Re: [R-SIG-Mac] X11 missing? ... was Re: [R] rgl persp3d bounding box color problem.

Rob Goedman Tue, 03 Mar 2009 14:17:23 -0800

David,

On my system libpng-config and xmkmf are in /usr/X11/bin, as on yoursystem.Adding /usr/X11/bin to my path did not help. I think /usr/X11R6 isjust 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.gzgot 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 knowthis 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 probablyrelates 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.ctfsysDesktop DB User Guides AndInformation netDesktop DFUsers optDeveloperVolumes privateLibrarybin sbinNetworkcores tempxx.txtProject Planning Spreadsheet v2.xlsdev test.htmlSession Feb 14.ag interact.retc tmpSession.Feb16,2009.txthome usrSystemmach_kernel var


bash-3.2$ cd usr
bash-3.2$ ls

X11 bin lib localshare texbinX11R6 include libexec sbinstandalone


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 setxkbmapxcutsel xinput xmkmf xtrapinXephyr fc-list libpng12-config showfontxditview xkbbell xmodmap xtrapinfoXfake fc-match listres showrgbxdm xkbcomp xmore xtrapoutXnest font_cache lndir startxxdmshell xkbevd xon xtrapprotoXquartz fontname.sh luit sxpmxdpr xkbprint xpr xtrapresetXvfb fontprop.sh makedepend twmxdpyinfo xkbvleds xprop xtrapstatsappres fonttosfnt makeg ucs2anyxedit xkbwatch xrandr xvinfoatobm freetype-config makestrs uxtermxev xkill xrdb xwdbdftopcf fslsfonts mergelib viewresxeyes xload xrefresh xwininfobdftruncate fstobdf mkdirhier x11perfxfd xlogo xset xwudbitmap gccmakedep mkfontdir x11perfcompxfontsel xlsatoms xsetmodebmtoa glxgears mkfontscale xauthxfs xlsclients xsetpointerccmakedep glxinfo mkhtmlindex xcalcxfsinfo xlsfonts xsetrootcleanlinks iceauth oclock xclipboard xft-config xmag xsmcxpm ico resize xclockxgc xman xstdcmapeditres imake revpath xconsolexhost xmessage xtermfc-cache koi8rxterm sessreg xcursorgenxinit 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.applibpng-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 allthe 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 emailaddresses

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 aswell.

These listings I think correspond to what you and prof Ripley showin

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.oPrimitiveSet.oQuadSet.o RenderContext.o Shape.o SphereMesh.o SphereSet.oSpriteSet.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 adirectory

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 fromsource

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 loadsunder

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 methodsbase


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'tbe

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: murd...@stats.uwo.ca
To: bozhou1...@hotmail.com
CC: remkoduur...@gmail.com; r-h...@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 yourOpenGL

driver...

Duncan Murdoch

Thanks!

Bo

Date: Mon, 2 Mar 2009 09:28:31 +1100
Subject: Re: [R] rgl persp3d bounding box color problem.
From: remkoduur...@gmail.com
To: bozhou1...@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 <bozhou1...@hotmail.com

wrote:

Thanks, Duncan.

What's your platform? Could this be an issues related tomyplatform? I'm on Ubuntu 8.10 64bit using cran's Rpackage. Ibuilt rgl package on my machine usinginstall.packages(). I'm

going to give it a try in windows.

I would be very grateful if anyone using similar setupcould

give it a try.

Thanks,
Bo

Date: Sun, 1 Mar 2009 07:03:10 -0500
From: murd...@stats.uwo.ca
To: bozhou1...@hotmail.com
CC: r-h...@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 andsee whythe first persp3d gives a red bounding box and thesecond
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 codelooks

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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and provide commented, minimal, self-contained,
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_________________________________________________________________


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______________________________________________
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible
code.


______________________________________________
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproduciblecode.


______________________________________________
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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: