[R-SIG-Mac] Loading rgl fails on 2.7.0
Simon Urbanek
simon.urbanek at r-project.org
Thu Feb 14 13:48:00 CET 2008
Michael, please read yesterday's rgl thread on the SIG-Mac mailing
list - it explains both the cause and fixes.
Thanks,
Simon
On Feb 13, 2008, at 8:41 PM, Michael Kubovy wrote:
> Hi Simon,
>
> Here is the rgl/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 2.59. Invocation command line was
>
> $ ./configure
>
> ## --------- ##
> ## Platform. ##
> ## --------- ##
>
> hostname = MK-MacPro.local
> uname -m = i386
> uname -r = 9.1.0
> uname -s = Darwin
> uname -v = Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT
> 2007; root:xnu-1228.0.2~1/RELEASE_I386
>
> /usr/bin/uname -p = i386
> /bin/uname -X = unknown
>
> /bin/arch = unknown
> /usr/bin/arch -k = unknown
> /usr/convex/getsysinfo = unknown
> hostinfo = Mach kernel version:
> Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007;
> root:xnu-1228.0.2~1/RELEASE_I386
> Kernel configured for up to 4 processors.
> 4 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: 120 tasks, 589 threads, 4 processors
> Load average: 1.09, Mach factor: 2.90
> /bin/machine = unknown
> /usr/bin/oslevel = unknown
> /bin/universe = unknown
>
> PATH: /usr/X11/bin
> PATH: /usr/X11/bin
> PATH: /usr/X11/bin
> PATH: /bin
> PATH: /sbin
> PATH: /usr/bin
> PATH: /usr/sbin
> PATH: /usr/local/bin
> PATH: /usr/local/sbin
> PATH: /usr/local/bin
> PATH: /usr/local/sbin
> PATH: /usr/local/teTeX/ bin/powerpc-apple-darwin-current
> PATH: /usr/X11/bin
> PATH: /usr/local/bin
> PATH: /usr/texbin
>
>
> ## ----------- ##
> ## Core tests. ##
> ## ----------- ##
>
> configure:1391: checking for gcc
> configure:1417: result: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99
> configure:1661: checking for C compiler version
> configure:1664: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 --version </dev/
> null >&5
> i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> Copyright (C) 2005 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:1667: $? = 0
> configure:1669: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -v </dev/null >&5
> Using built-in specs.
> Target: i686-apple-darwin9
> Configured with: /var/tmp/gcc/gcc-5465~16/src/configure --disable-
> checking -enable-werror --prefix=/usr --mandir=/share/man --enable-
> languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/
> s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/
> usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-
> tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9
> Thread model: posix
> gcc version 4.0.1 (Apple Inc. build 5465)
> configure:1672: $? = 0
> configure:1674: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -V </dev/null >&5
> gcc-4.0: argument to `-V' is missing
> configure:1677: $? = 1
> configure:1700: checking for C compiler default output file name
> configure:1703: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -g -O2 -
> march=nocona conftest.c >&5
> configure:1706: $? = 0
> configure:1752: result: a.out
> configure:1757: checking whether the C compiler works
> configure:1763: ./a.out
> configure:1766: $? = 0
> configure:1783: result: yes
> configure:1790: checking whether we are cross compiling
> configure:1792: result: no
> configure:1795: checking for suffix of executables
> configure:1797: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -o conftest -g -
> O2 -march=nocona conftest.c >&5
> configure:1800: $? = 0
> configure:1825: result:
> configure:1831: checking for suffix of object files
> configure:1852: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -c -g -O2 -
> march=nocona conftest.c >&5
> configure:1855: $? = 0
> configure:1877: result: o
> configure:1881: checking whether we are using the GNU C compiler
> configure:1905: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -c -g -O2 -
> march=nocona conftest.c >&5
> configure:1911: $? = 0
> configure:1915: test -z
> || test ! -s conftest.err
> configure:1918: $? = 0
> configure:1921: test -s conftest.o
> configure:1924: $? = 0
> configure:1937: result: yes
> configure:1943: checking whether gcc -arch i386 -isysroot /Developer/
> SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 accepts -g
> configure:1964: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -c -g
> conftest.c >&5
> configure:1970: $? = 0
> configure:1974: test -z
> || test ! -s conftest.err
> configure:1977: $? = 0
> configure:1980: test -s conftest.o
> configure:1983: $? = 0
> configure:1994: result: yes
> configure:2011: checking for gcc -arch i386 -isysroot /Developer/
> SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 option to
> accept ANSI C
> configure:2081: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -c -g -O2 -
> march=nocona conftest.c >&5
