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RGL package installation problem on Centos
5 messages · john herbert, Duncan Murdoch, Mike Marchywka
On 11-05-23 9:43 AM, john herbert wrote:
Dear R users,
I have installed the latest version of R from source on Centos (using
configure and make install).
This seemed to work fine, with no Errors reported and R at the command line
starts R.
However, if I try and installed the package rgl using;
install.packages("rgl")
I get the following error;
The error sounds like one reported back in November on Ubuntu. As in that case, I don't know what the cause is, but the debugging advice I gave then might help you to determine it. Here's a copy of a recent message on the topic. Duncan Murdoch
FYI, I have downloaded the latest version of rgl from CRAN and successfully installed and used it on my 64-bit Ubuntu (10.10) build of R-2.13.0. I don't know what has changed (exactly) for it to work now versus when we communicated six-months ago, but thanks for maintaining such an excellent resource for the R community.
cheers...
Brandon
On 23 November 2010 18:31, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
On 23/11/2010 1:02 PM, Brandon Whitcher wrote:
Apologies for emailing you directly, but I wanted to ask for your help as
quickly as possible. I have R 2.12.0 installed on my Ubuntu 64-bit 10.04
laptop. I have installed rgl (from CRAN) and it does compile/install.
However, when it is loaded into R, I get a segmentation fault (end of
message). The configuration doesn't throw up anything obvious to me... but
I'm not such an expert. Any suggestions would be great.
I'd try building and running it in 32 bit mode. I don't have a 64 bit Ubuntu machine to run on. I have run it on 32 bit Ubuntu (on a Mac laptop).
You could also try installing it in 64 bit mode without the automatic test load (use --no-test-load on the INSTALL command line), and see if it segfaults in a regular situation; my guess is that it will. But in this case you can run it under a debugger, and maybe get some more information about what's going wrong.
Duncan Murdoch
* installing *source* package 'rgl' ...
checking for gcc... gcc -m64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
checking for gcc... (cached) gcc -m64 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -m64 -std=gnu99 accepts -g... (cached) yes
checking for gcc -m64 -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... yes
checking for gluProject in -lGLU... yes
checking for freetype-config... yes
configure: using Freetype and FTGL
configure: creating ./config.status
config.status: creating src/Makevars
cheers...
Brandon
** testing if installed package can be loaded
*** caught segfault ***
address 0x4, cause 'memory not mapped'
Traceback:
1: .Call(rgl_init, initValue)
2: rgl.init(initValue)
3: fun(...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(...), error = identity)
8: runHook(".onLoad", package, env, package.lib, package)
9: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(expr, error = function(e) { call<- conditionCall(e) if
(!is.null(call)) { if (identical(call[[1L]],
quote(doTryCatch))) call<- sys.call(-4L) dcall<-
deparse(call)[1L] prefix<- paste("Error in", dcall, ": ")
LONG<- 75L msg<- conditionMessage(e) sm<- strsplit(msg,
"\n")[[1L]] w<- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type
= "w") if (is.na(w)) w<- 14L + nchar(dcall, type = "b")
+ nchar(sm[1L], type = "b") if (w> LONG)
prefix<- paste(prefix, "\n ", sep = "") } else prefix<- "Error :
" msg<- paste(prefix, conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1L])) if (!silent&&
identical(getOption("show.error.messages"), TRUE)) { cat(msg,
file = stderr()) .Internal(printDeferredWarnings()) }
invisible(structure(msg, class = "try-error"))})
14: try({ ns<- loadNamespace(package, c(which.lib.loc, lib.loc),
keep.source = keep.source) dataPath<- file.path(which.lib.loc, package,
"data") env<- attachNamespace(ns, pos = pos, dataPath =
dataPath, deps)})
15: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return =
TRUE)
16: withCallingHandlers(expr, packageStartupMessage = function(c)
invokeRestart("muffleMessage"))
17: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE))
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(expr, error = function(e) { call<- conditionCall(e) if
(!is.null(call)) { if (identical(call[[1L]],
quote(doTryCatch))) call<- sys.call(-4L) dcall<-
deparse(call)[1L] prefix<- paste("Error in", dcall, ": ")
LONG<- 75L msg<- conditionMessage(e) sm<- strsplit(msg,
"\n")[[1L]] w<- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type
= "w") if (is.na(w)) w<- 14L + nchar(dcall, type = "b")
+ nchar(sm[1L], type = "b") if (w> LONG)
prefix<- paste(prefix, "\n ", sep = "") } else prefix<- "Error :
" msg<- paste(prefix, conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1L])) if (!silent&&
identical(getOption("show.error.messages"), TRUE)) { cat(msg,
file = stderr()) .Internal(printDeferredWarnings()) }
invisible(structure(msg, class = "try-error"))})
22: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE)))
23: do_install_source(pkg_name, instdir, pkg, desc)
24: do_install(pkg)
25: tools:::.install_packages()
aborting ...
