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.
(3 replies) Hi all, I encountered difficulties when I tried to install the rgl package. I'm using R devel (2.7.0) on Mac OS X 10.5.1. Below is the message popping up when compiling the package from source. I'd be grateful if someone can help me solve the problem. (1 reply) I've been working to build a set of R functions that require rgl, specifically phytools. I'm using R v. 2.15.2 (built using homebrew; I've already run this particular issue through the homebrew group and so I can at least exclude that particular source of error) on a mac machine running os 10.8.
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 system('dpkg -l grep libglu1')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 system('dpkg -l grep libpng')ii libpng12-0:amd64 1.2.50-1ubuntu2.14.04.2 amd64 PNG library - runtime 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, INSTALLopts='-no-multiarch', configure.args=c(rgl='-with-gl-includes=/usr/include/GL')) Thanks so much for your help!
Santosh alternative HTML version deleted mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. 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 system('dpkg -l grep libglu1')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 system('dpkg -l grep libpng')ii libpng12-0:amd64 1.2.50-1ubuntu2.14.04.2 amd64 PNG library - runtime 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=TINSTALLopts='-no-multiarch'configure.args=c(rgl='-with-gl-includes=/usr/include/GL')) Thanks so much for your help! Santosh alternative HTML version deleted mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. On 6:05 PM, Santosh wrote: Hi RxpertsI 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. 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 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. 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 system('dpkg -l grep libglu1')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 system('dpkg -l grep libpng')ii libpng12-0:amd64 1.2.50-1ubuntu2.14.04.2 amd64 PNG library - runtime 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=TINSTALLopts='-no-multiarch'configure.args=c(rgl='-with-gl-includes=/usr/include/GL')) mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. On Nov 23, 2017 6:16 PM, 'Duncan Murdoch' wrote: On 6:05 PM, Santosh wrote: Hi RxpertsI 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.
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.
Fortunately there is no need to memorize them: apt-get build-dep r-cran-rgl should be all you need. Duncan Murdoch. 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 system('dpkg -l grep libglu1')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 system('dpkg -l grep libpng')ii libpng12-0:amd64 1.2.50-1ubuntu2.14.04.2 amd64 PNG library - runtime 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=TINSTALLopts='-no-multiarch'configure.args=c(rgl='-with-gl-includes=/usr/include/GL')) Thanks so much for your help! Santosh alternative HTML version deleted mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide ng-guide.html and provide commented, minimal, self-contained, reproducible code. mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. alternative HTML version deleted mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. 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 - @eddelbuettel mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. 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 - @eddelbuettel alternative HTML version deleted mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code.
On 2:30 PM, Santosh wrote: Hi All, Duncan, Rolf, Ista, DIrkThanks for the suggestions and I tried all of them (as suggested by DuncanRolf, 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'. That's the include file.
The error is saying you don't have libGL.so, which it is looking for in /usr/lib/x8664-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. On 24 November 2017 at 11:30, Santosh wrote: Hi All, Duncan, Rolf, Ista, DIrkThanks for the suggestions and I tried all of them (as suggested by DuncanRolf, 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 messageplease 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 - @eddelbuettel mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. On 24 November 2017 at 11:30, Santosh wrote: Hi All, Duncan, Rolf, Ista, DIrkThanks for the suggestions and I tried all of them (as suggested by DuncanRolf, 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 messageplease 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.
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 mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. On 5:45 PM, Dirk Eddelbuettel wrote: On 24 November 2017 at 11:30, Santosh wrote: Hi All, Duncan, Rolf, Ista, DIrkThanks for the suggestions and I tried all of them (as suggested by DuncanRolf, 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 messageplease 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. 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 alternative HTML version deleted mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. 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 wrote. Hi DuncanThanks 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 wrote: On 5:45 PM, Dirk Eddelbuettel wrote: On 24 November 2017 at 11:30, Santosh wrote: Hi All, Duncan, Rolf, Ista, DIrkThanks for the suggestions and I tried all of them (as suggested by DuncanRolf, 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 messageplease 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. 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 alternative HTML version deleted mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. On 3:05 PM, Santosh wrote: Hi RxpertsI 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.
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/x8664-linux-gnu/mesa/libGL.so.1.2.0. Duncan Murdoch. installing.source.
package ‘rgl’. package ‘rgl’ successfully unpacked and MD5 sums checked 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. Librariesheaders 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. No configure: error: missing required header GL/gl.h ERROR: 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 wrote: Hi DuncanThanks 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 wrote: On 5:45 PM, Dirk Eddelbuettel wrote: On 24 November 2017 at 11:30, Santosh wrote: Hi All, Duncan, Rolf, Ista, DIrkThanks for the suggestions and I tried all of them (as suggested by DuncanRolf, 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 messageplease 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.
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 itmaking sure there's no remnant of Mesa anywhere, then reinstalling it. Duncan Murdoch mailing list - To UNSUBSCRIBE and more, see PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code.
CRAN - Package rgl rgl: 3D Visualization Using OpenGL Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d, etc.) as well as functions for constructing representations of geometric objects (cube3d, etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.