[R-SIG-Mac] X11 missing? ... was Re: [R] rgl persp3d bounding box color problem.
Prof Brian Ripley
ripley at stats.ox.ac.uk
Tue Mar 3 17:37:42 CET 2009
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.
>>>>>>>>>
>>>>>>>
>>>>>>> _________________________________________________________________
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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.
>>>>>>>
>>>>>>
>>>>>> ______________________________________________
>>>>>> 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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--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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