Segmentation fault
The downloaded packages are in
'/tmp/RtmpFC4Uwq/downloaded_packages'
Warning message:
In install.packages("rgl") :
installation of package 'rgl' had non-zero exit status
Continuing with John's post...
installing to /usr/local/lib64/R/library/rgl/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
*** caught segfault ***
address (nil), cause 'memory not mapped'
aborting ...
sh: line 1: 23732 Segmentation fault '/usr/local/lib64/R/bin/R'
--no-save --slave< /tmp/RtmpkvIjOb/file6d97876
ERROR: loading failed
* removing ?/usr/local/lib64/R/library/rgl?
The downloaded packages are in
?/tmp/Rtmp5OaGuQ/downloaded_packages?
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages("rgl") :
installation of package 'rgl' had non-zero exit status
I read that Open GL header files have to be present and are in
/usr/include/GL.
I also read about different graphics cards causing problems but I don't know
how to find this info out.
Any help appreciated and full error message included below.
Thanks,
sessionInfo()
R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base #################### full error ######################
install.packages("rgl")
--- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/rgl_0.92.798.tar.gz' Content type 'application/x-gzip' length 1677772 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb * installing *source* package ?rgl? ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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... yes checking for gluProject in -lGLU... yes checking for freetype-config... yes configure: using Freetype and FTGL configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c BBoxDeco.cpp -o BBoxDeco.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Background.cpp -o Background.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Color.cpp -o Color.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Disposable.cpp -o Disposable.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Light.cpp -o Light.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c LineSet.cpp -o LineSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c LineStripSet.cpp -o LineStripSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Material.cpp -o Material.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c PointSet.cpp -o PointSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c PrimitiveSet.cpp -o PrimitiveSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c QuadSet.cpp -o QuadSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c RenderContext.cpp -o RenderContext.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Shape.cpp -o Shape.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SphereMesh.cpp -o SphereMesh.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SphereSet.cpp -o SphereSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SpriteSet.cpp -o SpriteSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c String.cpp -o String.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Surface.cpp -o Surface.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c TextSet.cpp -o TextSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Texture.cpp -o Texture.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Viewpoint.cpp -o Viewpoint.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c api.cpp -o api.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c assert.cpp -o assert.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c callbacks.cpp -o callbacks.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c device.cpp -o device.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c devicemanager.cpp -o devicemanager.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c fps.cpp -o fps.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c ftgl.cpp -o ftgl.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c geom.cpp -o geom.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -fpic -g -O2 -c gl2ps.c -o gl2ps.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c glErrors.cpp -o glErrors.