X11 missing? ... was Re: [R] rgl persp3d bounding box color problem.
Tried that method: The compilation proceeded without error and was reported: <snip quite a bit of material attached as rgl-compile.log> ** building package indices ... * DONE (rgl) However, in R refreshing the Package Manager and attempting to load rgl fails to load with this error report: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Users/davidwinsemius/Library/R/2.8/ library/rgl/libs/x86_64/rgl.so': dlopen(/Users/davidwinsemius/Library/R/2.8/library/rgl/libs/x86_64/ rgl.so, 6): Symbol not found: _FT_Attach_File Referenced from: /Users/davidwinsemius/Library/R/2.8/library/rgl/ libs/x86_64/rgl.so Expected in: dynamic lookup Error : .onLoad failed in 'loadNamespace' for 'rgl' Error: package/namespace load failed for 'rgl' -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: rgl-compile-log.txt URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20090303/0d6ec75e/attachment-0001.txt> -------------- next part -------------- -- thanks for all the eyeballs and ideas David Winsemius
On Mar 3, 2009, at 5:16 PM, Rob Goedman wrote:
David, On my system libpng-config and xmkmf are in /usr/X11/bin, as on your system. Adding /usr/X11/bin to my path did not help. I think /usr/X11R6 is just a link back to /usr/X11. Did you try the terminal suggestion? Download rgl_0.83-3.tar.gz from CRAN, then in a terminal Robs-Intel:~ rob$ pwd /Users/rob Robs-Intel:~ rob$ cd Downloads/ # To wherever the rgl.....tar.gz got stored Robs-Intel:Downloads rob$ ls Cappuccino_Developer_Tools.pkg Changes.app Fluid_0.9.6.zip iphone_sdk_for_iphone_os_2.2.19m2621afinal.dmg rgl_0.83-3.tar.gz ... Robs-Intel:Downloads rob$ R_ARCH=/x86_64 R CMD INSTALL --configure- args='--disable-carbon' rgl_0.83-3.tar.gz * Installing to library ?/Library/Frameworks/R.framework/Resources/ library? * Installing *source* package ?rgl? ... checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no ... I know, it is not the ultimate solution, but it might help to know this works on your system. Rob On Mar 3, 2009, at 1:08 PM, David Winsemius wrote:
I think the problem in my case may be different, (and probably relates to my UNIX-challenged status) since: david-winsemiuss-mac-pro:~ davidwinsemius$ $PATH -bash: /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/ usr/X11/bin: No such file or directory I am not sure what the system is telling me, since there *is* a / usr/X11/bin directory. Bear with me as I navigate to it from the root: bash-3.2$ ls Applications TC.creat.BMI.A- G.r mach_kernel.ctfsys Desktop DB User Guides And Information net Desktop DF Users opt Developer Volumes private Library bin sbin Network cores tempxx.txt Project Planning Spreadsheet v2.xls dev test.html Session Feb 14.ag interact.r etc tmp Session.Feb16,2009.txt home usr System mach_kernel var bash-3.2$ cd usr bash-3.2$ ls X11 bin lib local share texbin X11R6 include libexec sbin standalone bash-3.2$ cd X11 bash-3.2$ ls bin include lib libexec man share var bash-3.2$ cd bin bash-3.2$ ls X fc-cat libpng-config setxkbmap xcutsel xinput xmkmf xtrapin Xephyr fc-list libpng12-config showfont xditview xkbbell xmodmap xtrapinfo Xfake fc-match listres showrgb xdm xkbcomp xmore xtrapout Xnest font_cache lndir startx xdmshell xkbevd xon xtrapproto Xquartz fontname.sh luit sxpm xdpr xkbprint xpr xtrapreset Xvfb fontprop.sh makedepend twm xdpyinfo xkbvleds xprop xtrapstats appres fonttosfnt makeg ucs2any xedit xkbwatch xrandr xvinfo atobm freetype-config makestrs uxterm xev xkill xrdb xwd bdftopcf fslsfonts mergelib viewres xeyes xload xrefresh xwininfo bdftruncate fstobdf mkdirhier x11perf xfd xlogo xset xwud bitmap gccmakedep mkfontdir x11perfcomp xfontsel xlsatoms xsetmode bmtoa glxgears mkfontscale xauth xfs xlsclients xsetpointer ccmakedep glxinfo mkhtmlindex xcalc xfsinfo xlsfonts xsetroot cleanlinks iceauth oclock xclipboard xft- config xmag xsm cxpm ico resize xclock xgc xman xstdcmap editres imake revpath xconsole xhost xmessage xterm fc-cache koi8rxterm sessreg xcursorgen xinit xmh xtrapchar bash-3.2$ -- David Winsemius On Mar 3, 2009, at 11:37 AM, Prof Brian Ripley wrote:
It looks to me as if this is a path issue, as inside the R.app libpng-config is not found. On my system it is in /usr/local/bin. And I think the X configuration expects to find /usr/X11/bin/xmkmf (R's version certainly does). So I suggests putting /usr/local/bin and /usr/X11/bin in your path. (My CRAN build of R.app is showing /usr/local/bin but not /usr/X11/ bin in its path.) There are configure arguments and variables you can use to set all the pieces, but getting the right paths should be easier. On Tue, 3 Mar 2009, Rob Goedman wrote:
David, Apologies if you get this twice, I changed some of my email addresses recently... To install 64-bit rgl, on my system, I install it from within a terminal as shown (abbreviated) below. From inside R.app it always fails. I appended the error I get as well. These listings I think correspond to what you and prof Ripley show in the emails. I also use XQuartz 2.3.. Regards, Rob ----------------In a terminal--------------------------- Robs-Intel:Downloads rob$ R_ARCH=/x86_64 R CMD INSTALL -- configure- args='--disable-carbon' rgl_0.83-3.tar.gz * Installing to library ?/Library/Frameworks/R.framework/Resources/ library? * Installing *source* package ?rgl? ... checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc-4.2 -arch x86_64 - std=gnu99 -E checking for gcc... (cached) gcc-4.2 -arch x86_64 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... (cached) yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... (cached) none needed checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage checking for X... libraries /usr/X11/lib, headers /usr/X11/include checking for glEnd in -lGL... yes checking for gluProject in -lGLU... yes checking for freetype-config... yes configure: using Freetype and FTGL configure: creating ./config.status config.status: creating src/Makevars ** libs ** arch - x86_64 g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/ x86_64 -I/ System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - I/ usr/X11/include/libpng12 -I/usr/X11/include -DDarwin - DNO_GL_PREFIX -I/ usr/X11R6/include -DHAVE_FREETYPE -Iext/ftgl -I/usr/X11/include/ freetype2 -I/usr/X11/include -Iext -I/usr/local/include -g -O2 - fPIC -g -O2 -c BBoxDeco.cpp -o BBoxDeco.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/ x86_64 -I/ System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - I/ usr/X11/include/libpng12 -I/usr/X11/include -DDarwin - DNO_GL_PREFIX -I/ usr/X11R6/include -DHAVE_FREETYPE -Iext/ftgl -I/usr/X11/include/ freetype2 -I/usr/X11/include -Iext -I/usr/local/include -g -O2 - fPIC -g -O2 -c Background.cpp -o Background.o ... g++-4.2 -arch x86_64 -dynamiclib -Wl,- headerpad_max_install_names - undefined dynamic_lookup -single_module -multiply_defined suppress -L/ usr/local/lib -o rgl.so BBoxDeco.o Background.o Color.o Disposable.o Light.o LineSet.o LineStripSet.o Material.o PointSet.o PrimitiveSet.o QuadSet.o RenderContext.o Shape.o SphereMesh.o SphereSet.o SpriteSet.o String.o Surface.o TextSet.o Texture.o Viewpoint.o api.o assert.o callbacks.o device.o devicemanager.o fps.o ftgl.o geom.o gl2ps.o glErrors.o glgui.o gui.o init.o math.o osxgui.o osxlib.o par3d.o pixmap.o render.o rglview.o scene.o select.o win32gui.o win32lib.o x11gui.o x11lib.o -lGLU -lGL -framework OpenGL -dylib_file /System/ Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ libGL.dylib:/ System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ libGL.dylib -L/usr/X11/lib -lpng12 -L/usr/X11/lib -lX11 -L/usr/ X11/ lib -lfreetype -lz -Wl,-framework,CoreServices -Wl,- framework,ApplicationServices -F/Library/Frameworks/ R.framework/.. - framework R -Wl,-framework -Wl,CoreFoundation ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices
Building/Updating help pages for package 'rgl'
Formats: text html latex example 3dobjects text html latex example aspect3d text html latex example axes3d text html latex example bbox text html latex example bg text html latex example ... spin3d text html latex example sprites text html latex example subdivision3d text html latex example surface text html latex example surface3d text html latex example texts text html latex example viewpoint text html latex example ** building package indices ... * DONE (rgl) Robs-Intel:Downloads rob$ ----------------Inside R.app------------------------------------------------------ trying URL 'http://cran.stat.ucla.edu/src/contrib/ rgl_0.83-3.tar.gz' Content type 'application/x-tar' length 1653379 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb * Installing *source* package ?rgl? ... checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc-4.2 -arch x86_64 - std=gnu99 -E checking for gcc... (cached) gcc-4.2 -arch x86_64 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... (cached) yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... (cached) none needed checking for libpng-config... no checking libpng... checking for grep that handles long lines and - e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking png.h usability... no checking png.h presence... no checking for png.h... no checking for png_read_update_info in -lpng... no configure: libpng header and lib found configure: using libpng dynamic linkage checking for X... no configure: error: X11 not found but required, configure aborted. ERROR: configuration failed for package ?rgl? * Removing ?/Library/Frameworks/R.framework/Versions/2.9/Resources/ library/rgl? * Restoring previous ?/Library/Frameworks/R.framework/Versions/2.9/ Resources/library/rgl? The downloaded packages are in ?/private/var/folders/RC/RC96PNSWFMORQM4VyHEgik+++TI/-Tmp-/ RtmpZR2jwu/ downloaded_packages?
