[R-SIG-Mac] rpy on macbook

[Ruedi Fries]

Simon,

I tried the 2.3.1 binary. It doesn't make a difference.

There are actually two problems:

[macbook:/rpy-0.99.2] fries% python setup.py build
RHOMES= []
Setting RHOMES to  ['/Library/Frameworks/R.framework/Resources']
Traceback (most recent call last):
  File "setup.py", line 80, in ?
    RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
  File "/rpy-0.99.2/rpy_tools.py", line 102, in get_R_VERSION
    raise RuntimeError("Couldn't obtain version number from output\n"
RuntimeError: Couldn't obtain version number from output
of `R --version'.

I changed lines 80 and 81 of setup.py  to

RVERSION = '2.3.1'
RVER     = '2031'

Then I get the following:

[macbook:/rpy-0.99.2] fries% python setup.py build
RHOMES= []
Setting RHOMES to  ['/Library/Frameworks/R.framework/Resources']
### Using R verion 3.2.1 installed at 
/Library/Frameworks/R.framework/Resources ###
RHOME= /Library/Frameworks/R.framework/Resources
copying src/rpymodule.c -> src/rpymodule3021.c
copying src/R_eval.c -> src/R_eval3021.c
copying src/io.c -> src/io3021.c
running build
running build_py
running build_ext
building '_rpy3021' extension
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g 
-bundle -undefined dynamic_lookup 
build/temp.macosx-10.4-fat-2.4/src/rpymodule3021.o build/temp.macosx-
4-fat-2.4/src/R_eval3021.o build/temp.macosx-10.4-fat-2.4/src/io3021.o 
-L/Library/Frameworks/R.framework/Resources/bin 
-L/Library/Frameworks/R.framework/Resources/lib -LC -L
nGW\lib;C -L\WinNT\System32;C -L\Windows\System32 
-L/Library/Frameworks/R.framework/Resources/bin 
-L/Library/Frameworks/R.framework/Resources/lib -lR -o build/lib.macosx-10.
at-2.4/_rpy3021.so
/usr/bin/ld: warning -L: directory name (C) does not exist
/usr/bin/ld: warning -L: directory name (\MinGW\lib;C) does not exist
/usr/bin/ld: warning -L: directory name (\WinNT\System32;C) does not exist
/usr/bin/ld: warning -L: directory name (\Windows\System32) does not exist
/usr/bin/ld: for architecture i386
/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgfortran.0.dylib 
referenced fro
/Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)
/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib 
referenced from
Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)
/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib 
referenced f
: /Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)
/usr/bin/ld: Undefined symbols:
_add_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_clear_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_history_truncate_file referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_read_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_handler_install referenced from libR expected to be defined 
in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_handler_remove referenced from libR expected to be defined 
in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_read_char referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_stifle_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_tilde_expand referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_write_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
___divdc3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___muldc3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___moddi3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
__gfortran_compare_string referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgfortran.0.dylib
collect2: ld returned 1 exit status
/usr/bin/ld: warning -L: directory name (C) does not exist
/usr/bin/ld: warning -L: directory name (\MinGW\lib;C) does not exist
/usr/bin/ld: warning -L: directory name (\WinNT\System32;C) does not exist
/usr/bin/ld: warning -L: directory name (\Windows\System32) does not exist
/usr/bin/ld: for architecture ppc
/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgfortran.0.dylib 
referenced fro
/Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)
/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib 
referenced from
Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)

/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib 
referenced f
: /Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)
/usr/bin/ld: Undefined symbols:
_add_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_clear_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_history_truncate_file referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_read_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_handler_install referenced from libR expected to be defined 
in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_handler_remove referenced from libR expected to be defined 
in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_read_char referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_stifle_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_tilde_expand referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_write_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
___divdc3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___muldc3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___moddi3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
__gfortran_compare_string referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgfortran.0.dylib
collect2: ld returned 1 exit status
/usr/bin/ld: warning -L: directory name (C) does not exist
/usr/bin/ld: warning -L: directory name (\MinGW\lib;C) does not exist
/usr/bin/ld: warning -L: directory name (\WinNT\System32;C) does not exist
/usr/bin/ld: warning -L: directory name (\Windows\System32) does not exist
/usr/bin/ld: for architecture ppc
/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgfortran.0.dylib 
referenced fro
/Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)
/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib 
referenced from
Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)
/usr/bin/ld: warning can't open dynamic library: 
/Developer/SDKs/MacOSX10.4u.sdk/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib 
referenced f
: /Library/Frameworks/R.framework/Resources/lib/libR.dylib (checking for 
undefined symbols may be affected) (No such file or directory, errno = 2)
/usr/bin/ld: Undefined symbols:
_add_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_clear_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_history_truncate_file referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_read_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_handler_install referenced from libR expected to be defined 
in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_handler_remove referenced from libR expected to be defined 
in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_rl_callback_read_char referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_stifle_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_tilde_expand referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
_write_history referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libreadline.5.1.dylib
___floatdidf referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___fixdfdi referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___gcc_qadd referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___gcc_qdiv referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___divdc3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___muldc3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___gcc_qmul referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___gcc_qsub referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
___moddi3 referenced from libR expected to be defined in 
/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
collect2: ld returned 1 exit status
lipo: can't open input file: /var/tmp//ccxdJXvQ.out (No such file or 
directory)
error: command 'gcc' failed with exit status 1

Ruedi Fries