> configure:2087: $? = 0
> configure:2091: test -z
> || test ! -s conftest.err
> configure:2094: $? = 0
> configure:2097: test -s conftest.o
> configure:2100: $? = 0
> configure:2118: result: none needed
> configure:2136: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -c -g -O2 -
> march=nocona conftest.c >&5
> conftest.c:2: error: syntax error before 'me'
> configure:2142: $? = 1
> configure: failed program was:
> | #ifndef __cplusplus
> | choke me
> | #endif
> configure:2280: checking how to run the C preprocessor
> configure:2315: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -E conftest.c
> configure:2321: $? = 0
> configure:2353: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -E conftest.c
> conftest.c:9:28: error: ac_nonexistent.h: No such file or directory
> configure:2359: $? = 1
> configure: failed program was:
> | /* confdefs.h. */
> |
> | #define PACKAGE_NAME ""
> | #define PACKAGE_TARNAME ""
> | #define PACKAGE_VERSION ""
> | #define PACKAGE_STRING ""
> | #define PACKAGE_BUGREPORT ""
> | /* end confdefs.h. */
> | #include <ac_nonexistent.h>
> configure:2398: result: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -E
> configure:2422: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -E conftest.c
> configure:2428: $? = 0
> configure:2460: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -E conftest.c
> conftest.c:9:28: error: ac_nonexistent.h: No such file or directory
> configure:2466: $? = 1
> configure: failed program was:
> | /* confdefs.h. */
> |
> | #define PACKAGE_NAME ""
> | #define PACKAGE_TARNAME ""
> | #define PACKAGE_VERSION ""
> | #define PACKAGE_STRING ""
> | #define PACKAGE_BUGREPORT ""
> | /* end confdefs.h. */
> | #include <ac_nonexistent.h>
> configure:2555: checking for gcc
> configure:2581: result: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99
> configure:2825: checking for C compiler version
> configure:2828: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 --version </dev/
> null >&5
> i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> Copyright (C) 2005 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:2831: $? = 0
> configure:2833: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -v </dev/null >&5
> Using built-in specs.
> Target: i686-apple-darwin9
> Configured with: /var/tmp/gcc/gcc-5465~16/src/configure --disable-
> checking -enable-werror --prefix=/usr --mandir=/share/man --enable-
> languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/
> s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/
> usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-
> tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9
> Thread model: posix
> gcc version 4.0.1 (Apple Inc. build 5465)
> configure:2836: $? = 0
> configure:2838: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -V </dev/null >&5
> gcc-4.0: argument to `-V' is missing
> configure:2841: $? = 1
> configure:2844: checking whether we are using the GNU C compiler
> configure:2900: result: yes
> configure:2906: checking whether gcc -arch i386 -isysroot /Developer/
> SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 accepts -g
> configure:2957: result: yes
> configure:2974: checking for gcc -arch i386 -isysroot /Developer/
> SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 option to
> accept ANSI C
> configure:3081: result: none needed
> configure:3099: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -c -g -O2 -
> march=nocona conftest.c >&5
> conftest.c:2: error: syntax error before 'me'
> configure:3105: $? = 1
> configure: failed program was:
> | #ifndef __cplusplus
> | choke me
> | #endif
> configure:3274: checking for libpng-config
> configure:3290: found /usr/X11/bin/libpng-config
> configure:3301: result: yes
> configure:3311: using libpng-config
> configure:3315: using libpng dynamic linkage
> configure:3842: checking for X
> configure:4072: result: libraries /usr/X11/lib, headers /usr/X11/
> include
> configure:4293: checking for glEnd in -lGL
> configure:4323: gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -o conftest -g -
> O2 -march=nocona -I/System/Library/Frameworks/OpenGL.framework/
> Headers -DHAVE_PNG_H -I/usr/X11/include -I/usr/X11/include -DDarwin
> -DNO_GL_PREFIX -I/usr/X11R6/include conftest.c -lGL -framework
> OpenGL -L/usr/X11/lib -Wl,-rpath,/usr/X11/lib -lpng12 -lz -lm -L/
> usr/X11/lib -lX11 >&5
> ld: -rpath can only be used when targeting Mac OS X 10.5 or later
>
> collect2: ld returned 1 exit status
> configure:4329: $? = 1
> configure: failed program was:
> | /* confdefs.h. */
> |
> | #define PACKAGE_NAME ""
> | #define PACKAGE_TARNAME ""
> | #define PACKAGE_VERSION ""
> | #define PACKAGE_STRING ""
> | #define PACKAGE_BUGREPORT ""
> | /* end confdefs.h. */
> |
