Re: [R-SIG-Mac] Lion and X11
I tried CRAN R again, and could NOT reproduce this error, at least not this time. Maybe I inadvertently used my own compiled version last time I tried CRAN R. I may try the folks at homebrew to trace this issue. Thank you so much to everybody who chimed in. Cheers, Martin On 28 Jan 2012, at 20:35 , Simon Urbanek wrote: Martin, On Jan 28, 2012, at 9:31 PM, Simon Urbanek wrote: On Jan 28, 2012, at 8:21 PM, Martin Renner wrote: Thank you to everybody who replied! Simon, on my machine, I can reproduce this segfault every time using these steps: - open Terminal.app (or iTerm or Aquamacs), start R --vanilla (RStudio, or R.app) in R: - x11() (in Terminal, my R defaults to x11, without me doing anything; in R.app or RStudio, I call x11() to reproduce this segfault. - plot (1:10) or any other plotting command. Can you send us your sessionInfo(), please? Never mind - you did in your first e-mail. But from that info it is clear that you're not using CRAN R, so I fear we can't really help you since this problem is specific to your own R build. You should try the R release on CRAN to see if you can reproduce it with that. If not, you may want to use gdb to trace the issue (R -d gdb) - it could be R or some library you're using ... If you want us to look int that, you'd have to provide exact details on how you compiled that R (compiler versions, configure flags etc.). Cheers, Simon I am not aware of any other conscious or subconscious steps I'm taking. Plotting to quartz() or pdf() works fine. My .bashrc sets R_LIBS and the usual additions to the default PATH, nothing that should affect R or x11. Since I haven't heard back a flood of people saying, 'yes, me too', I suspect, this issue is specific to my setup. I've tried clearing out any preference files related to x11, to no affect. When calling plot (1:10), I get a new x11 graphics window, ten circles and an x-axis with tick-marks, and a segfault. No box(), no y-axis. There's no .Rprofile in my home directory. Are there any other preference files that could be corrupted? My display variable looks fine, so Christian seems to have a different issue than me. Sys.getenv (DISPLAY) [1] /tmp/launch-EepjEz/org.x:0 Cheers, Martin On 28 Jan 2012, at 10:17 , Simon Urbanek wrote: Martin, can you specify more precisely what you're doing? Issuing the code you sent would use Quartz, so apparently you're doing other things that you didn't mention - so can you share those so we can try to reproduce it? Thanks, Simon On Jan 27, 2012, at 7:17 PM, Martin Renner wrote: Hi All, Is anybody else experiencing problems with X11 and R under Mac OS X 10.7 (Lion)? If yes, maybe it's not specific to my machine. R segfaults when I try to plot to a X11 device, e.g. open R in the terminal and calling plot (1:10) (see below). Plotting to a quartz device works fine. I'm using R-2.14.1 (see below), compiled from source using homebrew. I've seen the same issue with the CRAN binaries, with a vanilla compile from source of R-2.14.1 and even with an old R-2.9.2. I wonder whether I'd have to wait for a fix from Apple, or whether there's a work-around like something that can be done during configuration? Cheers, Martin plot (1:10) *** caught segfault *** address 0x0, cause 'memory not mapped' Traceback: 1: axis(side = side, at = at, labels = labels, ...) 2: Axis.default(...) 3: Axis(...) 4: localAxis(if (is.null(y)) xy$x else x, side = 1, ...) 5: plot.default(1:10) 6: plot(1:10) sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin11.2.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Lion and X11
For what it is worth I don't see this problem on Snow Leopard, self-compiled. You can make quartz the default device by putting Sys.setenv(R_INTERACTIVE_DEVICE = quartz) in your .Rprofile. Kasper On Fri, Jan 27, 2012 at 7:17 PM, Martin Renner greatauk...@gmail.com wrote: Hi All, Is anybody else experiencing problems with X11 and R under Mac OS X 10.7 (Lion)? If yes, maybe it's not specific to my machine. R segfaults when I try to plot to a X11 device, e.g. open R in the terminal and calling plot (1:10) (see below). Plotting to a quartz device works fine. I'm using R-2.14.1 (see below), compiled from source using homebrew. I've seen the same issue with the CRAN binaries, with a vanilla compile from source of R-2.14.1 and even with an old R-2.9.2. I wonder whether I'd have to wait for a fix from Apple, or whether there's a work-around like something that can be done during configuration? Cheers, Martin plot (1:10) *** caught segfault *** address 0x0, cause 'memory not mapped' Traceback: 1: axis(side = side, at = at, labels = labels, ...) 2: Axis.default(...) 3: Axis(...) 4: localAxis(if (is.null(y)) xy$x else x, side = 1, ...) 5: plot.default(1:10) 6: plot(1:10) sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin11.2.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ 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] Lion and X11
