Re: [R-SIG-Mac] installing rgl with the 3.0 RC
Hi Duncan,
Rgl v0.93.925 (yesterday) 0.93.926 (this morning) installed fine from within
R.app.
Thanks a lot,
Rob J. Goedman
goed...@icloud.com
On Feb 5, 2013, at 10:22 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
On 05/02/2013 11:07 AM, 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
I have just updated the configure script in rgl on R-forge. It successfully
detected freetype-config in /usr/X11/bin on my 10.6.8 system when I hid the
default one in /usr/local/bin, but I don't suppose that means it's sure to
work on your system.
So could you please download the version 0.93.925 of rgl as soon as it
becomes available, and try that? You shouldn't need the --disable-cocoa any
more, but you will still need to match 32 vs 64 bits.
Duncan Murdoch
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/jchvcqm92rd7bjh6hzkd1cqcgn/T/RtmpgyhrHG/downloaded_packages
ERROR: compilation failed for package
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
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@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
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/jchvcqm92rd7bjh6hzkd1cqcgn/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/jchvcqm92rd7bjh6hzkd1cqcgn/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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
On 05/02/2013 13:25, Duncan Murdoch 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. On Mountain Lion it's part of XQuartz which has a different layout than Apple's X11 had. freetype-config is in /usr/X11/bin, and that is not by default on the path. You need it for the X11 part too. -- 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, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
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/jchvcqm92rd7bjh6hzkd1cqcgn/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/jchvcqm92rd7bjh6hzkd1cqcgn/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
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
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 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/jchvcqm92rd7bjh6hzkd1cqcgn/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/jchvcqm92rd7bjh6hzkd1cqcgn/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,
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
On 05/02/2013 10:46 AM, Prof Brian Ripley wrote: On 05/02/2013 13:25, Duncan Murdoch 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. On Mountain Lion it's part of XQuartz which has a different layout than Apple's X11 had. freetype-config is in /usr/X11/bin, and that is not by default on the path. You need it for the X11 part too. Thanks, that's helpful. I'll see if an update to autoconf is enough to find it. If not, I'll try a manual addition to configure.ac. And then I'll try sending the update to CRAN... Duncan Murdoch ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
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/jchvcqm92rd7bjh6hzkd1cqcgn/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/jchvcqm92rd7bjh6hzkd1cqcgn/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
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
On 05/02/2013 11:07 AM, 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 I have just updated the configure script in rgl on R-forge. It successfully detected freetype-config in /usr/X11/bin on my 10.6.8 system when I hid the default one in /usr/local/bin, but I don't suppose that means it's sure to work on your system. So could you please download the version 0.93.925 of rgl as soon as it becomes available, and try that? You shouldn't need the --disable-cocoa any more, but you will still need to match 32 vs 64 bits. Duncan Murdoch 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/jchvcqm92rd7bjh6hzkd1cqcgn/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
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
[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 rip...@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 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
Re: [R-SIG-Mac] installing rgl with the 3.0 RC
On 13-02-04 9:06 PM, Bryan Hanson wrote: I don't think I've seen this reported yet (apologies if I missed it). The version on CRAN is out of date. You want to get the one from R-forge. Duncan Murdoch There has previously been a problem similar to this, which was fixed by removing aglrgl.so (documented here: http://r-forge.r-project.org/tracker/index.php?func=detailaid=1996group_id=234atid=946). Trying to install the binary version, it downloads fine, reporting as follows: install.packages(rgl) Installing package into ‘/Users/bryanhanson/Library/R/3.0/library’ (as ‘lib’ is unspecified) There is a binary version available (and will be installed) but the source version is later: binary source rgl 0.92.894 0.93.921 Next: library(rgl) Error : .onLoad failed in loadNamespace() for 'rgl', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/bryanhanson/Library/R/3.0/library/rgl/libs/x86_64/aglrgl.so': dlopen(/Users/bryanhanson/Library/R/3.0/library/rgl/libs/x86_64/aglrgl.so, 6): Symbol not found: _R_pretty0 Referenced from: /Users/bryanhanson/Library/R/3.0/library/rgl/libs/x86_64/aglrgl.so Expected in: /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libR.dylib Error: package or namespace load failed for ‘rgl’ This is NOT the same missing symbol as previously reported. The output from installing from source is appended at the very bottom of this message. For kicks, I tried deleting aglrgl.so which was the previous fix. That doesn't work here, it just pushes the problem to rgl.so and if you delete that, it really tanks. I hope this is clear. Anyone have a suggestion? Thanks, Bryan *** sessionInfo() R Under development (unstable) (2013-02-03 r61829) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets [7] methods base other attached packages: [1] ggplot2_0.9.3 lattice_0.20-13 plyr_1.8 [4] sos_1.3-5 brew_1.0-6 loaded via a namespace (and not attached): [1] amap_0.8-7 chemometrics_1.3.8 class_7.3-5 [4] colorspace_1.2-0 dichromat_1.2-4digest_0.6.1 [7] e1071_1.6-1gtable_0.1.2 labeling_0.1 [10] MASS_7.3-23munsell_0.4mvoutlier_1.9.9 [13] mvtnorm_0.9-9994 nnet_7.3-5 pcaPP_1.9-48 [16] pls_2.3-0 proto_0.3-10 RColorBrewer_1.0-5 [19] reshape2_1.2.2 robustbase_0.9-4 rpart_4.1-0 [22] scales_0.2.3 seriation_1.0-9som_0.3-5 [25] stringr_0.6.2 tools_3.0.0TSP_1.0-7 ** Output from source build: install.packages(rgl, type = source) Installing package into ‘/Users/bryanhanson/Library/R/3.0/library’ (as ‘lib’ is unspecified) trying URL 'http://cran.at.r-project.org/src/contrib/rgl_0.93.921.tar.gz' Content type 'application/x-gzip' length 1731089 bytes (1.7 Mb) opened URL == downloaded 1.7 Mb Loading Bryan's .Rprofile Loading required package: brew Completed Bryan's .Rprofile GET TO WORK! * installing *source* package ‘rgl’ ... ** package ‘rgl’ successfully unpacked and MD5 sums checked checking for gcc... gcc -arch x86_64 -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 -arch x86_64 -std=gnu99 accepts -g... yes checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -arch x86_64 -std=gnu99 -E checking for gcc... (cached) gcc -arch x86_64 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc -arch x86_64 -std=gnu99 accepts -g... (cached) yes checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89... (cached) none needed checking for libpng-config... no checking libpng... checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking png.h usability... no checking png.h presence... no checking for png.h... no checking for png_read_update_info in -lpng... no configure: libpng header and lib found configure: using libpng dynamic linkage checking for X... libraries /usr/X11/lib, headers /usr/X11/include checking for glEnd
