Re: [R] rgl build warnings and loading error on Linux
On Wed, Apr 9, 2008 at 9:30 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: I've never seen that. Is there something unusual about the filesystem so it does not recognize rgl/configure is executable? (We've seen that on SMB filesystems with the wrong mount options.) In /etc/fstab, I have the following. tmpfs /tmptmpfs defaults,size=100M,mode=1777,noexec,nosuid 0 0 Mounting /tmp with noexec is a security measure, since /tmp may easily become a vulnerable spot on a Linux system. What I suggest you try is - unpack the rgl tarball. - cd rgl - R CMD ./configure - cd .. - R CMD INSTALL rgl Running R CMD INSTALL rgl from my reiserfs / partition was enough for the ./configure script to get executed and for rgl to build properly [1]. Now I can dyn.load() rgl with no error messages, although it is somewhat crashy. I will report here if I get any meaningful error messages. Thanks goes to all who contributed with their suggestions. Best regards, Liviu [1] http://www.geocities.com/landroni/rgl_build_02.txt __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
From the 'R Installation and Administration Manual':
Note that @env{TMPDIR} will be used to execute @command{configure}
scripts when installing packages, so if @code{/tmp} has been mounted as
@samp{noexec}, @env{TMPDIR} needs to be set to a directory from which
execution is allowed.
'If all else fails, read the manual'.
On Thu, 10 Apr 2008, Liviu Andronic wrote:
On Wed, Apr 9, 2008 at 9:30 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote:
I've never seen that. Is there something unusual about the filesystem so
it does not recognize rgl/configure is executable? (We've seen that on SMB
filesystems with the wrong mount options.)
In /etc/fstab, I have the following.
tmpfs /tmptmpfs
defaults,size=100M,mode=1777,noexec,nosuid 0 0
Mounting /tmp with noexec is a security measure, since /tmp may
easily become a vulnerable spot on a Linux system.
I suggest you talk to an expert about that.
What I suggest you try is
- unpack the rgl tarball.
- cd rgl
- R CMD ./configure
- cd ..
- R CMD INSTALL rgl
Running R CMD INSTALL rgl from my reiserfs / partition was enough
for the ./configure script to get executed and for rgl to build
properly [1]. Now I can dyn.load() rgl with no error messages,
although it is somewhat crashy. I will report here if I get any
meaningful error messages.
Thanks goes to all who contributed with their suggestions.
Best regards,
Liviu
[1] http://www.geocities.com/landroni/rgl_build_02.txt
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@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.
Re: [R] rgl build warnings and loading error on Linux
Dear R users, This is a follow-up of a recent discussion on building rgl on Gentoo Linux. Please read bellow. On Tue, Mar 18, 2008 at 7:24 PM, Charles C. Berry [EMAIL PROTECTED] wrote: Below substitute 'nvidia-drivers' or whatever you use for your-video-drivers emerge -D mesa your-video-drivers revdep-rebuild -X R install.packages(rgl) I have entirely updated my system using emerge -tva -DNu world, also meaning that I switched to R version 2.6.2. I have rebuilt all packages broken by this update using revdep-rebuild -i -tva -X. Just to make sure, afterwards I have also emerge -tva mesa xf86-video-i810. My mesa USE flags look like this: localhost liviu # eix mesa media-libs/mesa Installed versions: 7.0.2(15:23:17 09/04/08)(video_cards_i810 -debug -doc -kernel_FreeBSD -motif -nptl -pic [..]) Building and loading rgl has only switched the error message: dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) Error in dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) : unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glNormal3f Previously it was: undefined