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c glgui.cpp -o glgui.o glgui.cpp: In constructor ?GLFTFont::GLFTFont(const char*, int, double, const char*)?: glgui.cpp:118: warning: converting to ?unsigned int? from ?double? g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c gui.cpp -o gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c init.cpp -o init.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c osxgui.cpp -o osxgui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c osxlib.cpp -o osxlib.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c par3d.cpp -o par3d.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c pixmap.cpp -o pixmap.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c render.cpp -o render.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c rglmath.cpp -o rglmath.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c rglview.cpp -o rglview.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c scene.cpp -o scene.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c select.cpp -o select.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c win32gui.cpp -o win32gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c win32lib.cpp -o win32lib.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c x11gui.cpp -o x11gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c x11lib.cpp -o x11lib.o g++ -shared -L/usr/local/lib64 -o rgl.so BBoxDeco.o Background.o Color.o Disposable.o Light.o LineSet.o LineStripSet.o Material.o PointSet.o PrimitiveSet.o QuadSet.o RenderContext.o Shape.o SphereMesh.o SphereSet.o SpriteSet.o String.o Surface.o TextSet.o Texture.o Viewpoint.o api.o assert.o callbacks.o device.o devicemanager.o fps.o ftgl.o geom.o gl2ps.o glErrors.o glgui.o gui.o init.o osxgui.o osxlib.o par3d.o pixmap.o render.o rglmath.o rglview.o scene.o select.o win32gui.o win32lib.o x11gui.o x11lib.o -lGLU -lGL -L/usr/lib64 -lpng12 -lX11 -lfreetype installing to /usr/local/lib64/R/library/rgl/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded *** caught segfault *** address (nil), cause 'memory not mapped' aborting ... sh: line 1: 23732 Segmentation fault '/usr/local/lib64/R/bin/R' --no-save --slave< /tmp/RtmpkvIjOb/file6d97876 ERROR: loading failed * removing ?/usr/local/lib64/R/library/rgl? The downloaded packages are in ?/tmp/Rtmp5OaGuQ/downloaded_packages? Updating HTML index of packages in '.Library' Making packages.html ... done Warning message: In install.packages("rgl") : installation of package 'rgl' had non-zero exit status [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
----------------------------------------
Date: Mon, 23 May 2011 14:43:59 +0100
From: arraystruggles at gmail.com
To: r-help at r-project.org
Subject: [R] RGL package installation problem on Centos
Dear R users,
I have installed the latest version of R from source on Centos (using
configure and make install).
This seemed to work fine, with no Errors reported and R at the command line
starts R.
However, if I try and installed the package rgl using;
install.packages("rgl")
I get the following error;
installing to /usr/local/lib64/R/library/rgl/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
*** caught segfault ***
address (nil), cause 'memory not mapped'
I just did install of R from source built with various
options to support Rapache and tried to load rgl.
First it complained no display so I went back
to bash and did "export DISPLAY=:0" and it seemed
to load ok. Do you have X running and a display set?
Not sure what happens if you have R without X11 support
for example.
I probably installed with dep=TRUE and only cygwin I do recall
some issues with missing dependencies.? Try setting dependencies to
true and see if that helps.
aborting ...
sh: line 1: 23732 Segmentation fault '/usr/local/lib64/R/bin/R'
--no-save --slave < /tmp/RtmpkvIjOb/file6d97876
ERROR: loading failed
* removing ?/usr/local/lib64/R/library/rgl?
The downloaded packages are in
?/tmp/Rtmp5OaGuQ/downloaded_packages?
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages("rgl") :
installation of package 'rgl' had non-zero exit status
I read that Open GL header files have to be present and are in
/usr/include/GL.
I also read about different graphics cards causing problems but I don't know
how to find this info out.
Any help appreciated and full error message included below.
