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

[Martyn Plummer]

On Sun, 2004-08-08 at 22:22, Prof Brian Ripley wrote:
> 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.

This could be my fault. It transpires that this is not set correctly in
the RPMs for RH9 and 8.x.  I will look into it (this is most probably
due to a missing BuildRequires).  This isn't the first time someone has
had this problem. I apologize for not fixing it, but at the time I was
convinced the RPMS were OK.

Martyn