[R] Can't install rgl: installed package can't be loaded; 'memory not mapped'
Hi, I can't install package rgl. The last lines from the install process talking about the error are: ** testing if installed package can be loaded sh: line 1: 11949 Segmentation fault '/files3/R/R-3.2.1_install/lib64/R/bin/R' --no-save --slave 21 '/tmp/RtmpQCpp6N/file2b115f4f8e1d' *** caught segfault *** address (nil), cause 'memory not mapped' aborting ... ERROR: loading failed I realize this is probably not an R problem, but a Google search turns up nothing that helps, and I'm hoping someone here can help anyway. Below are my sessionInfo() output and the contents of the first file generated with R CMD check rgl_0.95.1247.tar.gz. sessionInfo() R version 3.2.1 (2015-06-18) 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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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 loaded via a namespace (and not attached): [1] tools_3.2.1 # R CMD check rgl_0.95.1247.tar.gz * 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 whether __attribute__((visibility())) is supported... yes checking whether gcc -std=gnu99 accepts -fvisibility... yes checking whether accepts -fvisibility... no 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/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c BBoxDeco.cpp -o BBoxDeco.o BBoxDeco.cpp: In member function 'int rgl::AxisInfo::getNticks(float, float)': BBoxDeco.cpp:239: warning: converting to 'int' from 'float' g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c Background.cpp -o Background.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c ClipPlane.cpp -o ClipPlane.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c Color.cpp -o Color.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c Disposable.cpp -o Disposable.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c Light.cpp -o Light.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c LineSet.cpp -o LineSet.o g++
Re: [R] Can't install rgl: installed package can't be loaded; 'memory not mapped'
On 08/08/2015 1:32 PM, Waichler, Scott R wrote: Hi, I can't install package rgl. The last lines from the install process talking about the error are: I'd guess you have an OpenGL problem. Does glxgears run? Duncan Murdoch ** testing if installed package can be loaded sh: line 1: 11949 Segmentation fault '/files3/R/R-3.2.1_install/lib64/R/bin/R' --no-save --slave 21 '/tmp/RtmpQCpp6N/file2b115f4f8e1d' *** caught segfault *** address (nil), cause 'memory not mapped' aborting ... ERROR: loading failed I realize this is probably not an R problem, but a Google search turns up nothing that helps, and I'm hoping someone here can help anyway. Below are my sessionInfo() output and the contents of the first file generated with R CMD check rgl_0.95.1247.tar.gz. sessionInfo() R version 3.2.1 (2015-06-18) 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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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 loaded via a namespace (and not attached): [1] tools_3.2.1 # R CMD check rgl_0.95.1247.tar.gz * 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 whether __attribute__((visibility())) is supported... yes checking whether gcc -std=gnu99 accepts -fvisibility... yes checking whether accepts -fvisibility... no 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/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c BBoxDeco.cpp -o BBoxDeco.o BBoxDeco.cpp: In member function 'int rgl::AxisInfo::getNticks(float, float)': BBoxDeco.cpp:239: warning: converting to 'int' from 'float' g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c Background.cpp -o Background.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c ClipPlane.cpp -o ClipPlane.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c Color.cpp -o Color.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c Disposable.cpp -o Disposable.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c Light.cpp -o Light.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG
Re: [R] Can't install rgl: installed package can't be loaded; 'memory not mapped'
Hi, I can't install package rgl. The last lines from the install process talking about the error are: I'd guess you have an OpenGL problem. Does glxgears run? Yes, it does. I wasn't aware of the program before you mentioned it, but a display opens with 3 gears and here is some output: [root@hokulea R-3.2.1_install]# glxgears -info GL_RENDERER = Mesa GLX Indirect GL_VERSION= 1.2 (1.5 Mesa 6.5.1) GL_VENDOR = Mesa project: www.mesa3d.org GL_EXTENSIONS = GL_ARB_depth_texture GL_ARB_imaging GL_ARB_multitexture GL_ARB_point_parameters GL_ARB_point_sprite GL_ARB_shadow GL_ARB_texture_border_clamp GL_ARB_texture_cube_map GL_ARB_texture_env_add GL_ARB_texture_env_combine GL_ARB_texture_env_crossbar GL_ARB_texture_env_dot3 GL_ARB_texture_mirrored_repeat GL_ARB_texture_non_power_of_two GL_ARB_window_pos GL_EXT_abgr GL_EXT_bgra GL_EXT_blend_color GL_EXT_blend_func_separate GL_EXT_blend_minmax GL_EXT_blend_subtract GL_EXT_draw_range_elements GL_EXT_framebuffer_object GL_EXT_fog_coord GL_EXT_multi_draw_arrays GL_EXT_packed_pixels GL_EXT_rescale_normal GL_EXT_secondary_color GL_EXT_separate_specular_color GL_EXT_shadow_funcs GL_EXT_stencil_wrap