symbol: glTexCoordPointer. Does this look like an rgl or a Gentoo Linux issue? Would any of the disabled mesa USE flags be worth enabling? Thank you in advance, Liviu __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On 4/9/2008 10:53 AM, Liviu Andronic wrote: Dear R users, This is a follow-up of a recent discussion on building rgl on Gentoo Linux. Please read bellow. On Tue, Mar 18, 2008 at 7:24 PM, Charles C. Berry [EMAIL PROTECTED] wrote: Below substitute 'nvidia-drivers' or whatever you use for your-video-drivers emerge -D mesa your-video-drivers revdep-rebuild -X R install.packages(rgl) I have entirely updated my system using emerge -tva -DNu world, also meaning that I switched to R version 2.6.2. I have rebuilt all packages broken by this update using revdep-rebuild -i -tva -X. Just to make sure, afterwards I have also emerge -tva mesa xf86-video-i810. My mesa USE flags look like this: localhost liviu # eix mesa media-libs/mesa Installed versions: 7.0.2(15:23:17 09/04/08)(video_cards_i810 -debug -doc -kernel_FreeBSD -motif -nptl -pic [..]) Building and loading rgl has only switched the error message: dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) Error in dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) : unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glNormal3f Previously it was: undefined symbol: glTexCoordPointer. Does this look like an rgl or a Gentoo Linux issue? Would any of the disabled mesa USE flags be worth enabling? glNormal3f and glTexCoordPointer are both OpenGL entry points used by rgl, so the messages are indicating a linking problem. But I don't know enough about Linux to recognize whether that's because of something wrong with Gentoo or what you did, or something wrong with the rgl configure script. Duncan Murdoch Thank you in advance, Liviu __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
We'll need to see the output from install.packages(rgl) to have much idea: R CMD ldd /usr/lib/R/library/rgl/libs/rgl.so would also be informative. On Wed, 9 Apr 2008, Duncan Murdoch wrote: On 4/9/2008 10:53 AM, Liviu Andronic wrote: Dear R users, This is a follow-up of a recent discussion on building rgl on Gentoo Linux. Please read bellow. On Tue, Mar 18, 2008 at 7:24 PM, Charles C. Berry [EMAIL PROTECTED] wrote: Below substitute 'nvidia-drivers' or whatever you use for your-video-drivers emerge -D mesa your-video-drivers revdep-rebuild -X R install.packages(rgl) I have entirely updated my system using emerge -tva -DNu world, also meaning that I switched to R version 2.6.2. I have rebuilt all packages broken by this update using revdep-rebuild -i -tva -X. Just to make sure, afterwards I have also emerge -tva mesa xf86-video-i810. My mesa USE flags look like this: localhost liviu # eix mesa media-libs/mesa Installed versions: 7.0.2(15:23:17 09/04/08)(video_cards_i810 -debug -doc -kernel_FreeBSD -motif -nptl -pic [..]) Building and loading rgl has only switched the error message: dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) Error in dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) : unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glNormal3f Previously it was: undefined symbol: glTexCoordPointer. Does this look like an rgl or a Gentoo Linux issue? Would any of the disabled mesa USE flags be worth enabling? glNormal3f and glTexCoordPointer are both OpenGL entry points used by rgl, so the messages are indicating a linking problem. But I don't know enough about Linux to recognize whether that's because of something wrong with Gentoo or what you did, or something wrong with the rgl configure script. Duncan Murdoch Thank you in advance, Liviu __ R-help@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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
