Hi,
A possible fix has been to re-install the Xcode command line tools: rpy2 seems
now to install and work, though I confess that all the reports of the Xcode
tools show no change in version number etc following the re-install. Still, it
has worked.
Jeremy
On 24 Jan 2013, at 15:55, Jeremy Harbinson <jeremy_harbin...@me.com> wrote:
> 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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