rgl on 10.7: has anyone tried it?

The issue seem in your setup - you should be using libraries from /usr/X11/lib (which is the default) but you are using stuff from /opt/local which is incomplete. Make sure your /opt/.. paths are *last* on your PATH, definitely after /usr/X11/bin.

Cheers,
Simon


On Oct 11, 2011, at 6:44 PM, Marius Hofert wrote:

On 2011-10-12, at 00:37 , Simon Urbanek wrote:

On Oct 11, 2011, at 6:33 PM, Marius Hofert wrote:

On 2011-10-12, at 00:12 , Simon Urbanek wrote:

On Oct 11, 2011, at 6:01 PM, Marius Hofert wrote:

On 2011-10-11, at 23:30 , Simon Urbanek wrote:

On Oct 11, 2011, at 5:16 PM, Marius Hofert wrote:

On 2011-10-11, at 23:04 , Simon Urbanek wrote:

On Oct 11, 2011, at 4:10 PM, Marius Hofert wrote:

Dear all,

I tried to install the package rgl on 10.7. Here's the output:

##############################################################################

install.packages("rgl", type="source")

install.packages("rgl", type="source")
Installing package(s) into ?/Library/Frameworks/R.framework/library?
(as ?lib? is unspecified)
trying URL 'http://stat.ethz.ch/CRAN/src/contrib/rgl_0.92.798.tar.gz'
Content type 'application/x-gzip' length 1677772 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

* installing *source* package ?rgl? ...
checking for gcc... gcc -arch x86_64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... libraries , headers 
checking for glEnd in -lGL... no
configure: error: missing required library GL
ERROR: configuration failed for package ?rgl?
* removing ?/Library/Frameworks/R.framework/library/rgl?

The downloaded packages are in
	?/private/var/folders/5r/fpc7qzk55ll71t9j8l9d1d_00000gn/T/RtmpQ6nuVK/downloaded_packages?
Warning message:
In install.packages("rgl", type = "source") :
installation of package 'rgl' had non-zero exit status

##############################################################################

Apparently, I'm missing the "GL" library. But how can I install it? I searched for it on the web and mainly found that the Mac should have Open GL already installed (?).

Are you sure you installed X11 and Xcode4?

yes, both are installed.

I have no problem with the *configuration* on vanilla Lion.

I installed about 30 packages today, everything worked fine. Hmmm... seems challenging to detect where the problem is.

If you want to do that, have a look at rgl/config.log - it will tell you what went wrong.

Hi Simon,

do you know the full path of this file? I can't find it.0

It's in the rgl directory after you run R CMD INSTALL rgl

that's removed after the configure-trial:

bash-3.2$ R CMD INSTALL rgl_0.92.798.tar.gz 
* installing to library ?/Library/Frameworks/R.framework/library?
* installing *source* package ?rgl? ...
checking for gcc... gcc -arch x86_64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... libraries , headers 
checking for glEnd in -lGL... no
configure: error: missing required library GL
ERROR: configuration failed for package ?rgl?
* removing ?/Library/Frameworks/R.framework/library/rgl?
bash-3.2$ 

=> there is no rgl folder (neither in /Library/Frameworks/R.framework/library nor in the folder in which the .tar.gz resides). 

As I said use R CMD INSTALL rgl, not on the tar ball
S

Ahh, okay, now I get it :-)
Here's the config.log:

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by configure, which was
generated by GNU Autoconf 2.64.  Invocation command line was

$ ./configure 

## --------- ##
## Platform. ##
## --------- ##

hostname = 80-218-246-245.dclient.hispeed.ch
uname -m = x86_64
uname -r = 11.0.1
uname -s = Darwin
uname -v = Darwin Kernel Version 11.0.1: Thu Jul 28 02:01:39 PDT 2011; root:xnu-1699.23.4~1/RELEASE_X86_64