Thanks,
sessionInfo()
R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base #################### full error ######################
install.packages("rgl")
--- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/rgl_0.92.798.tar.gz' Content type 'application/x-gzip' length 1677772 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb * installing *source* package ?rgl? ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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... yes checking for gluProject in -lGLU... yes checking for freetype-config... yes configure: using Freetype and FTGL configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c BBoxDeco.cpp -o BBoxDeco.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Background.cpp -o Background.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Color.cpp -o Color.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Disposable.cpp -o Disposable.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Light.cpp -o Light.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c LineSet.cpp -o LineSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c LineStripSet.cpp -o LineStripSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Material.cpp -o Material.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c PointSet.cpp -o PointSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c PrimitiveSet.cpp -o PrimitiveSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c QuadSet.cpp -o QuadSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c RenderContext.cpp -o RenderContext.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Shape.cpp -o Shape.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SphereMesh.cpp -o SphereMesh.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SphereSet.cpp -o SphereSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SpriteSet.cpp -o SpriteSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c String.cpp -o String.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Surface.cpp -o Surface.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c TextSet.cpp -o TextSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Texture.cpp -o Texture.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Viewpoint.cpp -o Viewpoint.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c api.cpp -o api.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c assert.cpp -o assert.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c callbacks.cpp -o callbacks.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c device.cpp -o device.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c devicemanager.cpp -o devicemanager.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c fps.cpp -o fps.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c ftgl.cpp -o ftgl.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c geom.cpp -o geom.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -fpic -g -O2 -c gl2ps.c -o gl2ps.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c glErrors.cpp -o glErrors.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c glgui.cpp -o glgui.o glgui.cpp: In constructor ?GLFTFont::GLFTFont(const char*, int, double, const char*)?: glgui.cpp:118: warning: converting to ?unsigned int? from ?double? g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c gui.cpp -o gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c init.cpp -o init.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c osxgui.cpp -o osxgui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c osxlib.cpp -o osxlib.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c par3d.cpp -o par3d.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c pixmap.cpp -o pixmap.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c render.cpp -o render.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c rglmath.cpp -o rglmath.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c rglview.cpp -o rglview.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c scene.cpp -o scene.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c select.cpp -o select.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c win32gui.cpp -o win32gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c win32lib.cpp -o win32lib.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c x11gui.cpp -o x11gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c x11lib.cpp -o x11lib.o g++ -shared -L/usr/local/lib64 -o rgl.so BBoxDeco.o Background.o Color.o Disposable.o Light.o LineSet.o LineStripSet.o Material.o PointSet.o PrimitiveSet.o QuadSet.o RenderContext.o Shape.o SphereMesh.o SphereSet.o SpriteSet.o String.o Surface.o TextSet.o Texture.o Viewpoint.o api.o assert.o callbacks.o device.o devicemanager.o fps.o ftgl.o geom.o gl2ps.o glErrors.o glgui.o gui.o init.o osxgui.o osxlib.o par3d.o pixmap.o render.o rglmath.o rglview.o scene.o select.o win32gui.o win32lib.o x11gui.o x11lib.o -lGLU -lGL -L/usr/lib64 -lpng12 -lX11 -lfreetype installing to /usr/local/lib64/R/library/rgl/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded *** caught segfault *** address (nil), cause 'memory not mapped' aborting ... sh: line 1: 23732 Segmentation fault '/usr/local/lib64/R/bin/R' --no-save --slave < /tmp/RtmpkvIjOb/file6d97876 ERROR: loading failed * removing ?