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installing "rgl" package

14 messages · Rolf Turner, Dirk Eddelbuettel, Duncan Murdoch +1 more

Original
Santosh
# 
Hi Rxperts,
I am trying to install 'rgl' package in Ubuntu.. Would highly appreciate
your assistance .. I tried several leads available on various discussion
fora and nothing helped so far.


* installing *source* package ?rgl? ...checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -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 , headers
checking GL/gl.h usability... yes
checking GL/gl.h presence... yes
checking for GL/gl.h... yes
checking GL/glu.h usability... yes
checking GL/glu.h presence... yes
checking for GL/glu.h... yes
checking for glEnd in -lGL... noconfigure: error: missing required
library GLERROR: configuration failed for package ?rgl?* removing
?/data/R/lib/rgl?Warning in install.packages :
  installation of package ?rgl? had non-zero exit status

Checking the system dependencies based on README..

system('dpkg -l |grep  libgl1')ii  libgl1-mesa-dev
  10.1.3-0ubuntu0.6                       amd64        free
implementation of the OpenGL API -- GLX development files
ii  libglu1-mesa-dev                      9.0.0-2
           amd64        Mesa OpenGL utility library -- development
files
ii  libpng12-dev                          1.2.50-1ubuntu2.14.04.2
           amd64        PNG library - development

I also tried installing .. using the following command..
install.packages("rgl",dep=T,
INSTALL_opts="--no-multiarch",
configure.args=c(rgl="--with-gl-includes=/usr/include/GL"))

Thanks so much for your help!
Santosh
Duncan Murdoch
#
On 23/11/2017 6:05 PM, Santosh wrote:
Your message is really hard to follow, since you posted in HTML.  You 
need the OpenGL development packages.  On Ubuntu, that probably means 
MesaGL, but I don't know the names of the development packages.

Duncan Murdoch
Rolf Turner
#
On 24/11/17 12:10, Duncan Murdoch wrote:
The installation of rgl runs without complaint on my system, so 
apparently I have whatever libraries are needed.

I did "apt-show-versions | grep mesa" on my laptop (a trick I just 
learned from Berwin Turlach; thanks Berwin!) and got a slew of bumff:
(There were also a bunch of lines referring to i386 versions not being
installed; I deleted these to save space.)

So it would seem that you need to do at least:

     sudo apt-get install libegl1-mesa
     sudo apt-get install libegl1-mesa-dev

Doing this may result in the other bumff that is referred to getting 
installed automatically.  Try it and see if it works.  If not, keep 
doing the sudo apt-get install thing to the other bits and pieces until 
it does work.

Hope this helps; kind of a case of the blind leading the blind, but I 
*think* this should get you going with rgl.

cheers,

Rolf Turner
Dirk Eddelbuettel
#
On 23 November 2017 at 15:05, Santosh wrote:
| I am trying to install 'rgl' package in Ubuntu.. Would highly appreciate
| your assistance .. I tried several leads available on various discussion
| fora and nothing helped so far.

Install the _pre-built binary package_ via

    sudo apt install r-cran-rgl

Dirk
Santosh
# 
Hi All, Duncan, Rolf, Ista, DIrk,

Thanks for the suggestions and I tried all of them (as suggested by Duncan,
Rolf, Ista and Dirk)... I still get similar error as before while
installing 'rgl' package.. I also tried to manually configure "rgl" and got
an error message (please see below for the verbatim output).  Would highly
any further ideas/suggestions!

*In my system, "GL" library is present under "/usr/include/GL"*

Here are the libraries available (as suggested by Rolf)

After installing some of them, I continue to get the same error message,
please below the output messages in config.log after I ran "./configure")


"ii  r-cran-rgl                            0.93.996-1
        amd64        GNU R package for three-dimensional visualisation
using OpenGL"

"ii  libegl1-mesa:amd64                    10.1.3-0ubuntu0.6
       amd64        free implementation of the EGL API -- runtime"

"ii  libegl1-mesa-dev                      10.1.3-0ubuntu0.6
       amd64        free implementation of the EGL API -- development files"

"ii  libegl1-mesa-drivers:amd64            10.1.3-0ubuntu0.6
       amd64        free implementation of the EGL API -- hardware drivers"

"ii  libgl1-mesa-dev                       10.1.3-0ubuntu0.6
       amd64        free implementation of the OpenGL API -- GLX
development files"