On Mar 2, 2009, at 4:13 PM, David Winsemius wrote:
I tried to install the current version of rgl on R-forge from source from the 64 bit R-GUI and get this error during installation : <entire listing copied below> checking for X... no configure: error: X11 not found but required, configure aborted. ERROR: configuration failed for package 'rgl' ** Removing '/Library/Frameworks/R.framework/Resources/library/ rgl' ** Restoring previous '/Library/Frameworks/R.framework/Resources/ library/rgl' The downloaded packages are in /private/var/folders/xS/xSUsVXTIHEiP7OLJg2OXmU+++TI/-Tmp-/ Rtmp3Z2KtQ/downloaded_packages I do have an X11 installation, XQuartz 2.3.1 (xorg-server 1.4.2- apple17), and wonder whether I need to do something to make X11's availability visible to the Installer? I believe that it loads under the 32 bit GUI although the version appears to be 0.82-2. -- David Winsemius
sessionInfo()
R version 2.8.1 Patched (2009-01-07 r47515)
i386-apple-darwin9.6.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] mapproj_1.1-7.2 maps_2.0-40
loaded via a namespace (and not attached):
[1] grid_2.8.1 lattice_0.17-20 tools_2.8.1
Warning message:
In install.packages(c("rgl"), lib = "/Library/Frameworks/
R.framework/
Resources/library/", :
installation of package 'rgl' had non-zero exit status
capabilities()
jpeg png tiff tcltk X11 aqua http/ftp sockets libxml fifo cledit iconv TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NLS profmem cairo TRUE FALSE TRUE ---- intall listing follows---- trying URL 'http://R-Forge.R-project.org/src/contrib/rgl_0.83-751.tar.gz' Content type 'application/x-gzip' length 1656674 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb * Installing *source* package 'rgl' ... checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc-4.2 -arch x86_64 - std=gnu99 -E checking for gcc... (cached) gcc-4.2 -arch x86_64 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... (cached) yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... (cached) none needed checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage checking for X... no configure: error: X11 not found but required, configure aborted. ERROR: configuration failed for package 'rgl' ** Removing '/Library/Frameworks/R.framework/Resources/library/ rgl' ** Restoring previous '/Library/Frameworks/R.framework/Resources/ library/rgl' The downloaded packages are in /private/var/folders/xS/xSUsVXTIHEiP7OLJg2OXmU+++TI/-Tmp-/ Rtmp3Z2KtQ/downloaded_packages ----end listing---- On Mar 2, 2009, at 4:39 PM, Duncan Murdoch wrote:
On 3/2/2009 2:48 PM, chaogai wrote:
Oops, sorry R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE = en_US .UTF -8 ;LC_NUMERIC = C ;LC_TIME = en_US .UTF -8 ;LC_COLLATE = en_US .UTF -8 ;LC_MONETARY = C ;LC_MESSAGES = en_US .UTF -8 ;LC_PAPER = en_US .UTF -8 ;LC_NAME = C ;LC_ADDRESS =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rgl_0.81 svGUI_0.9-44 svSocket_0.9-43 svMisc_0.9-46
0.81 isn't the current version of rgl on CRAN. Please try that one, or even better, the development version on R-forge. Duncan Murdoch
Duncan Murdoch wrote:
On 3/2/2009 2:00 PM, chaogai wrote:
Whatever it is, it is also happening on my Acer, Suse 11.1, 32 bits, self build R.