Dear Duncan and Brian, thank you for the quick replies. Please see bellow. On Wed, Apr 9, 2008 at 6:11 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: We'll need to see the output from install.packages(rgl) to have much idea: localhost liviu # R CMD INSTALL /home/liviu/inst/dwn_R/rgl_0.77.tar.gz [ http://www.geocities.com/landroni/rgl_build.txt ] R CMD ldd /usr/lib/R/library/rgl/libs/rgl.so localhost liviu # R CMD ldd /usr/lib/R/library/rgl/libs/rgl.so linux-gate.so.1 = (0xe000) libR.so = /usr/lib/R/lib/libR.so (0xb7c9a000) libstdc++.so.6 = /usr/lib/gcc/i686-pc-linux-gnu/4.1.2/libstdc++.so.6 (0xb7b92000) libm.so.6 = /lib/libm.so.6 (0xb7b6c000) libgcc_s.so.1 = /usr/lib/gcc/i686-pc-linux-gnu/4.1.2/libgcc_s.so.1 (0xb7b6) libc.so.6 = /lib/libc.so.6 (0xb7a2f000) libblas.so.0 = /usr/lib/libblas.so.0 (0xb79dd000) libgfortran.so.1 = /usr/lib/gcc/i686-pc-linux-gnu/4.1.2/libgfortran.so.1 (0xb7962000) libreadline.so.5 = /lib/libreadline.so.5 (0xb793) libpcre.so.0 = /usr/lib/libpcre.so.0 (0xb7909000) libbz2.so.1 = /lib/libbz2.so.1 (0xb78f9000) libz.so.1 = /lib/libz.so.1 (0xb78e6000) libdl.so.2 = /lib/libdl.so.2 (0xb78e2000) /lib/ld-linux.so.2 (0x8000) libncurses.so.5 = /lib/libncurses.so.5 (0xb789e000) __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On Wed, 9 Apr 2008, Liviu Andronic wrote: Dear R users, This is a follow-up of a recent discussion on building rgl on Gentoo Linux. Please read bellow. On Tue, Mar 18, 2008 at 7:24 PM, Charles C. Berry [EMAIL PROTECTED] wrote: Below substitute 'nvidia-drivers' or whatever you use for your-video-drivers emerge -D mesa your-video-drivers revdep-rebuild -X R install.packages(rgl) I have entirely updated my system using emerge -tva -DNu world, also meaning that I switched to R version 2.6.2. I have rebuilt all packages broken by this update using revdep-rebuild -i -tva -X. Just to make sure, afterwards I have also emerge -tva mesa xf86-video-i810. My mesa USE flags look like this: localhost liviu # eix mesa media-libs/mesa Installed versions: 7.0.2(15:23:17 09/04/08)(video_cards_i810 -debug -doc -kernel_FreeBSD -motif -nptl -pic [..]) Building and loading rgl has only switched the error message: dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) Error in dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) : unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glNormal3f Previously it was: undefined symbol: glTexCoordPointer. Does this look like an rgl or a Gentoo Linux issue? Would any of the disabled mesa USE flags be worth enabling? A couple of guesses here. --- Does 'glxgears' work or give you a similar error message?? Obviously, if it breaks, your system is the issue. --- You can get some sense of what is going on by setting export LD_DEBUG_OUTPUT=tmp.debug export LD_DEBUG=all running something - like glxgears or R (invoking library(rgl)) then grep glNormal3f tmp.debug.* For one of my gentoo systems running an ati video card, I get this after glxgears [EMAIL PROTECTED] ~ $ grep glNormal3f tmp.debug.* 6846: symbol=glNormal3f; lookup in file=glxgears [0] 6846: symbol=glNormal3f; lookup in file=/usr/lib/libglut.so.3 [0] 6846: symbol=glNormal3f; lookup in file=/usr/lib/libGLU.so.1 [0] 6846: symbol=glNormal3f; lookup in file=//usr/lib64/opengl/ati/lib/libGL.so.1 [0] 6864: binding file glxgears [0] to //usr/lib64/opengl/ati/lib/libGL.so.1 [0]: normal symbol `glNormal3f' and after R return library(rgl) I get many more lines, but again ending with this long (wrapped) line 6857: binding file /home/cberry/lib.loc/rgl/libs/rgl.so [0] to //usr/lib64/opengl/ati/lib/libGL.so.1 [0]: normal symbol `glNormal3f' Maybe this helps: http://www.linux.org/docs/ldp/howto/Program-Library-HOWTO/shared-libraries.html --- Have you tried opengl-update? HTH, Chuck Thank you in advance, Liviu __ R-help@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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