"ii  libgl1-mesa-dri:amd64                 10.1.3-0ubuntu0.6
       amd64        free implementation of the OpenGL API -- DRI modules"


"ii  libgl1-mesa-glx:amd64                 10.1.3-0ubuntu0.6
       amd64        free implementation of the OpenGL API -- GLX runtime"


"ii  libglapi-mesa:amd64                   10.1.3-0ubuntu0.6
       amd64        free implementation of the GL API -- shared library"

"ii  libglu1-mesa:amd64                    9.0.0-2
       amd64        Mesa OpenGL utility library (GLU)"

"ii  libglu1-mesa-dev                      9.0.0-2
       amd64        Mesa OpenGL utility library -- development files"

"ii  libwayland-client0:amd64              1.4.0-1ubuntu1
        amd64        wayland compositor infrastructure - client library"

"ii  libwayland-cursor0:amd64              1.4.0-1ubuntu1
        amd64        wayland compositor infrastructure - cursor library"

"ii  libwayland-dev                        1.4.0-1ubuntu1
        amd64        wayland compositor infrastructure - development files"

"ii  libwayland-egl1-mesa:amd64            10.1.3-0ubuntu0.6
       amd64        implementation of the Wayland EGL platform -- runtime"

"ii  libwayland-server0:amd64              1.4.0-1ubuntu1
        amd64        wayland compositor infrastructure - server library"

"ii  mesa-common-dev                       10.1.3-0ubuntu0.6
       amd64        Developer documentation for Mesa"

"ii  mesa-vdpau-drivers:amd64              10.1.3-0ubuntu0.6
       amd64        Mesa VDPAU video acceleration drivers"

"ii  mesa-utils                            8.1.0-2
       amd64        Miscellaneous Mesa GL utilities"


The error message when installing "rgl" library,

* installing *source* package ?rgl? ...

checking for gcc... gcc -std=gnu99

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc -std=gnu99 accepts -g... yes

checking for gcc -std=gnu99 option to accept ISO C89... none needed

checking how to run the C preprocessor... gcc -std=gnu99 -E

checking for gcc... (cached) gcc -std=gnu99

checking whether we are using the GNU C compiler... (cached) yes

checking whether gcc -std=gnu99 accepts -g... (cached) yes

checking for gcc -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 , headers

checking GL/gl.h usability... yes

checking GL/gl.h presence... yes

checking for GL/gl.h... yes

checking GL/glu.h usability... yes

checking GL/glu.h presence... yes

checking for GL/glu.h... yes

checking for glEnd in -lGL... no

configure: error: missing required library GL

ERROR: configuration failed for package ?rgl?

* removing ?/data/R/lib/rgl?

Warning in install.packages :

  installation of package ?rgl? had non-zero exit status


The error message as seen in config.log (after manually running
"./configure" under "rgl")

configure:4263: checking for glEnd in -lGL
configure:4288: gcc -std=gnu99 -o conftest -g -O2 -fstack-protector
--param=ssp-buffer-size=4 -Wformat -Werror=format-security
-D_FORTIFY_SOURCE=2 -g  -DHAVE_PNG_H -I/usr/include/libpng12
conftest.c -lGL   -L/usr/lib/x86_64-linux-gnu -lpng12 -lX11
collect2: error: ld returned 1 exit status
configure:4288: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_GL_GL_H 1
| #define HAVE_GL_GLU_H 1
| /* end confdefs.h.  */
|
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char glEnd ();
| int
| main ()
| {
| return glEnd ();
|   ;
|   return 0;
| }configure:4298: result: no
configure:4311: error: missing required library GL

Thanks a ton, again!
Santosh
On Fri, Nov 24, 2017 at 5:13 AM, Dirk Eddelbuettel <edd at debian.org> wrote:

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
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On 24/11/2017 2:30 PM, Santosh wrote:

            

      
      
      
    

        
That's the include file.  The error is saying you don't have libGL.so, 
which it is looking for in /usr/lib/x86_64-linux-gnu.  Do you have that 
file?  Is it there, and marked as executable?

It's probably a symbolic link; on an old Ubuntu system I just checked, 
it points to mesa/libGL.so, which is also a symlink, pointing to 
mesa/libGL.so.1.2.0, which is executable.

Duncan Murdoch

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Santosh
    

    

      
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Hi Duncan, and others..

Yes, below are the search results. it is linked to mesa/libGL.so and is
again point to libGL.so -> libGL.so.1.2.0 . However, I could not find
libGL.so.1.2.0 or its source. Where is libGL.so.1.2.0 expected to be
located?


