committee Member Association for Budgeting and Financial Management (ABFM) b.y.clark[at]csuohio.edu bit.ly/BenClark From: John Fox j...@mcmaster.ca Sent: Thursday, October 23, 2014 2:15 PM To: 'Simon Urbanek' Cc: 'Amos B. Elberg'; 'r-sig-mac'; 'Spencer Mass'; Benjamin Y Clark; 'peter dalgaard'; 'Marc Schwartz'; 'David Winsemius'; 'Hadley Wickham' Subject: RE: [R-SIG-Mac] Yosemite and R Dear Simon, I installed Yosemite a couple of days ago and everything seems to work fine so far, including the tcltk demo that caused problems for Peter, and the Rcmdr package, which gives Tcl/Tk a pretty good workout. I first reinstalled XQuartz, as suggested, and I also reinstalled R and updated all packages, though the latter two steps probably weren't necessary. I figured that it would help to hear positive experiences as well as problems. The only issue that I've encountered so far is specific to checking packages under RStudio, which doesn't appear to find pdflatex; OTOH, R CMD check runs fine in a terminal window. I haven't yet tried to resolve this problem. Best, John -Original Message- From: Simon Urbanek [mailto:simon.urba...@r-project.org] Sent: Tuesday, October 21, 2014 4:38 PM To: John Fox Cc: Amos B. Elberg; r-sig-mac; Spencer Mass; Ben Clark; peter dalgaard; Marc Schwartz; David Winsemius; Hadley Wickham Subject: Re: [R-SIG-Mac] Yosemite and R I wasn't able to reproduce but I suspect those are all red herrings - there are really no subprocesses involved at all in either case. On Oct 21, 2014, at 4:19 PM, John Fox j...@mcmaster.ca wrote: Dear all, I wonder whether this issue also accounts for the tcltk problems that have been reported. (I haven't yet upgraded to Yosemite myself, hoping to wait for the wrinkles to be ironed out, though I'll likely do so shortly if only to see what happens.) Best, John -Original Message- From: r-sig-mac-boun...@r-project.org [mailto:r-sig-mac-bounces@r- project.org] On Behalf Of Amos B. Elberg Sent: Tuesday, October 21, 2014 12:40 PM To: David Winsemius; Hadley Wickham Cc: r-sig-mac; Spencer Mass Subject: Re: [R-SIG-Mac] Yosemite and R If the full environment isn’t getting passed to R-spawned sub- processes, that might explain an error I’ve been having since the update: when R is launched from the command line, calls that should create an X11 window in the background fail unless an X11 window has already been created with the width and height specified: plot(rnorm(100)) Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : invalid 'width' or 'height' X11() Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : invalid 'width' or 'height' X11(width = 5, height = 5) plot(rnorm(100)) [now it works - and any number of additional windows can be spawned without repeating the error] [quitting R and reopening, without quitting XQuartz, and I get the same error calling plot() before X11(width = , height = ) This does not happen in RStudio. I don’t use the R.app gui; I opened it just now to test and I got a slew of path-related errors, but they’re as likely to have to do with my not-maintained R.app as with anything else. I had not reported this already because I wasn’t confident whether its a yosemite issue, an R-patched issue, or just something odd in the way I built R. If incomplete-environment-passing is the new normal, is this not going to be a common issue for packages that spawn sub-processes? From: Hadley Wickham h.wick...@gmail.com Reply: Hadley Wickham h.wick...@gmail.com Date: October 21, 2014 at 10:12:13 AM To: David Winsemius dwinsem...@comcast.net Cc: r-sig-mac r-sig-mac@r-project.org, Spencer Mass ma...@newpaltz.edu Subject: Re: [R-SIG-Mac] Yosemite and R No, it is not. It is expected that the path in the terminal be different to the path in R, it is _not_ expected that the path in R be different to the path in a subprocess started by R. (Well it is now expected, because this appears to be a new security feature in Yosemite) The best thread I could find on the problem is here: https://code.google.com/p/mactlmgr/issues/detail?id=102 -- http://had.co.nz/ ___ 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] Yosemite and R
Hi John, Regarding your issue in RStudio and pdflatex -- this is a general problem with any applications not launched from the terminal; presumedly it would be seen in R.app as well when not launched from the terminal (this is related to the forward-PATH-to-subprocesses problem discussed earlier) There is a prescription available on StackOverflow: http://stackoverflow.com/questions/26491934/running-system-command-from-r-console-cannot-locate-installed-programs-since-upg Cheers, Kevin On Thu, Oct 23, 2014 at 11:18 AM, Benjamin Y Clark b.y.cl...@csuohio.edu wrote: Update on my issue: Upon reinstalling Xquartz, as suggested, all of my previous issues went away. -Ben -- Benjamin Y. Clark, PhD Assistant Professor of Public Administration (Levin College) Assistant Professor of Public Health (CEOMPH) Cleveland State University Executive Committee Member Association for Budgeting and Financial Management (ABFM) b.y.clark[at]csuohio.edu bit.ly/BenClark From: John Fox j...