On 05/02/2013 16:07, Bryan Hanson wrote:
Thanks, I'll try that in a short while. But I'm still not sure exactly sure
how this issue arose, I only work with the 64 bit version (or so I thought).
Bryan
But the R you installed from CRAN is biarch and hence tries to install
packages for both i386 and x86_64. If you only want 64-bit packages,
use R CMD INSTALL --no-multiarch.
On Feb 5, 2013, at 11:01 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote:
On 05/02/2013 15:56, Bryan Hanson wrote:
Is that something I can control? I've never had to worry about that before,
never run into it. Clearly I'm near the edge of my expertise. Thanks, Bryan
See the --merge-multiarch argument to INSTALL, or 'Writing R Extensions'.
Since rgl has a configure script, you only installed it for x64_64.
On Feb 5, 2013, at 10:53 AM, Robert J Goedman <goed...@icloud.com> wrote:
Bryan,
It looks like it's mixing packages compiled for 32 and 64 bit.
Regards,
Rob J. Goedman
goed...@icloud.com
On Feb 5, 2013, at 7:46 AM, Bryan Hanson <han...@depauw.edu> wrote:
Thanks Rob, that's a very good trick to know.
Duncan's suggestion about using configure.args="--disable-cocoa" worked for me
- I have an rgl installation that works interactively. Now however, when I try to
install a source package that uses rgl, I get the following (also sent to Duncan
separately). Does this ring any bells? I'm not sure what the install process is doing
with dependent packages that is different, but obviously it doesn't like something.
Thank you. Bryan
* installing *source* package ‘ChemoSpec’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘panel.lines’ when loading ‘lattice’
** help
*** installing help indices
** building package indices
** installing vignettes
‘ChemoSpec.Rnw’
** testing if installed package can be loaded
*** arch - i386
********
******** Loading Bryan's .Rprofile
********
Loading required package: brew
********
******** Completed Bryan's .Rprofile GET TO WORK!
********
Warning: replacing previous import ‘panel.lines’ when loading ‘lattice’
Error : .onLoad failed in loadNamespace() for 'rgl', details:
call: library.dynam(dll, pkg, lib.loc = lib)
error: shared object ‘rgl.so’ not found
Error: loading failed
Execution halted
*** arch - x86_64
********
******** Loading Bryan's .Rprofile
********
Loading required package: brew
********
******** Completed Bryan's .Rprofile GET TO WORK!
********
Warning: replacing previous import ‘panel.lines’ when loading ‘lattice’
ERROR: loading failed for ‘i386’
* removing ‘/Users/bryanhanson/Library/R/3.0/library/ChemoSpec’
* restoring previous ‘/Users/bryanhanson/Library/R/3.0/library/ChemoSpec’
On Feb 5, 2013, at 10:35 AM, Robert J Goedman <goed...@icloud.com> wrote:
Bryan,
I've seen that issue a couple of times as well. Trying to install rgl 0.93.934
from R-Forge using R.app, I get (in the R.app console):
...
mv AGL/* .
MAKINGAGL=TRUE /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o
aglrgl.so *.cpp *.c \
osx/*.mm osx/*.cpp
mv: rename AGL/* to ./*: No such file or directory
make: [aglrgl.so] Error 1 (ignored)
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG
-DHAVE_PNG_H -DRGL_USE_COCOA -Iext -I/usr/local/include -g -O2 -fPIC -g -O2
-c x11gui.cpp -o x11gui.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG
-DHAVE_PNG_H -DRGL_USE_COCOA -Iext -I/usr/local/include -g -O2 -fPIC -g -O2
-c x11lib.cpp -o x11lib.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG
-DHAVE_PNG_H -DRGL_USE_COCOA -Iext -I/usr/local/include -fPIC -c
osx/osxgui.mm -o osx/osxgui.o
osx/osxgui.mm:9:2: error: #error Cocoa backend reguires FreeType font reneder
make[1]: *** [osx/osxgui.o] Error 1
make: *** [aglrgl.so] Error 1
The downloaded source packages are in
‘/private/var/folders/fl/jchvcqm92rd7bjh6hzkd1cqc0000gn/T/RtmpgyhrHG/downloaded_packages’
ERROR: compilation failed for package ‘rgl’
* removing ‘/Users/rob/Library/R/3.0/library/rgl’
* restoring previous ‘/Users/rob/Library/R/3.0/library/rgl’
On my system the following trick works. Make sure to keep a copy of the RGL
package you want to install (typically the version is in the directory
containing the downloaded packages, as printed at the end of the install
process in the R.app console). Notice that these are removed if you quit R.app!
So just keep R.app running.
I then use, in a terminal window:
cd
/private/var/folders/fl/jchvcqm92rd7bjh6hzkd1cqc0000gn/T/RtmpgyhrHG/downloaded_packages
R_ARCH=/X86_64 R CMD INSTALL rgl_0.93.924.tar.gz
Towards the end of the build/install I get:
...
installing to /Users/rob/Library/R/3.0/library/rgl/libs/X86_64
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning in rgl.init(initValue) : RGL: unable to open X11 display
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (rgl)
These last 2 warning messages only show up if XQuartz.app is not running.
Testing in R.app:
library(rgl)
demo(rgl)
works (at least on my system!).
Regards,
Rob J. Goedman
goed...@icloud.com
On Feb 5, 2013, at 5:25 AM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
On 13-02-05 8:07 AM, Bryan Hanson wrote:
Thanks for taking the time to look at this carefully Duncan. I don't see the
warning you mention, and I don't see the string R_pretty0 in the log either.
I'm appending right here in case there is something else you want to look at.
I restarted my computer but the result is the same. I'm on OSX OS X 10.8.2
(12C60). Thanks, Bryan
Okay, now you're getting a different error than you described before. This one
I think you can fix: you need Freetype, and rgl needs to be able to find it
when you do the install. Normally it does that using the freetype-config
utility, but you're not finding that:
[deletions]
checking for freetype-config... no
I thought (from online readings) that Freetype should be available in a
standard OSX install, so I'm not sure why it's not working for you. You can
disable the Cocoa (native) support by configuring with the configure option
install.packages("rgl", ..., configure.args="--disable-cocoa")
and then you should be able to get the install to complete, but it might be
better to figure out why freetype-config isn't working for you.
Duncan Murdoch
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
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, UK Fax: +44 1865 272595
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
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, UK Fax: +44 1865 272595
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