/usr/local/lib64/R/library/rgl? The downloaded packages are in ?/tmp/Rtmp5OaGuQ/downloaded_packages? Updating HTML index of packages in '.Library' Making packages.html ... done Warning message: In install.packages("rgl") : installation of package 'rgl' had non-zero exit status ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
1 day later
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On 11-05-25 6:08 AM, john herbert wrote:
Hi. Thank you for your help. From your suggestions, I tried the following; R CMD INSTALL --no-test-load rgl_0.92.798.tar.gz This seemed to load and install (starting R and issuing library(rgl) did not flag any problems But running the sphere example from rgl, it causes big problems :-) # R R version 2.13.0 (2011-04-13) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
library(rgl) open3d()
[1] 1
spheres3d(rnorm(10), rnorm(10), rnorm(10), radius=runif(10),
color=rainbow(10))
X Error of failed request: GLXUnsupportedPrivateRequest
Major opcode of failed request: 143 (GLX)
Minor opcode of failed request: 16 (X_GLXVendorPrivate)
Serial number of failed request: 75
Current serial number in output stream: 80
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: .C(rgl_spheres, success = as.integer(FALSE), idata,
as.numeric(vertex), as.numeric(radius), NAOK = TRUE)
2: rgl.spheres(x = c(0.506515614656334, -0.610549216480097,
1.08552683577513, 0.189935807154803, 1.3670636776769, 1.0181689602839,
-1.51133180077403, 1.41127485066926, 0.199668469858345, -1.22523054947931),
y = c(-0.323499291411831, -1.00507951141751, -0.901821819799205,
1.41189828512003, -0.131573335707317, -0.308459525548042, 1.50221794165404,
-0.154047787639801, 0.44717002689869, -0.93671163236924), z =
c(0.836709660070246, -0.251235618242673, -2.02289120416259,
0.499914144749108, -0.458094619767492, 1.48047512280956, 0.80987242929676,
-1.17963322744287, 0.81492625128413, 0.475181724036684), radius =
c(0.174093995941803, 0.75503840832971, 0.562892300076783, 0.541058518458158,
0.724675815086812, 0.828356854617596, 0.423405217472464, 0.540400178171694,
0.0765824350528419, 0.55016236170195), color = c("#FF0000FF", "#FF9900FF",
"#CCFF00FF", "#33FF00FF", "#00FF66FF", "#00FFFFFF", "#0066FFFF",
"#3300FFFF", "#CC00FFFF", "#FF0099FF"), alpha = 1, lit = TRUE, ambient =
"#000000", specular = "#FFFFFF", emission = "#000000", shininess = 50,
smooth = TRUE, front = "filled", back = "filled", size = 3, lwd = 1, fog
= FALSE, point_antialias = FALSE, line_antialias = FALSE, texture =
NULL, textype = "rgb", texmipmap = FALSE, texminfilter = "linear",
texmagfilter = "linear", texenvmap = FALSE)
3: do.call("rgl.spheres", c(list(x = x, y = y, z = z, radius = radius),
.fixMaterialArgs(..., Params = save)))
4: spheres3d(rnorm(10), rnorm(10), rnorm(10), radius = runif(10), color
= rainbow(10))
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Does this error message make anything clearer?
The problem is being reported by your X Windows system, because something that rgl is doing is not supported by it. If you Google for GLXUnsupportedPrivateRequest you'll see a lot of similar reports for this for various systems, but I don't see a lot of solutions. I suspect it's a badly implemented graphics driver for your graphics card. All I can suggest is that you contact the vendor to see if there's an update. Duncan Murdoch
On Mon, May 23, 2011 at 2:43 PM, john herbert<arraystruggles at gmail.com>wrote:
Dear R users,
I have installed the latest version of R from source on Centos (using
configure and make install).
This seemed to work fine, with no Errors reported and R at the command line
starts R.
However, if I try and installed the package rgl using;
install.packages("rgl")
I get the following error;
installing to /usr/local/lib64/R/library/rgl/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
*** caught segfault ***
address (nil), cause 'memory not mapped'
aborting ...
sh: line 1: 23732 Segmentation fault '/usr/local/lib64/R/bin/R'
--no-save --slave< /tmp/RtmpkvIjOb/file6d97876
ERROR: loading failed
* removing ?/usr/local/lib64/R/library/rgl?
The downloaded packages are in
?/tmp/Rtmp5OaGuQ/downloaded_packages?
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages("rgl") :
installation of package 'rgl' had non-zero exit status
I read that Open GL header files have to be present and are in
/usr/include/GL.
I also read about different graphics cards causing problems but I don't
know how to find this info out.