Martin, can you specify more precisely what you're doing? Issuing the code you sent would use Quartz, so apparently you're doing other things that you didn't mention - so can you share those so we can try to reproduce it? Thanks, Simon On Jan 27, 2012, at 7:17 PM, Martin Renner wrote: Hi All, Is anybody else experiencing problems with X11 and R under Mac OS X 10.7 (Lion)? If yes, maybe it's not specific to my machine. R segfaults when I try to plot to a X11 device, e.g. open R in the terminal and calling plot (1:10) (see below). Plotting to a quartz device works fine. I'm using R-2.14.1 (see below), compiled from source using homebrew. I've seen the same issue with the CRAN binaries, with a vanilla compile from source of R-2.14.1 and even with an old R-2.9.2. I wonder whether I'd have to wait for a fix from Apple, or whether there's a work-around like something that can be done during configuration? Cheers, Martin plot (1:10) *** caught segfault *** address 0x0, cause 'memory not mapped' Traceback: 1: axis(side = side, at = at, labels = labels, ...) 2: Axis.default(...) 3: Axis(...) 4: localAxis(if (is.null(y)) xy$x else x, side = 1, ...) 5: plot.default(1:10) 6: plot(1:10) sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin11.2.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Lion and X11
On Jan 28, 2012, at 1:46 PM, cstrato wrote: Yes, although I have started X11.app and run R from within an xterm I get: plot(1:8) No protocol specified Error in X11(d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, : unable to start device X11 In addition: Warning message: In function (display = , width, height, pointsize, gamma, bg, : unable to open connection to X11 display '' Chances are that you DISPLAY is unset - you possibly messed with it in your startup files so R can't use X11 unless you give it the proper display. On a clean OS X you will see it set properly, e.g.: Sys.getenv(DISPLAY) [1] /tmp/launch-byCZTH/org.x:0 Please check that your DISPLAY is set (and that you don't mess with R options, either). This is setting is automatic on SL/Lion. Cheers, Simon sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base I have never had this problem on Snow Leopard, Leopard or Tiger! Does someone have an idea what might be the reason? Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l:cstrato at aon.at _._._._._._._._._._._._._._._._._._ ___ 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] Lion and X11
Dear Simon, Thank you for your replies, I understand now your explanation about R.app. I do not think that the topic on the locale is unrelated to the plot problem, since adding to .bashrc: export LC_CTYPE=en_US.UTF-8 export LC_ALL=en_US.UTF-8 does solve the problem with plot(), as you can see from the following output: Sys.getenv(DISPLAY) [1] :0 sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base plot(1:8) It is still not clear to me why I need to add above lines to .bashrc, since on my Snow Leopard machine this is not necessary. The locale there is also only C. BTW, to run R I start always X11.app first and then start R from xterm, I do not use the Terminal. Best regards Christian On 1/29/12 12:03 AM, Simon Urbanek wrote: On Jan 28, 2012, at 1:46 PM, cstrato wrote: Yes, although I have started X11.app and run R from within an xterm I get: plot(1:8) No protocol specified Error in X11(d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, : unable to start device X11 In addition: Warning message: In function (display = , width, height, pointsize, gamma, bg, : unable to open connection to X11 display '' Chances are that you DISPLAY is unset - you possibly messed with it in your startup files so R can't use X11 unless you give it the proper display. On a clean OS X you will see it set properly, e.g.: Sys.getenv(DISPLAY) [1] /tmp/launch-byCZTH/org.x:0 Please check that your DISPLAY is set (and that you don't mess with R options, either). This is setting is automatic on SL/Lion. Cheers, Simon sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base I have never had this problem on Snow Leopard, Leopard or Tiger! Does someone have an idea what might be the reason? Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l:cstrato at aon.at _._._._._._._._._._._._._._._._._._ ___ 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] Lion and X11
