[R-SIG-Mac] X11 missing? ... was Re: [R] rgl persp3d bounding box color problem.
David Winsemius
dwinsemius at comcast.net
Tue Mar 3 22:08:36 CET 2009
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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _________________________________________________________________
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> [[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.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>> _________________________________________________________________
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> [[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.
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _________________________________________________________________
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> [[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.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>> _________________________________________________________________
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> [[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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>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>
> --
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
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