[R] R packages install problems linux - X not found (WhiteBoxEL 3)

Marc Schwartz MSchwartz at MedAnalytics.com
Sun Aug 8 21:46:46 CEST 2004

On Sun, 2004-08-08 at 14:10, Dr Mike Waters wrote:


> Thanks for the responses guys.
> I used to have RH9 installed on this machine and I found out about the
> separate developer packages then. I thought that I had got the relevant
> XFree devel package installed, but although it showed up in the rpm database
> as being present, the required files were not present. I did a forced rpm
> upgrade from the WhiteBox updates directory and that problem is now fixed,
> at least for car. Marc, thanks for the pointer on the rgl problem. However,
> I have a slightly different problem with the install of this package. It
> gets through to the point where it tries to make the rgl.so from the various
> .o files and fails then, as follows:
> --------------------------------------------------------------------
> g++ -I/usr/lib/R/include -I/usr/X11R6/include -DHAVE_PNG_H
> -I/usr/include -I/usr/local/include  -Wall -pedantic -fno-exceptions
> -fno-rtti -fPIC  -O2 -g -march=i386 -mcpu=i686 -c glgui.cpp -o glgui.o
> g++  -L/usr/local/lib -o rgl.so x11lib.o x11gui.o types.o math.o fps.o
> pixmap.o gui.o api.o device.o devicemanager.o rglview.o scene.o glgui.o
> -L/usr/X11R6/lib -L/usr/lib -lstdc++ -lX11 -lXext -lGL -lGLU -lpng
> /usr/lib/gcc-lib/i386-redhat-linux/3.2.3/../../../crt1.o(.text+0x18): In
> function `_start':
> : undefined reference to `main'
> x11lib.o(.text+0x84): In function `set_R_handler':
> /tmp/R.INSTALL.13414/rgl/src/x11gui.h:33: undefined reference to
> `R_InputHandlers'
> x11lib.o(.text+0x92):/tmp/R.INSTALL.13414/rgl/src/x11gui.h:33: undefined
> reference to `addInputHandler'
> x11lib.o(.text+0xfb): In function `unset_R_handler':
> /tmp/R.INSTALL.13414/rgl/src/x11lib.cpp:52: undefined reference to
> `R_InputHandlers'
> x11lib.o(.text+0x103):/tmp/R.INSTALL.13414/rgl/src/x11lib.cpp:52:
> undefined reference to `removeInputHandler'
> collect2: ld returned 1 exit status
> make: *** [rgl.so] Error 1
> ERROR: compilation failed for package 'rgl'
> ** Removing '/usr/lib/R/library/rgl'
> ---------------------------------------------------------------------
> No doubt another failed dependency........... DOH!
> Regards

I am concerned by your indications of previously having had RH9 on the
same box and that you had to force an update of the XFree Devel RPM.
Forcing the installation of an RPM is almost always a bad thing.

When you installed WB on the system, did you do a "clean" installation
or some type of "upgrade"?

If the latter, it is reasonable to consider that there may be some level
of mixing and matching of RPMS from the two distributions going on. This
could result in a level of marginally or wholly incompatible versions of
RPMS being installed.

Could you clarify that point?

Also, be sure that you have the same versions of the XFree series RPMS


rpm -qa | grep XFree

in a console and be sure that the RPMS return the same version schema.
If not, it is possible that one of your problems is the mixing of

Take note of the output of the above and be sure that the
XFree86-Mesa-libGL and XFree86-Mesa-libGLU RPMS are installed as well.

Some of the messages above would also suggest a problem finding R
related headers. How did you install R? This may be a red herring of
sorts, given the other problems, but may be helpful.


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