GL_EXT_texture3D GL_EXT_texture_edge_clamp GL_EXT_texture_env_add GL_EXT_texture_env_combine GL_EXT_texture_env_dot3 GL_EXT_texture_lod_bias GL_EXT_texture_object GL_EXT_vertex_array GL_ATI_texture_mirror_once GL_IBM_texture_mirrored_repeat GL_NV_blend_square GL_NV_texture_rectan! gle GL_NV_texgen_reflection GL_SGIS_generate_mipmap GL_SGIS_texture_lod GL_SGIX_depth_texture GL_SGIX_shadow 24839 frames in 6.0 seconds = 4153.389 FPS 7152 frames in 6.0 seconds = 1192.594 FPS . . . Scott ** testing if installed package can be loaded sh: line 1: 11949 Segmentation fault '/files3/R/R- 3.2.1_install/lib64/R/bin/R' --no-save --slave 21 '/tmp/RtmpQCpp6N/file2b115f4f8e1d' *** caught segfault *** address (nil), cause 'memory not mapped' aborting ... ERROR: loading failed I realize this is probably not an R problem, but a Google search turns up nothing that helps, and I'm hoping someone here can help anyway. Below are my sessionInfo() output and the contents of the first file generated with R CMD check rgl_0.95.1247.tar.gz. sessionInfo() R version 3.2.1 (2015-06-18) 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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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 loaded via a namespace (and not attached): [1] tools_3.2.1 # R CMD check rgl_0.95.1247.tar.gz * 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 whether __attribute__((visibility())) is supported... yes checking whether gcc -std=gnu99 accepts -fvisibility... yes checking whether accepts -fvisibility... no 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/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H - I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl - I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o g++ -I/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H - I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl - I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c
Re: [R] Can't install rgl: installed package can't be loaded; 'memory not mapped'
On 08/08/2015 5:19 PM, Waichler, Scott R wrote: Hi, I can't install package rgl. The last lines from the install process talking about the error are: I'd guess you have an OpenGL problem. Does glxgears run? Yes, it does. I wasn't aware of the program before you mentioned it, but a display opens with 3 gears and here is some output: [root@hokulea R-3.2.1_install]# glxgears -info GL_RENDERER = Mesa GLX Indirect GL_VERSION= 1.2 (1.5 Mesa 6.5.1) GL_VENDOR = Mesa project: www.mesa3d.org GL_EXTENSIONS = GL_ARB_depth_texture GL_ARB_imaging GL_ARB_multitexture GL_ARB_point_parameters GL_ARB_point_sprite GL_ARB_shadow GL_ARB_texture_border_clamp GL_ARB_texture_cube_map GL_ARB_texture_env_add GL_ARB_texture_env_combine GL_ARB_texture_env_crossbar GL_ARB_texture_env_dot3 GL_ARB_texture_mirrored_repeat GL_ARB_texture_non_power_of_two GL_ARB_window_pos GL_EXT_abgr GL_EXT_bgra GL_EXT_blend_color GL_EXT_blend_func_separate GL_EXT_blend_minmax GL_EXT_blend_subtract GL_EXT_draw_range_elements GL_EXT_framebuffer_object GL_EXT_fog_coord GL_EXT_multi_draw_arrays GL_EXT_packed_pixels GL_EXT_rescale_normal GL_EXT_secondary_color GL_EXT_separate_specular_color GL_EXT_shadow_funcs GL_EXT_stencil_wrap GL_EXT_texture3D GL_EXT_texture_edge_clamp GL_EXT_texture_env_add GL_EXT_texture_env_combine GL_EXT_texture_env_dot3 GL_EXT_texture_lod_bias GL_EXT_texture_object GL_EXT_vertex_array GL_ATI_texture_mirror_once GL_IBM_texture_mirrored_repeat GL_NV_blend_square GL_NV_texture_rect! angle GL_N V_texgen_reflection GL_SGIS_generate_mipmap GL_SGIS_texture_lod GL_SGIX_depth_texture GL_SGIX_shadow 24839 frames in 6.0 seconds = 4153.389 FPS 7152 frames in 6.0 seconds = 1192.594 FPS . . . So it looks as though OpenGL is working. I really have no idea what is causing the error you're seeing. rgl works for me, but I don't have a 64 bit Linux to try it on. (It does work in 32 bit Ubuntu.) Duncan Murdoch ** testing if installed package can be loaded sh: line 1: 11949 Segmentation fault '/files3/R/R- 3.2.1_install/lib64/R/bin/R' --no-save --slave 21 '/tmp/RtmpQCpp6N/file2b115f4f8e1d' *** caught segfault *** address (nil), cause 'memory not mapped' aborting ... ERROR: loading failed I realize this is probably not an R problem, but a Google search turns up nothing that helps, and I'm hoping someone here can help anyway. Below are my sessionInfo() output and the contents of the first file generated with R CMD check rgl_0.95.1247.tar.gz. sessionInfo() R version 3.2.1 (2015-06-18) 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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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 loaded via a namespace (and not attached): [1] tools_3.2.1 # R CMD check rgl_0.95.1247.tar.gz * 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 whether __attribute__((visibility())) is supported... yes checking whether gcc -std=gnu99 accepts -fvisibility... yes checking whether accepts -fvisibility... no 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/files3/R/R-3.2.1_install/lib64/R/include -DNDEBUG -DHAVE_PNG_H - I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl - I/usr/include/freetype2 -Iext -I/usr/local/include -g -O2 -fvisibility=hidden -fpic -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o