> | /* Override any gcc2 internal prototype to avoid an error. */
> | #ifdef __cplusplus
> | extern "C"
> | #endif
> | /* We use char because int might match the return type of a gcc2
> | builtin and then its argument prototype would still apply. */
> | char glEnd ();
> | int
> | main ()
> | {
> | glEnd ();
> | ;
> | return 0;
> | }
> configure:4355: result: no
> configure:4368: 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_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_exeext=
> ac_cv_have_x='have_x=yes ac_x_includes=/usr/X11/include
> ac_x_libraries=/usr/X11/lib'
> ac_cv_lib_GL___glEnd=no
> ac_cv_objext=o
> ac_cv_prog_CPP='gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -E'
> ac_cv_prog_HAVE_LIBPNG_CONFIG=yes
> ac_cv_prog_ac_ct_CC='gcc -arch i386 -isysroot /Developer/SDKs/
> MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99'
> ac_cv_prog_cc_g=yes
> ac_cv_prog_cc_stdc=
>
> ## ----------------- ##
> ## Output variables. ##
> ## ----------------- ##
>
> AGLCPPFLAGS=' -DHAVE_PNG_H -I/usr/X11/include -DRGL_USE_CARBON -I/
> System/Library/Frameworks/AGL.framework/Headers'
> AGLLIBS=' -L/usr/X11/lib -Wl,-rpath,/usr/X11/lib -lpng12 -lz -lm -
> framework AGL'
> BUILD_AGL_TRUE=''
> CC='gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -
> mmacosx-version-min=10.4 -std=gnu99'
> CFLAGS='-g -O2 -march=nocona'
> CPP='gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -
> mmacosx-version-min=10.4 -std=gnu99 -E'
> CPPFLAGS='-I/System/Library/Frameworks/OpenGL.framework/Headers -
> DHAVE_PNG_H -I/usr/X11/include -I/usr/X11/include -DDarwin -
> DNO_GL_PREFIX -I/usr/X11R6/include'
> CXXFLAGS='-g -O2 -march=nocona'
> DEFS=''
> ECHO_C='ECHO_N=''
> ECHO_T=''
> EGREP='/usr/bin/grep -E'
> EXEEXT=''
> HAVE_LIBPNG_CONFIG='yes'
> LDFLAGS=''
> LIBOBJS=''
> LIBS='-framework OpenGL -L/usr/X11/lib -Wl,-rpath,/usr/X11/lib -
> lpng12 -lz -lm -L/usr/X11/lib -lX11'
> LTLIBOBJS=''
> OBJEXT='o'
> PACKAGE_BUGREPORT=''
> PACKAGE_NAME=''
> PACKAGE_STRING=''
> PACKAGE_TARNAME=''
> PACKAGE_VERSION=''
> PATH_SEPARATOR=':'
> SHELL='/bin/sh'
> ac_ct_CC='gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -
> mmacosx-version-min=10.4 -std=gnu99'
> bindir='${exec_prefix}/bin'
> build_alias=''
> datadir='${prefix}/share'
> exec_prefix='NONE'
> host_alias=''
> includedir='${prefix}/include'
> infodir='${prefix}/info'
> libdir='${exec_prefix}/lib'
> libexecdir='${exec_prefix}/libexec'
> localstatedir='${prefix}/var'
> mandir='${prefix}/man'
> oldincludedir='/usr/include'
> prefix='NONE'
> program_transform_name='s,x,x,'
> sbindir='${exec_prefix}/sbin'
> sharedstatedir='${prefix}/com'
> sysconfdir='${prefix}/etc'
> target_alias=''
>
> ## ----------- ##
> ## confdefs.h. ##
> ## ----------- ##
>
> #define PACKAGE_BUGREPORT ""
> #define PACKAGE_NAME ""
> #define PACKAGE_STRING ""
> #define PACKAGE_TARNAME ""
> #define PACKAGE_VERSION ""
> ***********************************
>
> On Feb 12, 2008, at 12:39 PM, Simon Urbanek wrote:
>
>> are you sure you have put /usr/X11/bin on your PATH? That is
>> probably the most common mistake. The safest bet to see what went
>> wrong is to look at the configure output.
>>
>> Cheers,
>> Simon
>>
>> On Feb 12, 2008, at 10:20 AM, Michael Kubovy wrote:
>>
>>> Hi Simon,
>>>
>>> Thanks. So in Terminal:
>>>
>>> MK-MacPro:lib mk$ cd /usr/X11/lib
>>> MK-MacPro:lib mk$ sudo bash
>>> Password:
>>> bash-3.2# mv libGL.dylib libGL.dylib.apple
>>> bash-3.2# ln -s /System/Library/Frameworks/OpenGL.framework/
>>> Libraries/libGL.dylib .
>>>
>>> Then in R:
>>> > install.packages('rgl', type = 'source', lib = '/Library/
>>> Frameworks/R.framework/Versions/2.7/Resources/library')
>>> trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rgl_0.76.tar.gz'
>>> Content type 'application/x-gzip' length 803143 bytes (784 Kb)
>>>
>>> <snip>
>>>
>>> The downloaded packages are in
>>> /private/var/folders/TG/TG6nWu2pHYCI-BdWWiyMxU+++TI/-Tmp-/
>>> RtmpuLU92a/downloaded_packages
>>> Warning message:
>>> In install.packages("rgl", type = "source", lib = "/Library/
>>> Frameworks/R.framework/Versions/2.7/Resources/library") :
>>> installation of package 'rgl' had non-zero exit status
>>> no
>>> configure: error: X11 not found but required, configure aborted.
>>> ERROR: configuration failed for package 'rgl'
>>> ** Removing '/Library/Frameworks/R.framework/Versions/2.7/
>>> Resources/library/rgl'
>
> _____________________________
> Professor Michael Kubovy
> University of Virginia
> Department of Psychology
> USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
> Parcels: Room 102 Gilmer Hall
> McCormick Road Charlottesville, VA 22903
> Office: B011 +1-434-982-4729
> Lab: B019 +1-434-982-4751
> Fax: +1-434-982-4766
> WWW: http://www.people.virginia.edu/~mk9y/
>
>
>
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