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, though some other bits of Xcode seem to be more recent, in Xcode.app
for example) and the Enthought Python Distribution. I am not sure if the
problem lies with Rpy2 or with Xcode, 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:
e.g. 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.o in 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
------------------------------------------------------------------------------
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. ON SALE this month only -- learn more at:
http://p.sf.net/sfu/learnnow-d2d
_______________________________________________
rpy-list mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rpy-list