Martin, On Jan 28, 2012, at 9:31 PM, Simon Urbanek wrote: On Jan 28, 2012, at 8:21 PM, Martin Renner wrote: Thank you to everybody who replied! Simon, on my machine, I can reproduce this segfault every time using these steps: - open Terminal.app (or iTerm or Aquamacs), start R --vanilla (RStudio, or R.app) in R: - x11() (in Terminal, my R defaults to x11, without me doing anything; in R.app or RStudio, I call x11() to reproduce this segfault. - plot (1:10) or any other plotting command. Can you send us your sessionInfo(), please? Never mind - you did in your first e-mail. But from that info it is clear that you're not using CRAN R, so I fear we can't really help you since this problem is specific to your own R build. You should try the R release on CRAN to see if you can reproduce it with that. If not, you may want to use gdb to trace the issue (R -d gdb) - it could be R or some library you're using ... If you want us to look int that, you'd have to provide exact details on how you compiled that R (compiler versions, configure flags etc.). Cheers, Simon I am not aware of any other conscious or subconscious steps I'm taking. Plotting to quartz() or pdf() works fine. My .bashrc sets R_LIBS and the usual additions to the default PATH, nothing that should affect R or x11. Since I haven't heard back a flood of people saying, 'yes, me too', I suspect, this issue is specific to my setup. I've tried clearing out any preference files related to x11, to no affect. When calling plot (1:10), I get a new x11 graphics window, ten circles and an x-axis with tick-marks, and a segfault. No box(), no y-axis. There's no .Rprofile in my home directory. Are there any other preference files that could be corrupted? My display variable looks fine, so Christian seems to have a different issue than me. Sys.getenv (DISPLAY) [1] /tmp/launch-EepjEz/org.x:0 Cheers, Martin On 28 Jan 2012, at 10:17 , Simon Urbanek wrote: Martin, can you specify more precisely what you're doing? Issuing the code you sent would use Quartz, so apparently you're doing other things that you didn't mention - so can you share those so we can try to reproduce it? Thanks, Simon On Jan 27, 2012, at 7:17 PM, Martin Renner wrote: Hi All, Is anybody else experiencing problems with X11 and R under Mac OS X 10.7 (Lion)? If yes, maybe it's not specific to my machine. R segfaults when I try to plot to a X11 device, e.g. open R in the terminal and calling plot (1:10) (see below). Plotting to a quartz device works fine. I'm using R-2.14.1 (see below), compiled from source using homebrew. I've seen the same issue with the CRAN binaries, with a vanilla compile from source of R-2.14.1 and even with an old R-2.9.2. I wonder whether I'd have to wait for a fix from Apple, or whether there's a work-around like something that can be done during configuration? Cheers, Martin plot (1:10) *** caught segfault *** address 0x0, cause 'memory not mapped' Traceback: 1: axis(side = side, at = at, labels = labels, ...) 2: Axis.default(...) 3: Axis(...) 4: localAxis(if (is.null(y)) xy$x else x, side = 1, ...) 5: plot.default(1:10) 6: plot(1:10) sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin11.2.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ 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] Lion and X11
Hi All, Is anybody else experiencing problems with X11 and R under Mac OS X 10.7 (Lion)? If yes, maybe it's not specific to my machine. R segfaults when I try to plot to a X11 device, e.g. open R in the terminal and calling plot (1:10) (see below). Plotting to a quartz device works fine. I'm using R-2.14.1 (see below), compiled from source using homebrew. I've seen the same issue with the CRAN binaries, with a vanilla compile from source of R-2.14.1 and even with an old R-2.9.2. I wonder whether I'd have to wait for a fix from Apple, or whether there's a work-around like something that can be done during configuration? Cheers, Martin plot (1:10) *** caught segfault *** address 0x0, cause 'memory not mapped' Traceback: 1: axis(side = side, at = at, labels = labels, ...) 2: Axis.default(...) 3: Axis(...) 4: localAxis(if (is.null(y)) xy$x else x, side = 1, ...) 5: plot.default(1:10) 6: plot(1:10) sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin11.2.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
