The previous post ended up with no line breaks - hopefully this one, with
breaks, will be readable.
Hi,
I have had a problem installing Rpy2 versions 2.1.8 and 2.3.1 and Mac OSX
version 10.8.2 using Xcode 3.2 (this is the version that
is in my 'Developer' directory) and the Enthought Python Distribution. I am not
sure if the problem lies with Rpy2 or with R,
so my apologies if I have made a mistake in posting here.
When I first tried to instal Rpy2 2.3.1 I got the following error message:
python setup.py build install
running build
running build_py
running build_ext
/Library/Frameworks/R.framework/Resources/bin/config: line 142: make: command
not found
/Library/Frameworks/R.framework/Resources/bin/config: line 143: make: command
not found
R was not built as a library
Traceback (most recent call last):
File "setup.py", line 372, in <module>
[os.path.join('doc', 'source', 'rpy2_logo.png')])]
File
"/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/distutils/core.py",
line 152, in setup
dist.run_commands()
File
"/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/distutils/dist.py",
line 953, in run_commands
self.run_command(cmd)
File
"/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/distutils/dist.py",
line 972, in run_command
cmd_obj.run()
File
"/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/distutils/command/build.py",
line 127, in run
self.run_command(cmd_name)
File
"/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/distutils/cmd.py",
line 326, in run_command
self.distribution.run_command(command)
File
"/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/distutils/dist.py",
line 971, in run_command
cmd_obj.ensure_finalized()
File
"/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/distutils/cmd.py",
line 109, in ensure_finalized
self.finalize_options()
File "setup.py", line 111, in finalize_options
config += get_rconfig(r_home, about)
File "setup.py", line 264, in get_rconfig
rc = RConfig.from_string(rconfig)
File "setup.py", line 252, in from_string
+ '\nin string\n' + string)
ValueError: Invalid substring
in string
This is a reasonably widely reported problem. I got the same result with rpy
2.1.8. I checked I had a 'make' and I checked the
path statement in my Terminal app and sure enough the directory (there were
two) in which make was located was not in the path,
so I added one to the Terminal window path (hopefully this was the right thing
to do). Repeating the install, but using a
different procedure, in a terminal wondow with the new path allowed the install
to proceed further, but still ending in an
error:
sudo easy_install rpy2
Password:
Searching for rpy2
Reading http://pypi.python.org/simple/rpy2/
Reading http://rpy.sourceforge.net
Best match: rpy2 2.3.1
Downloading
http://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.1.tar.gz#md5=8d68dbd8947931975304dc633bbb843c
Processing rpy2-2.3.1.tar.gz
Writing /tmp/easy_install-66vvZU/rpy2-2.3.1/setup.cfg
Running rpy2-2.3.1/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-66vvZU/rpy2-2.3.1/egg-dist-tmp-xJsNct
returned an empty string.
returned an empty string.
Configuration for R as a library:
include_dirs: ('/Library/Frameworks/R.framework/Resources/include',
'/Library/Frameworks/R.framework/Resources/include/i386')
libraries: ()
library_dirs: ('/Library/Frameworks/R.framework/Resources/lib/i386',)
extra_link_args: ('-framework R', '-F/Library/Frameworks/R.framework/..')
# OSX-specific (included in extra_link_args)
framework_dirs: ('-F/Library/Frameworks/R.framework/..',)
frameworks: ('-framework R',)
warning: no previously-included files matching '*patch*' found anywhere in
distribution
warning: no previously-included files matching '*diff*' found anywhere in
distribution
warning: no previously-included files matching '.hg' found anywhere in
distribution
no previously-included directories found matching 'dist'
./rpy/rinterface/_rinterface.c: In function ‘init_rinterface’:
./rpy/rinterface/_rinterface.c:3550: warning: passing argument 1 of
‘PyLong_FromLong’ makes integer from pointer without a cast
ld: library not found for -lbundle1.o
collect2: ld returned 1 exit status
error: Setup script exited with error: command 'gcc' failed with exit status 1
Searching for the -lbundle1.o message on the web got some hits:
http://lists.apple.com/archives/darwin-dev/2011/Apr/msg00018.html
The suggestion was to replace the -l switch with the full path to bundle1.o
except I cannot find any reference to bundle1.oin
the rpy2 code. There is, nonetheless, a bundle1.o on my system:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/usr/lib/bundle1.o
but this path is not in the path of my Terminal window. I could add it, but I
guess I find it odd that this should necessary and
I wonder if something else is going wrong. Maybe my Xcode installation is
broken, or I am doing something fundamentally
misguided. I have little experience of compiling code so I also feel that at
the moment I am just tampering with things
in a rather naive way
all the best,
Jeremy
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