[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 09:43:57 CET 2009
On Mon, 2 Mar 2009, 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
I am using the Apple version of X from Xcode, and building rgl works
for me under an x86_64 build of R: it says
checking for X... libraries /usr/X11/lib, headers /usr/X11/include
checking for glEnd in -lGL... yes
checking for gluProject in -lGLU... yes
...
It's a while since I used XQuartz, but my recollection is that it
used those locations.
rgl's configure uses the standard AC_PATH_X, which supports
X features:
--x-includes=DIR X include files are in DIR
--x-libraries=DIR X library files are in DIR
so that is how you specify the paths if you need to.
I used the command line to do this, as source package builds
ultimately call command-line R as in
~/R/R64/bin/R CMD INSTALL rgl_0.83-751.tar.gz
> 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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>>>>>>
>>>>>>
>>>>>> ______________________________________________
>>>>>> 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/
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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