Any help appreciated and full error message included below.
Thanks,
sessionInfo()
R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base #################### full error ######################
install.packages("rgl")
--- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/rgl_0.92.798.tar.gz' Content type 'application/x-gzip' length 1677772 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb * installing *source* package ?rgl? ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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... yes checking for gluProject in -lGLU... yes checking for freetype-config... yes configure: using Freetype and FTGL configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c BBoxDeco.cpp -o BBoxDeco.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Background.cpp -o Background.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Color.cpp -o Color.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Disposable.cpp -o Disposable.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Light.cpp -o Light.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c LineSet.cpp -o LineSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c LineStripSet.cpp -o LineStripSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Material.cpp -o Material.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c PointSet.cpp -o PointSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c PrimitiveSet.cpp -o PrimitiveSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c QuadSet.cpp -o QuadSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c RenderContext.cpp -o RenderContext.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Shape.cpp -o Shape.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SphereMesh.cpp -o SphereMesh.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SphereSet.cpp -o SphereSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c SpriteSet.cpp -o SpriteSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c String.cpp -o String.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Surface.cpp -o Surface.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c TextSet.cpp -o TextSet.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Texture.cpp -o Texture.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c Viewpoint.cpp -o Viewpoint.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c api.cpp -o api.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c assert.cpp -o assert.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c callbacks.cpp -o callbacks.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c device.cpp -o device.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c devicemanager.cpp -o devicemanager.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c fps.cpp -o fps.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c ftgl.cpp -o ftgl.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c geom.cpp -o geom.o gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -fpic -g -O2 -c gl2ps.c -o gl2ps.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c glErrors.cpp -o glErrors.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c glgui.cpp -o glgui.o glgui.cpp: In constructor ?GLFTFont::GLFTFont(const char*, int, double, const char*)?: glgui.cpp:118: warning: converting to ?unsigned int? from ?double? g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c gui.cpp -o gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c init.cpp -o init.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c osxgui.cpp -o osxgui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c osxlib.cpp -o osxlib.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c par3d.cpp -o par3d.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c pixmap.cpp -o pixmap.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c render.cpp -o render.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c rglmath.cpp -o rglmath.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c rglview.cpp -o rglview.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c scene.cpp -o scene.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c select.cpp -o select.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c win32gui.cpp -o win32gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c win32lib.cpp -o win32lib.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c x11gui.cpp -o x11gui.o g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fpic -g -O2 -c x11lib.cpp -o x11lib.o g++ -shared -L/usr/local/lib64 -o rgl.so BBoxDeco.o Background.o Color.o Disposable.o Light.o LineSet.o LineStripSet.o Material.o PointSet.o PrimitiveSet.o QuadSet.o RenderContext.o Shape.o SphereMesh.o SphereSet.o SpriteSet.o String.o Surface.o TextSet.o Texture.o Viewpoint.o api.o assert.o callbacks.o device.o devicemanager.o fps.o ftgl.o geom.o gl2ps.o glErrors.o glgui.o gui.o init.o osxgui.o osxlib.o par3d.o pixmap.o render.o rglmath.o rglview.o scene.o select.o win32gui.o win32lib.o x11gui.o x11lib.o -lGLU -lGL -L/usr/lib64 -lpng12 -lX11 -lfreetype installing to /usr/local/lib64/R/library/rgl/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded *** caught segfault *** address (nil), cause 'memory not mapped' aborting ... sh: line 1: 23732 Segmentation fault '/usr/local/lib64/R/bin/R' --no-save --slave< /tmp/RtmpkvIjOb/file6d97876 ERROR: loading failed * removing ?/usr/local/lib64/R/library/rgl? The downloaded packages are in ?/tmp/Rtmp5OaGuQ/downloaded_packages? Updating HTML index of packages in '.Library' Making packages.html ... done Warning message: In install.packages("rgl") : installation of package 'rgl' had non-zero exit status
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