Versions of R and rgl? Duncan Murdoch
Kees Bo Zhou wrote:
Thanks Duncan. I haven't got a chance to try it in windows yet. But I won't be surprised if it's my driver's fault. I had OpenGL problems on this dell laptop before.....
Date: Sun, 1 Mar 2009 18:29:20 -0500 From: murdoch at stats.uwo.ca To: bozhou1981 at hotmail.com CC: remkoduursma at gmail.com; r-help at r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 01/03/2009 5:54 PM, Bo Zhou wrote:
site down......
here is the code
library(rgl)
plot1:
persp3d(x=1:11,y=1:210,z=matrix(rep(1,11*210),
11,210),col=matrix(rep("#FF0000",11*210),11,210))
plot2:
persp3d(x=1:11,y=1:10,z=matrix(rep(1,11*10),
11,10),col=matrix(rep("#FF0000",11*10),11,10))
Works fine on Mac OS 10.5 too. Looks like a bug in your OpenGL driver... Duncan Murdoch
Thanks! Bo
Date: Mon, 2 Mar 2009 09:28:31 +1100 Subject: Re: [R] rgl persp3d bounding box color problem. From: remkoduursma at gmail.com To: bozhou1981 at hotmail.com I would not mind trying, but the link no longer works... Remko ------------------------------------------------- Remko Duursma Post-Doctoral Fellow Centre for Plant and Food Science University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia Mobile: +61 (0)422 096908 On Mon, Mar 2, 2009 at 8:16 AM, Bo Zhou <bozhou1981 at hotmail.com
wrote:
Thanks, Duncan. What's your platform? Could this be an issues related to my platform? I'm on Ubuntu 8.10 64bit using cran's R package. I built rgl package on my machine using install.packages(). I'm going to give it a try in windows. I would be very grateful if anyone using similar setup could give it a try. Thanks, Bo
Date: Sun, 1 Mar 2009 07:03:10 -0500 From: murdoch at stats.uwo.ca To: bozhou1981 at hotmail.com CC: r-help at r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 28/02/2009 4:20 PM, Bo Zhou wrote:
Hi guys, I hit on a problem when I use rgl. Could you try to run the code here in this link and see why the first persp3d gives a red bounding box and the second shows black?
They both show as black on my system. Duncan Murdoch
http://rafb.net/p/g1i7ur33.html (sorry for not pasting the code here directly but my previous email got filtered by this list so I suspect my code looks like spam to the spam filter) I'm expecting black color to be the right result but the code is virtually same except different data size. Looks like a mem bug to me? BTW you will need to install the rgl package Thanks, Bo
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_________________________________________________________________ [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
_________________________________________________________________ [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
_________________________________________________________________ Hotmail? is up to 70% faster. Now good news travels really fast. [[alternative HTML version deleted]] ------------------------------------------------------------------------ ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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On Mar 2, 2009, at 4:13 PM, David Winsemius wrote:
I tried to install the current version of rgl on R-forge from source from the 64 bit R-GUI and get this error during installation : <entire listing copied below> checking for X... no configure: error: X11 not found but required, configure aborted. ERROR: configuration failed for package 'rgl' ** Removing '/Library/Frameworks/R.framework/Resources/library/ rgl' ** Restoring previous '/Library/Frameworks/R.framework/Resources/ library/rgl' The downloaded packages are in /private/var/folders/xS/xSUsVXTIHEiP7OLJg2OXmU+++TI/-Tmp-/ Rtmp3Z2KtQ/downloaded_packages I do have an X11 installation, XQuartz 2.3.1 (xorg-server 1.4.2- apple17), and wonder whether I need to do something to make X11's availability visible to the Installer? I believe that it loads under the 32 bit GUI although the version appears to be 0.82-2. -- David Winsemius
sessionInfo()
R version 2.8.1 Patched (2009-01-07 r47515)
i386-apple-darwin9.6.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] mapproj_1.1-7.2 maps_2.0-40
loaded via a namespace (and not attached):
[1] grid_2.8.1 lattice_0.17-20 tools_2.8.1
Warning message:
In install.packages(c("rgl"), lib = "/Library/Frameworks/
R.framework/
Resources/library/", :
installation of package 'rgl' had non-zero exit status
capabilities()
