[R-SIG-Mac] installing rgl with the 3.0 RC
Bryan Hanson
hanson at depauw.edu
Tue Feb 5 20:15:58 CET 2013
[Fixed it with everyone's help and learned something useful along the way. Here's how I worked it out, mainly for my records. Bryan]
Alright, let me try to pull some ideas from the different answers together here. When I did:
install.packages("rgl", repos = "http://r-forge.r-project.org/", type = "source", configure.args = "--no-cocoa")
because rgl has it's own configure script, it detected that I am on x86_64 and did not install the i386 version. For building my own package I'd like to use both arch's and so when I tried to build it, it saw there were no i386 resources and stopped. I think this much is right (please correct me if not). This is the main problem.
Now, after reading R-inst, I thought the solution would be to do this:
install.packages("rgl", repos = "http://r-forge.r-project.org/", type = "source", configure.args = c("--no-cocoa", "--arch=i386", "--libs-only"))
But that does not work, it does not recognize any of the configure.args (tried each separately). I was thinking this might be because rgl's configure script overrode these. So, using Rob's idea, I moved to one of the tempdirs of these unsuccessful installations, and tried it from the command line:
R CMD INSTALL --libs-only rgl_0.93.924.tar.gz
but this doesn't give me the needed framework either, probably still auto-detecting the arch. After several variations and re-reading R-inst,
R --arch=i386 CMD INSTALL --libs-only rgl_0.93.924.tar.gz
worked, in which I discovered that the flags have to be in the right place (!). In particular, --arch must be with R and not CMD. I'm sure I knew this once.
Thanks for all your patience and help. I seem to be running. Bryan
On Feb 5, 2013, at 11:09 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
> 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 <ripley at 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 <goedman at icloud.com> wrote:
>>>>
>>>>> Bryan,
>>>>>
>>>>> It looks like it's mixing packages compiled for 32 and 64 bit.
>>>>>
>>>>> Regards,
>>>>> Rob J. Goedman
>>>>> goedman at icloud.com
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Feb 5, 2013, at 7:46 AM, Bryan Hanson <hanson at 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 <goedman at 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
>>>>>>> goedman at icloud.com
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Feb 5, 2013, at 5:25 AM, Duncan Murdoch <murdoch.duncan at 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
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> R-SIG-Mac at r-project.org
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>>>
>>> --
>>> Brian D. Ripley, ripley at 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
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>
>
> --
> Brian D. Ripley, ripley at 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
More information about the R-SIG-Mac
mailing list