/usr/lib/libGL.so.1

/usr/lib/x86_64-linux-gnu/libGL.so
/usr/lib/x86_64-linux-gnu/libGL.so.1
/usr/lib/x86_64-linux-gnu/mesa/libGL.so


Thanks again,
Santosh

On Fri, Nov 24, 2017 at 12:39 PM, Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
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On 24/11/2017 5:24 PM, Santosh wrote:

            

      
      
      
    

        
Mine was in /usr/lib/x86_64-linux-gnu/mesa/.

Duncan Murdoch

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 24 November 2017 at 11:30, Santosh wrote:

        
| Hi All, Duncan, Rolf, Ista, DIrk,
| 
| Thanks for the suggestions and I tried all of them (as suggested by Duncan,
| Rolf, Ista and Dirk)... I still get similar error as before while
| installing 'rgl' package.. I also tried to manually configure "rgl" and got
| an error message (please see below for the verbatim output).  Would highly
| any further ideas/suggestions!
| 
| *In my system, "GL" library is present under "/usr/include/GL"*
| 
| Here are the libraries available (as suggested by Rolf)
| 
| After installing some of them, I continue to get the same error message,
| please below the output messages in config.log after I ran "./configure")
| 
| 
| "ii  r-cran-rgl                            0.93.996-1
|         amd64        GNU R package for three-dimensional visualisation
| using OpenGL"

That means you _have_ the rgl package installed, and can stop everything you
are doing.

You do _not_ need to install it from source via R. You have it from Ubuntu.

Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Santosh
    

    

      
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Hi Duncan, Dirk, & Others,

Mine has also like this...
/usr/lib/x86_64-linux-gnu/libGL.so -> mesa/libGL.so  ->  libGL.so.1.2.0

however, I could not find the source of libGL.so.1.2.0

Dirk, I just now saw your response... Yes, r-cran-rgl and ibgl1-mesa-glx
<https://packages.ubuntu.com/quantal/libgl1-mesa-glx-dbg> are the latest
available now.  How do I install R package "rgl" successfully? it gives the
error about glEnd... and removes the  R package "rgl".

Thanks again,
Santosh


On Fri, Nov 24, 2017 at 2:33 PM, Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
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On 24/11/2017 5:45 PM, Dirk Eddelbuettel wrote:

            

      
      
      
    

        
Actually the version on CRAN is pretty old, so I'd recommend people do 
install it from source, getting the source from R-forge.  Since that is 
a development site the quality varies over time, but right at this 
minute I would say it is better than the CRAN version.

Re Santosh's error messages:  it looks as though the Mesa installation 
is messed up.  I'd recommend uninstalling it, making sure there's no 
remnant of Mesa anywhere, then reinstalling it.

Duncan Murdoch

  
  


  


      

    

    

      
      

        


  

        

      Santosh
    

    

      
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Hi Duncan,
Thanks for the suggestions. How do I uninstall mesa related installations?
Do I need to uninstall all of "mesa" or only the specific ones?

Santosh

On Fri, Nov 24, 2017 at 3:05 PM, Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

            

      
      
      
    

        

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Santosh
    

    

      
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Hi Rxperts,

I tried with r-cran-rgl (based on the default installation of Ubuntu) with
reinstalled rgl package from R-forge.. I get the missing GL/gl.h header.
Didn't reinstall Mesa libraries per recommendations of Duncan.

* installing *source* package ?rgl? ...** package ?rgl? successfully
unpacked and MD5 sums checkedchecking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -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 , headers
checking GL/gl.h usability... no
checking GL/gl.h presence... no
checking for GL/gl.h... no
checking GL/glu.h usability... no
checking GL/glu.h presence... no
checking for GL/glu.h... noconfigure: error: missing required header
GL/gl.hERROR: configuration failed for package ?rgl?
* removing ?/data/R/lib/rgl?Warning in install.packages :
  installation of package ?rgl? had non-zero exit status

        
On Fri, Nov 24, 2017 at 3:45 PM, Santosh <santosh2005 at gmail.com> wrote:

        

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
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On 26/11/2017 3:05 PM, Santosh wrote:

            

      
      
      
    

        
None of your messages have indicated that the header is missing.  You're 
missing the library.  According to one of your earlier messages, it 
sounded as though the missing file is 
/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0.

Duncan Murdoch