Right, that shows that the rgl configure script is not being run and no linking is being done to any GL libraries. I've never seen that. Is there something unusual about the filesystem so it does not recognize rgl/configure is executable? (We've seen that on SMB filesystems with the wrong mount options.) What I suggest you try is - unpack the rgl tarball. - cd rgl - R CMD ./configure - cd .. - R CMD INSTALL rgl Hopefully that will either configure or explain why it is not being run. On Wed, 9 Apr 2008, Liviu Andronic wrote: Dear Duncan and Brian, thank you for the quick replies. Please see bellow. On Wed, Apr 9, 2008 at 6:11 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: We'll need to see the output from install.packages(rgl) to have much idea: localhost liviu # R CMD INSTALL /home/liviu/inst/dwn_R/rgl_0.77.tar.gz [ http://www.geocities.com/landroni/rgl_build.txt ] R CMD ldd /usr/lib/R/library/rgl/libs/rgl.so localhost liviu # R CMD ldd /usr/lib/R/library/rgl/libs/rgl.so linux-gate.so.1 = (0xe000) libR.so = /usr/lib/R/lib/libR.so (0xb7c9a000) libstdc++.so.6 = /usr/lib/gcc/i686-pc-linux-gnu/4.1.2/libstdc++.so.6 (0xb7b92000) libm.so.6 = /lib/libm.so.6 (0xb7b6c000) libgcc_s.so.1 = /usr/lib/gcc/i686-pc-linux-gnu/4.1.2/libgcc_s.so.1 (0xb7b6) libc.so.6 = /lib/libc.so.6 (0xb7a2f000) libblas.so.0 = /usr/lib/libblas.so.0 (0xb79dd000) libgfortran.so.1 = /usr/lib/gcc/i686-pc-linux-gnu/4.1.2/libgfortran.so.1 (0xb7962000) libreadline.so.5 = /lib/libreadline.so.5 (0xb793) libpcre.so.0 = /usr/lib/libpcre.so.0 (0xb7909000) libbz2.so.1 = /lib/libbz2.so.1 (0xb78f9000) libz.so.1 = /lib/libz.so.1 (0xb78e6000) libdl.so.2 = /lib/libdl.so.2 (0xb78e2000) /lib/ld-linux.so.2 (0x8000) libncurses.so.5 = /lib/libncurses.so.5 (0xb789e000) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On Mon, Mar 17, 2008 at 11:07 PM, Liviu Andronic [EMAIL PROTECTED] wrote: This is what I have on my system: localhost liviu # locate libGL.so /usr/lib/opengl/xorg-x11/lib/libGL.so.1 /usr/lib/opengl/xorg-x11/lib/libGL.so.1.2 /usr/lib/opengl/xorg-x11/lib/libGL.so /usr/lib/libGL.so However, the funny thing is that /usr/lib/libGL.so belongs to no package, while the other libGL.so belongs to media-libs/mesa. I moved /usr/lib/libGL.so to /usr/lib/libGL.so.bak (it seemed like a broken soft link) and recreated a /usr/lib/libGL.so that linked to /usr/lib/opengl/xorg-x11/lib/libGL.so.1.2. [EMAIL PROTECTED] ~ $ ls -l /usr/lib/libGL.so lrwxrwxrwx 1 root root 32 2008-03-18 12:16 /usr/lib/libGL.so - opengl/xorg-x11/lib/libGL.so.1.2 However, the problem was not solved. A rebuilt rgl generates the same error on library load: dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) Error in dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) : unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glTexCoordPointer Is there anything else that I could try? __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On Tue, 18 Mar 2008, Liviu Andronic wrote: On Mon, Mar 17, 2008 at 11:07 PM, Liviu Andronic [EMAIL PROTECTED] wrote: This is what I have on my system: localhost liviu # locate libGL.so /usr/lib/opengl/xorg-x11/lib/libGL.so.1 /usr/lib/opengl/xorg-x11/lib/libGL.so.1.2 /usr/lib/opengl/xorg-x11/lib/libGL.so /usr/lib/libGL.so However, the funny thing is that /usr/lib/libGL.so belongs to no package, while the other libGL.so belongs to media-libs/mesa. I moved /usr/lib/libGL.so to /usr/lib/libGL.so.bak (it seemed like a broken soft link) and recreated a /usr/lib/libGL.so that linked to /usr/lib/opengl/xorg-x11/lib/libGL.so.1.2. [EMAIL PROTECTED] ~ $ ls -l /usr/lib/libGL.so lrwxrwxrwx 1 root root 32 2008-03-18 12:16 /usr/lib/libGL.so - opengl/xorg-x11/lib/libGL.so.1.2 However, the