@mcmaster.ca Sent: Thursday, October 23, 2014 2:15 PM To: 'Simon Urbanek' Cc: 'Amos B. Elberg'; 'r-sig-mac'; 'Spencer Mass'; Benjamin Y Clark; 'peter dalgaard'; 'Marc Schwartz'; 'David Winsemius'; 'Hadley Wickham' Subject: RE: [R-SIG-Mac] Yosemite and R Dear Simon, I installed Yosemite a couple of days ago and everything seems to work fine so far, including the tcltk demo that caused problems for Peter, and the Rcmdr package, which gives Tcl/Tk a pretty good workout. I first reinstalled XQuartz, as suggested, and I also reinstalled R and updated all packages, though the latter two steps probably weren't necessary. I figured that it would help to hear positive experiences as well as problems. The only issue that I've encountered so far is specific to checking packages under RStudio, which doesn't appear to find pdflatex; OTOH, R CMD check runs fine in a terminal window. I haven't yet tried to resolve this problem. Best, John -Original Message- From: Simon Urbanek [mailto:simon.urba...@r-project.org] Sent: Tuesday, October 21, 2014 4:38 PM To: John Fox Cc: Amos B. Elberg; r-sig-mac; Spencer Mass; Ben Clark; peter dalgaard; Marc Schwartz; David Winsemius; Hadley Wickham Subject: Re: [R-SIG-Mac] Yosemite and R I wasn't able to reproduce but I suspect those are all red herrings - there are really no subprocesses involved at all in either case. On Oct 21, 2014, at 4:19 PM, John Fox j...@mcmaster.ca wrote: Dear all, I wonder whether this issue also accounts for the tcltk problems that have been reported. (I haven't yet upgraded to Yosemite myself, hoping to wait for the wrinkles to be ironed out, though I'll likely do so shortly if only to see what happens.) Best, John -Original Message- From: r-sig-mac-boun...@r-project.org [mailto:r-sig-mac-bounces@r- project.org] On Behalf Of Amos B. Elberg Sent: Tuesday, October 21, 2014 12:40 PM To: David Winsemius; Hadley Wickham Cc: r-sig-mac; Spencer Mass Subject: Re: [R-SIG-Mac] Yosemite and R If the full environment isn’t getting passed to R-spawned sub- processes, that might explain an error I’ve been having since the update: when R is launched from the command line, calls that should create an X11 window in the background fail unless an X11 window has already been created with the width and height specified: plot(rnorm(100)) Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : invalid 'width' or 'height' X11() Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : invalid 'width' or 'height' X11(width = 5, height = 5) plot(rnorm(100)) [now it works - and any number of additional windows can be spawned without repeating the error] [quitting R and reopening, without quitting XQuartz, and I get the same error calling plot() before X11(width = , height = ) This does not happen in RStudio. I don’t use the R.app gui; I opened it just now to test and I got a slew of path-related errors, but they’re as likely to have to do with my not-maintained R.app as with anything else. I had not reported this already because I wasn’t confident whether its a yosemite issue, an R-patched issue, or just something odd in the way I built R. If incomplete-environment-passing is the new normal, is this not going to be a common issue for packages that spawn sub-processes? From: Hadley Wickham h.wick...@gmail.com Reply: Hadley Wickham h.wick...@gmail.com Date: October 21, 2014 at 10:12:13 AM To: David Winsemius dwinsem...@comcast.net Cc: r-sig-mac r-sig-mac@r-project.org, Spencer Mass ma...@newpaltz.edu Subject: Re: [R-SIG-Mac] Yosemite and R No, it is not. It is expected that the path in the terminal be different to the path in R, it is _not_ expected that the path in R be different to the path in a subprocess started by R. (Well it is
[R-SIG-Mac] sh: convert: command not found
Dear Mac R community,
I wonder if anyone else has come across this issue. After installing the
new Mac OS10.10 Yosemite, I am now having a strange problem.
I'm trying to use movie3d and run similar functions based on this I have
written myself.
Specifically, when I run
system(convert --version)
sh: convert: command not found
yet, it is not a path issue.
Sys.getenv(PATH)
[1]
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:
*/opt/ImageMagick/bin*:/usr/texbin
This shows clearly that the imagemagick path is listed (and so isn't the
same as the problem in this previous discussion:
http://r.789695.n4.nabble.com/convert-command-not-found-in-movie3d-rgl-package-in-Mac-OS-X-td4320734.html
)
Also, in Terminal,
echo $PATH
/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/git/bin:
*/opt/ImageMagick/bin*:/usr/texbin
The only way I have been able to get it to work is:
system(/opt/ImageMagick/bin/convert --version)
[1] Version: ImageMagick 6.8.9-8 Q16 x86_64 2014-10-08
http://www.imagemagick.org;
[2] Copyright: Copyright (C) 1999-2014 ImageMagick Studio LLC
[3] Features: DPC OpenCL
[4] Delegates: bzlib fftw jng jpeg lcms lzma png tiff webp xml zlib
[5]
However, this workaround does not work for me using movie3d{rgl}
Any ideas most appreciated
Emma
~~~
Emma Sherratt, PhD.
Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L118 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5038
email: emma.sherr...@une.edu.au
Caecilians are legless amphibians...
* __
(\ .-. .-. /_)
\\_//^\\_//^\\_//
`` `` ``*
learn more about them here: www.emmasherratt.com/caecilians
[[alternative HTML version deleted]]
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Re: [R-SIG-Mac] sh: convert: command not found
On Oct 24, 2014, at 12:22 AM, Emma Sherratt emma.sherr...@gmail.com wrote:
Dear Mac R community,
I wonder if anyone else has come across this issue. After installing the
new Mac OS10.10 Yosemite, I am now having a strange problem.
I'm trying to use movie3d and run similar functions based on this I have
written myself.
Specifically, when I run
system(convert --version)
sh: convert: command not found
yet, it is not a path issue.
Sys.getenv(PATH)
[1]
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:
*/opt/ImageMagick/bin*:/usr/texbin
It is, because Yosemite ignores PATH for processes started from a GUI
application. You will see if you run
system(echo $PATH)
You have to use full paths in Yosemite for anything that is not on the
sanctioned PATH -- or use R from the shell.
Cheers,
Simon
This shows clearly that the imagemagick path is listed (and so isn't the
same as the problem in this previous discussion:
http://r.789695.n4.nabble.com/convert-command-not-found-in-movie3d-rgl-package-in-Mac-OS-X-td4320734.html
)
Also, in Terminal,
echo $PATH
/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/git/bin:
*/opt/ImageMagick/bin*:/usr/texbin
The only way I have been able to get it to work is:
system(/opt/ImageMagick/bin/convert --version)
[1] Version: ImageMagick 6.8.9-8 Q16 x86_64 2014-10-08
http://www.imagemagick.org;
[2] Copyright: Copyright (C) 1999-2014 ImageMagick Studio LLC
[3] Features: DPC OpenCL
[4] Delegates: bzlib fftw jng jpeg lcms lzma png tiff webp xml zlib
[5]
However, this workaround does not work for me using movie3d{rgl}
Any ideas most appreciated
Emma
~~~
Emma Sherratt, PhD.
Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L118 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5038
email: emma.sherr...@une.edu.au
Caecilians are legless amphibians...
* __
(\ .-. .-. /_)
\\_//^\\_//^\\_//
`` `` ``*
learn more about them here: www.emmasherratt.com/caecilians
[[alternative HTML version deleted]]
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Re: [R-SIG-Mac] sh: convert: command not found
On Oct 24, 2014, at 1:10 AM, Marc Girondot marc_...@yahoo.fr wrote:
Look at here:
http://max2.ese.u-psud.fr/epc/conservation/Girondot/Publications/Blog_r/Entrees/2014/7/6_Using_system()_in_MacOSX.html
I think it is the solution.
Nope - that only applies for systems before Yosemite (and the former is in the
FAQ - no need to quote a random blog ;)).
Cheers,
S
Sincerely,
Marc
Le 24/10/2014 06:22, Emma Sherratt a écrit :
Dear Mac R community,
I wonder if anyone else has come across this issue. After installing the
new Mac OS10.10 Yosemite, I am now having a strange problem.
I'm trying to use movie3d and run similar functions based on this I have
written myself.
Specifically, when I run
system(convert --version)
sh: convert: command not found
yet, it is not a path issue.
Sys.getenv(PATH)
[1]
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:
*/opt/ImageMagick/bin*:/usr/texbin
This shows clearly that the imagemagick path is listed (and so isn't the
same as the problem in this previous discussion:
http://r.789695.n4.nabble.com/convert-command-not-found-in-movie3d-rgl-package-in-Mac-OS-X-td4320734.html
)
Also, in Terminal,
echo $PATH
/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/git/bin:
*/opt/ImageMagick/bin*:/usr/texbin
The only way I have been able to get it to work is:
system(/opt/ImageMagick/bin/convert --version)
[1] Version: ImageMagick 6.8.9-8 Q16 x86_64 2014-10-08
http://www.imagemagick.org;
[2] Copyright: Copyright (C) 1999-2014 ImageMagick Studio LLC
[3] Features: DPC OpenCL
[4] Delegates: bzlib fftw jng jpeg lcms lzma png tiff webp xml zlib
[5]
However, this workaround does not work for me using movie3d{rgl}
Any ideas most appreciated
Emma
~~~
Emma Sherratt, PhD.
Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L118 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5038
email: emma.sherr...@une.edu.au
Caecilians are legless amphibians...
* __
(\ .-. .-. /_)
\\_//^\\_//^\\_//
`` `` ``*
learn more about them here: www.emmasherratt.com/caecilians
[[alternative HTML version deleted]]
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