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

[Prof Brian Ripley]

On Sun, 8 Aug 2004, Marc Schwartz wrote:

> On Sun, 2004-08-08 at 14:10, Dr Mike Waters wrote:
> 
> snip
> 
> > 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
> installed.
> 
> Use:
> 
> 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
> versions.
> 
> 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.

I think it is the exact point.  Those entry points are in R.bin, 
so should be missing.  The g++ line is missing `-shared', which is picked 
up from R_HOME/etc/Makeconf, specifically from

SHLIB_CXXLDFLAGS = -shared

So the R installation doesn't have the right flags.

-- 
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