problem was not solved. A rebuilt rgl generates the same error on library load: dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) Error in dyn.load(/usr/lib/R/library/rgl/libs/rgl.so) : unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glTexCoordPointer Is there anything else that I could try? Below substitute 'nvidia-drivers' or whatever you use for your-video-drivers emerge -D mesa your-video-drivers revdep-rebuild -X R install.packages(rgl) __ R-help@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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On Sun, Mar 16, 2008 at 7:38 PM, Liviu Andronic [EMAIL PROTECTED] wrote: I have several problems in using rgl-0.77 (and recent earlier versions) on Gentoo Linux with a custom-built v. 2.6.22 kernel. Currently I use R-2.6.1. When I build rgl, # R CMD INSTALL /home/liviu/inst/dwn/R/rgl_0.77.tar.gz or install.packages(rgl, dependencies=TRUE, method =wget), I notice the following warning messages: i686-pc-linux-gnu-g++ -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -march=pentium-m -pipe -fomit-frame-pointer -std=gnu99 -c api.cpp -o api.o cc1plus: warning: command line option -std=gnu99 is valid for C/ObjC but not for C++ The warning message itself is repeated during the entire build process. However, the package builds fine, but fails to load: library(rgl) Error in dyn.load(file, ...) : unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glTexCoordPointer Error : .onLoad failed in 'loadNamespace' for 'rgl' Error: package/namespace load failed for 'rgl' I had the exact same error message with rgl_0.76. Could anyone suggest how to make rgl build correctly? What is your Linux distribution? Paul __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On Sun, Mar 16, 2008 at 10:00 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: It sounds as though it is not finding the OpenGL libs when it configures. That function should be in libGL.so. This is what I have on my system: localhost liviu # locate libGL.so /usr/lib/opengl/xorg-x11/lib/libGL.so.1 /usr/lib/opengl/xorg-x11/lib/libGL.so.1.2 /usr/lib/opengl/xorg-x11/lib/libGL.so /usr/lib/libGL.so However, the funny thing is that /usr/lib/libGL.so belongs to no package, while the other libGL.so belongs to media-libs/mesa. localhost liviu # equery b /usr/lib/libGL.so [ Searching for file(s) /usr/lib/libGL.so in *... ] localhost liviu # equery b /usr/lib/opengl/xorg-x11/lib/libGL.so [ Searching for file(s) /usr/lib/opengl/xorg-x11/lib/libGL.so in *... ] media-libs/mesa-7.0.2 (/usr/lib/opengl/xorg-x11/lib/libGL.so - libGL.so.1.2) localhost liviu # eix media-libs/mesa [I] media-libs/mesa Available versions: 6.5.2-r1 (~)7.0.2 Installed versions: 7.0.2(22:55:32 26/02/08) Do you think removing /usr/lib/libGL.so is reasonable? __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On Mon, Mar 17, 2008 at 1:54 AM, Charles C. Berry [EMAIL PROTECTED] wrote: emerge -pD R to see what would get rebuilt. (This should rebuild out-of-date dependencies.) emerge -tvaD R proposes me to emerge all out-dated packages found on my system, from gimp to dbus (currently 292,146 kB). Do you think it is possible to simply emerge/pinpoint R's out-dated dependencies? (I haven't yet found how to do this.) Thanks, Liviu __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On Mon, 17 Mar 2008, Liviu Andronic wrote: On Mon, Mar 17, 2008 at 1:54 AM, Charles C. Berry [EMAIL PROTECTED] wrote: emerge -pD R to see what would get rebuilt. (This should rebuild out-of-date dependencies.) emerge -tvaD R proposes me to emerge all out-dated packages found on my system, from gimp to dbus (currently 292,146 kB). Do you think it is possible to simply emerge/pinpoint R's out-dated dependencies? (I haven't yet found how to do this.) Are you sure?! Perhaps you slipped