/usr/bin/uname -p = i386
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = Mach kernel version:
	 Darwin Kernel Version 11.0.1: Thu Jul 28 02:01:39 PDT 2011; root:xnu-1699.23.4~1/RELEASE_X86_64
Kernel configured for up to 4 processors.
2 processors are physically available.
4 processors are logically available.
Processor type: i486 (Intel 80486)
Processors active: 0 1 2 3
Primary memory available: 4.00 gigabytes
Default processor set: 107 tasks, 499 threads, 4 processors
Load average: 0.91, Mach factor: 3.08
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /opt/local/bin
PATH: /opt/local/sbin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /usr/local/bin
PATH: /usr/X11/bin
PATH: /usr/texbin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2106: checking for gcc
configure:2133: result: gcc -arch x86_64 -std=gnu99
configure:2362: checking for C compiler version
configure:2371: gcc -arch x86_64 -std=gnu99 --version >&5
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2382: $? = 0
configure:2371: gcc -arch x86_64 -std=gnu99 -v >&5
Using built-in specs.
Target: i686-apple-darwin11
Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2335.15~25/src/configure --disable-checking --enable-werror --prefix=/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2335.15~25/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)
configure:2382: $? = 0
configure:2371: gcc -arch x86_64 -std=gnu99 -V >&5
llvm-gcc-4.2: argument to `-V' is missing
configure:2382: $? = 1
configure:2371: gcc -arch x86_64 -std=gnu99 -qversion >&5
i686-apple-darwin11-llvm-gcc-4.2: no input files
configure:2382: $? = 1
configure:2404: checking for C compiler default output file name
configure:2426: gcc -arch x86_64 -std=gnu99 -g -O2   conftest.c  >&5
configure:2430: $? = 0
configure:2467: result: a.out
configure:2483: checking whether the C compiler works
configure:2492: ./a.out
configure:2496: $? = 0
configure:2511: result: yes
configure:2518: checking whether we are cross compiling
configure:2520: result: no
configure:2523: checking for suffix of executables
configure:2530: gcc -arch x86_64 -std=gnu99 -o conftest -g -O2   conftest.c  >&5
configure:2534: $? = 0
configure:2556: result: 
configure:2562: checking for suffix of object files
configure:2584: gcc -arch x86_64 -std=gnu99 -c -g -O2  conftest.c >&5
configure:2588: $? = 0
configure:2609: result: o
configure:2613: checking whether we are using the GNU C compiler
configure:2632: gcc -arch x86_64 -std=gnu99 -c -g -O2  conftest.c >&5
configure:2632: $? = 0
configure:2641: result: yes
configure:2650: checking whether gcc -arch x86_64 -std=gnu99 accepts -g
configure:2670: gcc -arch x86_64 -std=gnu99 -c -g  conftest.c >&5
configure:2670: $? = 0
configure:2711: result: yes
configure:2728: checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89
configure:2792: gcc -arch x86_64 -std=gnu99  -c -g -O2  conftest.c >&5
configure:2792: $? = 0
configure:2805: result: none needed
configure:2830: checking how to run the C preprocessor
configure:2900: result: gcc -arch x86_64 -std=gnu99 -E
configure:2920: gcc -arch x86_64 -std=gnu99 -E  conftest.c
configure:2920: $? = 0
configure:2934: gcc -arch x86_64 -std=gnu99 -E  conftest.c
conftest.c:9:28: error: ac_nonexistent.h: No such file or directory
configure:2934: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3010: checking for gcc
configure:3037: result: gcc -arch x86_64 -std=gnu99
configure:3266: checking for C compiler version
configure:3275: gcc -arch x86_64 -std=gnu99 --version >&5
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3286: $? = 0
configure:3275: gcc -arch x86_64 -std=gnu99 -v >&5
Using built-in specs.
Target: i686-apple-darwin11
Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2335.15~25/src/configure --disable-checking --enable-werror --prefix=/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2335.15~25/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)
configure:3286: $? = 0
configure:3275: gcc -arch x86_64 -std=gnu99 -V >&5
llvm-gcc-4.2: argument to `-V' is missing
configure:3286: $? = 1
configure:3275: gcc -arch x86_64 -std=gnu99 -qversion >&5
i686-apple-darwin11-llvm-gcc-4.2: no input files
configure:3286: $? = 1
configure:3290: checking whether we are using the GNU C compiler
configure:3318: result: yes
configure:3327: checking whether gcc -arch x86_64 -std=gnu99 accepts -g
configure:3388: result: yes
configure:3405: checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89
configure:3482: result: none needed
configure:3545: checking for libpng-config
configure:3561: found /opt/local/bin/libpng-config
configure:3573: result: yes
configure:3584: using libpng-config
configure:3588: using libpng dynamic linkage
configure:3955: checking for X
configure:4063: gcc -arch x86_64 -std=gnu99 -E  -DHAVE_PNG_H -I/opt/local/include/libpng14 conftest.c
configure:4063: $? = 0
configure:4094: gcc -arch x86_64 -std=gnu99 -o conftest -g -O2  -DHAVE_PNG_H -I/opt/local/include/libpng14  conftest.c -lX11  -L/opt/local/lib -lpng14 >&5
configure:4094: $? = 0
configure:4144: result: libraries , headers 
configure:4229: checking for glEnd in -lGL
configure:4254: gcc -arch x86_64 -std=gnu99 -o conftest -g -O2 -I/System/Library/Frameworks/OpenGL.framework/Headers  -DHAVE_PNG_H -I/opt/local/include/libpng14 -DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include  conftest.c -lGL  -framework OpenGL -dylib_file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib  -L/opt/local/lib -lpng14 -lX11 >&5
ld: library not found for -lGL
collect2: ld returned 1 exit status
configure:4254: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| 
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char glEnd ();
| int
| main ()
| {
| return glEnd ();
|   ;
|   return 0;
| }
configure:4264: result: no
configure:4278: error: missing required library GL

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_c_compiler_gnu=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_XMKMF_set=
ac_cv_env_XMKMF_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_have_x='have_x=yes	ac_x_includes='\'''\''	ac_x_libraries='\'''\'''
ac_cv_lib_GL___glEnd=no
ac_cv_objext=o
ac_cv_prog_CPP='gcc -arch x86_64 -std=gnu99 -E'
ac_cv_prog_HAVE_LIBPNG_CONFIG=yes
ac_cv_prog_ac_ct_CC='gcc -arch x86_64 -std=gnu99'
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

AGLCPPFLAGS=''
AGLLIBS=''
BUILD_AGL_TRUE='#'
CC='gcc -arch x86_64 -std=gnu99'
CFLAGS='-g -O2'
CPP='gcc -arch x86_64 -std=gnu99 -E'
CPPFLAGS='-I/System/Library/Frameworks/OpenGL.framework/Headers  -DHAVE_PNG_H -I/opt/local/include/libpng14 -DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include'
CXXFLAGS='-g -O2'
DEFS=''
ECHO_C='\c'
ECHO_N=''
ECHO_T=''
EGREP=''
EXEEXT=''
GREP=''
HAVE_FREETYPE_CONFIG=''
HAVE_LIBPNG_CONFIG='yes'
LDFLAGS=''
LIBOBJS=''
LIBS='-framework OpenGL -dylib_file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib  -L/opt/local/lib -lpng14 -lX11'
LTLIBOBJS=''
OBJEXT='o'
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_URL=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
SHELL='/bin/sh'
XMKMF=''
ac_ct_CC='gcc -arch x86_64 -std=gnu99'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE}'
dvidir='${docdir}'
exec_prefix='NONE'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define PACKAGE_STRING ""
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""

configure: exit 1

There is still an issue in the rgl 0.92.798 code (opengl.hpp), though, it's including AGL/* instead of OpenGL/* which fails (hence CC to Duncan), but that's at compilation stage, not configuration.

BTW: why don't you just use
install.packages("rgl")
that works on Lion as well...

I installed all packages from source since I installed R from source and I remember reading somewhere that one should do it this way since the binaries are built to work with CRAN's binary installation of R. But if this does not create problems (please let me know), I'll give it a try.

As long as your configuration is compatible (essentially you have to set r_arch properly) it works. It's not guaranteed to work if you use different compilers.

I tried:
install.packages("rgl", configure.args="--r_arch=x86_64")

Naw, you got wrong - I was talking about R configuration. Never mind then (you may want to read up on building R - see the R for Mac FAQ).

Cheers,
Simon

but the outcome was:

install.packages("rgl", configure.args="--r_arch=x86_64")

install.packages("rgl", configure.args="--r_arch=x86_64")
Installing package(s) into ?/Library/Frameworks/R.framework/library?
(as ?lib? is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://stat.ethz.ch/CRAN/src/contrib/rgl_0.92.798.tar.gz'
Content type 'application/x-gzip' length 1677772 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

* installing *source* package ?rgl? ...
configure: error: unrecognized option: `--r_arch=x86_64'
Try `./configure --help' for more information.
ERROR: configuration failed for package ?rgl?
* removing ?/Library/Frameworks/R.framework/library/rgl?

The downloaded packages are in
	?/private/var/folders/5r/fpc7qzk55ll71t9j8l9d1d_00000gn/T/RtmpzmXkSd/downloaded_packages?
Warning message:
In install.packages("rgl", configure.args = "--r_arch=x86_64") :
installation of package 'rgl' had non-zero exit status

How/Where should r_arch be specified?

Cheers,

Marius

I just remember something: I installed the 64bit R version. Is this a problem for rgl?

No.

Cheers,
Simon

Cheers,

Marius

Cheers,
Simon


[PS: while at it - I'm a bit confused about the current setup, though, since it uses the (non-X11) OpenGL framework yet links X11;  Also it crashes when GLX is not supported (e.g. ssh tunneling). I remember that at some point in the past it was building native and X11 versions but what is left is some mix of both...]

Cheers,

Marius