R help - Aug 2004 - R packages install problems linux - X not found (WhiteBoxEL 3)

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.

Marc

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

> 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.
>
> Marc
>
> ______________________________________________

Marc,

Sorry for the confusion yesterday - in my defence, it was very hot and humid
here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). 

What had happened was that I had done a clean install of WB Linux, including
the XFree86 and other developer packages. However, the on-line updating
system updated the XFree86 packages to a newer sub version. It seems that it
didn't do this correctly for the XFree86 developer package, which was
missing vital files. However it showed up in the rpm database as being
installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another
rpm for this manually and I only forced the upgrade because it was the same
version as already 'installed' (as far as the rpm database was
concerned). I
assumed that all dependencies were sorted out through the install in the
first place.

I only mentioned RH9 to show that I had some familiarity with the RedHat
policy of separating out the 'includes' etc into a separate developer
package.

Once all this had been sorted out, I was then left with a compilation error
which pointed to a missing dependency or similar, which was not due to
missing developer packages, but, as you and Prof Ripley correctly point out,
from the R installation itself. Having grown fat and lazy on using R under
the MS Windows environment, I was struggling to identify the precise nature
of this remaining problem.

As regards the R installation, I did this from the RH9 binary for version
1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate
here. Perhaps I should now compile from the source instead?

Regards

M