in a '-N' without noticing? On my Gentoo system, 'emerge -tvaD R' gives only the dependencies of R even though there are other things needing to be rebuilt. In any case, emerge -tvaD R should show you what dependencies of R will be rebuilt. But if it doesn't, dig into 'equery depgraph R'. HTH, Chuck p.s. you really should 'emerge system' and 'emerge world' fairly often to keep your system up to date. See http://gentoo-wiki.com/HOWTO_Maintain_Gentoo_-_%22Best_Practices%22 Thanks, Liviu __ R-help@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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On 16/03/2008 3:38 PM, Liviu Andronic wrote: Dear useRs, I have several problems in using rgl-0.77 (and recent earlier versions) on Gentoo Linux with a custom-built v. 2.6.22 kernel. Currently I use R-2.6.1. When I build rgl, # R CMD INSTALL /home/liviu/inst/dwn/R/rgl_0.77.tar.gz or install.packages(rgl, dependencies=TRUE, method =wget), I notice the following warning messages: i686-pc-linux-gnu-g++ -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -march=pentium-m -pipe -fomit-frame-pointer -std=gnu99 -c api.cpp -o api.o cc1plus: warning: command line option -std=gnu99 is valid for C/ObjC but not for C++ The warning message itself is repeated during the entire build process. However, the package builds fine, but fails to load: library(rgl) Error in dyn.load(file, ...) : unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glTexCoordPointer Error : .onLoad failed in 'loadNamespace' for 'rgl' Error: package/namespace load failed for 'rgl' I had the exact same error message with rgl_0.76. Could anyone suggest how to make rgl build correctly? It sounds as though it is not finding the OpenGL libs when it configures. That function should be in libGL.so. Duncan Murdoch __ R-help@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.
Re: [R] rgl build warnings and loading error on Linux
On 16 March 2008 at 17:00, Duncan Murdoch wrote: | On 16/03/2008 3:38 PM, Liviu Andronic wrote: | Dear useRs, | | I have several problems in using rgl-0.77 (and recent earlier | versions) on Gentoo Linux with a custom-built v. 2.6.22 kernel. | Currently I use R-2.6.1. | | When I build rgl, | # R CMD INSTALL /home/liviu/inst/dwn/R/rgl_0.77.tar.gz | or | install.packages(rgl, dependencies=TRUE, method =wget), | | I notice the following warning messages: | i686-pc-linux-gnu-g++ -I/usr/lib/R/include -I/usr/lib/R/include | -I/usr/local/include-fpic -O2 -march=pentium-m -pipe | -fomit-frame-pointer -std=gnu99 -c api.cpp -o api.o | cc1plus: warning: command line option -std=gnu99 is valid for C/ObjC | but not for C++ | | The warning message itself is repeated during the entire build | process. However, the package builds fine, but fails to load: | library(rgl) | Error in dyn.load(file, ...) : |unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so': |/usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glTexCoordPointer | Error : .onLoad failed in 'loadNamespace' for 'rgl' | Error: package/namespace load failed for 'rgl' | | I had the exact same error message with rgl_0.76. | | Could anyone suggest how to make rgl build correctly? | | It sounds as though it is not finding the OpenGL libs when it | configures. That function should be in libGL.so. For what it is worth, the Debian r-cran-rgl packages uses these Build-Depends which may or may not map into similar Gentoo packages: Build-Depends: debhelper (= 5.0.0), r-base-dev (= 2.6.2), cdbs, \ libgl1-mesa-dev | libgl-dev, libglu1-mesa-dev | libglu-dev, \ libpng12-dev, libx11-dev, libxt-dev, x-dev So try looking for libgl and libglu, possibly in their mesa implementations. Hth, Dirk -- Three out of two people have difficulties with fractions. __ R-help@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.