jpeg png tiff tcltk X11 aqua http/ftp sockets libxml fifo cledit iconv TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NLS profmem cairo TRUE FALSE TRUE ---- intall listing follows---- trying URL 'http://R-Forge.R-project.org/src/contrib/rgl_0.83-751.tar.gz' Content type 'application/x-gzip' length 1656674 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb * Installing *source* package 'rgl' ... checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc-4.2 -arch x86_64 - std=gnu99 -E checking for gcc... (cached) gcc-4.2 -arch x86_64 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... (cached) yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... (cached) none needed checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage checking for X... no configure: error: X11 not found but required, configure aborted. ERROR: configuration failed for package 'rgl' ** Removing '/Library/Frameworks/R.framework/Resources/library/ rgl' ** Restoring previous '/Library/Frameworks/R.framework/Resources/ library/rgl' The downloaded packages are in /private/var/folders/xS/xSUsVXTIHEiP7OLJg2OXmU+++TI/-Tmp-/ Rtmp3Z2KtQ/downloaded_packages ----end listing---- On Mar 2, 2009, at 4:39 PM, Duncan Murdoch wrote:
On 3/2/2009 2:48 PM, chaogai wrote:
Oops, sorry R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE = en_US .UTF -8 ;LC_NUMERIC = C ;LC_TIME = en_US .UTF -8 ;LC_COLLATE = en_US .UTF -8 ;LC_MONETARY = C ;LC_MESSAGES = en_US .UTF -8 ;LC_PAPER = en_US .UTF -8 ;LC_NAME = C ;LC_ADDRESS =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rgl_0.81 svGUI_0.9-44 svSocket_0.9-43 svMisc_0.9-46
0.81 isn't the current version of rgl on CRAN. Please try that one, or even better, the development version on R-forge. Duncan Murdoch
Duncan Murdoch wrote:
On 3/2/2009 2:00 PM, chaogai wrote:
Whatever it is, it is also happening on my Acer, Suse 11.1, 32 bits, self build R.
Versions of R and rgl? Duncan Murdoch
Kees Bo Zhou wrote:
Thanks Duncan. I haven't got a chance to try it in windows yet. But I won't be surprised if it's my driver's fault. I had OpenGL problems on this dell laptop before.....
Date: Sun, 1 Mar 2009 18:29:20 -0500 From: murdoch at stats.uwo.ca To: bozhou1981 at hotmail.com CC: remkoduursma at gmail.com; r-help at r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 01/03/2009 5:54 PM, Bo Zhou wrote:
site down......
here is the code
library(rgl)
plot1:
persp3d(x=1:11,y=1:210,z=matrix(rep(1,11*210),
11,210),col=matrix(rep("#FF0000",11*210),11,210))
plot2:
persp3d(x=1:11,y=1:10,z=matrix(rep(1,11*10),
11,10),col=matrix(rep("#FF0000",11*10),11,10))
Works fine on Mac OS 10.5 too. Looks like a bug in your OpenGL driver... Duncan Murdoch
Thanks! Bo
Date: Mon, 2 Mar 2009 09:28:31 +1100 Subject: Re: [R] rgl persp3d bounding box color problem. From: remkoduursma at gmail.com To: bozhou1981 at hotmail.com I would not mind trying, but the link no longer works... Remko ------------------------------------------------- Remko Duursma Post-Doctoral Fellow Centre for Plant and Food Science University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia Mobile: +61 (0)422 096908 On Mon, Mar 2, 2009 at 8:16 AM, Bo Zhou <bozhou1981 at hotmail.com
wrote:
Thanks, Duncan. What's your platform? Could this be an issues related to my platform? I'm on Ubuntu 8.10 64bit using cran's R package. I built rgl package on my machine using install.packages(). I'm going to give it a try in windows. I would be very grateful if anyone using similar setup could give it a try. Thanks, Bo
Date: Sun, 1 Mar 2009 07:03:10 -0500 From: murdoch at stats.uwo.ca To: bozhou1981 at hotmail.com CC: r-help at r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 28/02/2009 4:20 PM, Bo Zhou wrote:
Hi guys, I hit on a problem when I use rgl. Could you try to run the code here in this link and see why the first persp3d gives a red bounding box and the second shows black?
They both show as black on my system. Duncan Murdoch
http://rafb.net/p/g1i7ur33.html (sorry for not pasting the code here directly but my previous email got filtered by this list so I suspect my code looks like spam to the spam filter) I'm expecting black color to be the right result but the code is virtually same except different data size. Looks like a mem bug to me? BTW you will need to install the rgl package Thanks, Bo
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