Tried to install the version from pypi, and it worked!
thanks so much.
Just to note though, I have updated several dependencies that might
facilitated rpy2 2.1.7 to finally work.
On Oct 13, 2010, at 11:25 AM, Laurent Gautier wrote:
> On 10/13/10 10:07 AM, Alon philosof wrote:
>> Thanks for the reply.
>> I get this when trying easy_install:
>> Searching for rpy2
>> Best match: rpy2 2.1.0alpha3
>> Adding rpy2 2.1.0alpha3 to easy-install.pth file
>
> Strange. The latest release is 2.1.7.
> Can you fetch it from Pypi then ?
>
>> Using /Library/Frameworks/Python.framework/Versions/2.6/lib/
>> python2.6/
>> site-packages
>> Processing dependencies for rpy2
>> Finished processing dependencies for rpy2
>>
>>
>> Also, I have been unable to install rpy2 even with future versions
>> 2.1.6 and 2.2.0.
>>
>> On Oct 13, 2010, at 9:51 AM, Laurent Gautier wrote:
>>
>>> From the output, this seems to be an older release you are trying to
>>> install.
>>>
>>> What would give today ?
>>>
>>> easy_install rpy2 give
>>>
>>>
>>> On 10/13/10 9:38 AM, Alon philosof wrote:
>>>> Hello,
>>>> I'm bumping a question I've posted on stackexchange and biostar but
>>>> still can't solve.
>>>> before I give up I thought I might be able to get some help on this
>>>> list:
>>>> I have Xcode 3.1.4 installed and R 2.11.1, mac os x 10.5.8.
>>>> when I run:
>>>>
>>>> sudo python setup.py build install
>>>>
>>>> I get this:
>>>>
>>>>
>>>> running build
>>>> running build_py
>>>> running build_ext
>>>> building 'rpy2.rinterface.rinterface' extension
>>>> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch
>>>> i386 -
>>>> arch ppc -arch x86_64 -g -O2 -DNDEBUG -g -O3 -
>>>> DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DCSTACK_DEFNS=1 -
>>>> DRIF_HAS_RSIGHAND=1 -Irpy/rinterface -I/Library/Frameworks/
>>>> Python.framework/Versions/2.7/include/python2.7 -I/Library/
>>>> Frameworks/
>>>> R.framework/Resources/include -I/Library/Frameworks/R.framework/
>>>> Resources/include/i386 -c rpy/rinterface/rinterface.c -o build/
>>>> temp.macosx-10.5-fat3-2.7/rpy/rinterface/rinterface.o -F/Library/
>>>> Frameworks/R.framework/.. -framework R -L/Library/Frameworks/
>>>> R.framework/Resources/lib/i386 -lRlapack -L/Library/Frameworks/
>>>> R.framework/Resources/lib/i386 -lRblas
>>>> i686-apple-darwin9-gcc-4.0.1: -lRlapack: linker input file
>>>> unused because linking not done
>>>> i686-apple-darwin9-gcc-4.0.1: -lRblas: linker input file
>>>> unused because linking not done
>>>> i686-apple-darwin9-gcc-4.0.1: -lRlapack: linker input file
>>>> unused because linking not done
>>>> i686-apple-darwin9-gcc-4.0.1: -lRblas: linker input file
>>>> unused because linking not done
>>>> powerpc-apple-darwin9-gcc-4.0.1: -lRlapack: linker input
>>>> file
>>>> unused because linking not done
>>>> powerpc-apple-darwin9-gcc-4.0.1: -lRblas: linker input
>>>> file
>>>> unused because linking not done
>>>> gcc-4.0 -arch i386 -arch ppc -arch x86_64 -isysroot / -g -
>>>> bundle -undefined dynamic_lookup build/temp.macosx-10.5-fat3-2.7/
>>>> rpy/
>>>> rinterface/rinterface.o -L-F/Library/Frameworks/R.framework/.. -L-
>>>> framework -LR -L/Library/Frameworks/R.framework/Resources/modules -
>>>> L-F/
>>>> Library/Frameworks/R.framework/.. -L-framework -LR L/Library/
>>>> Frameworks/R.framework/Resources/modules -lR -o build/
>>>> lib.macosx-10.5-
>>>> fat3-2.7/rpy2/rinterface/rinterface.so
>>>> ld: library not found for -lR
>>>> ld: library not found for -lR
>>>> collect2: ld returned 1 exit status
>>>> ldcollect2: : library ld returned 1 exit status
>>>> not found for -lR
>>>> collect2: ld returned 1 exit status
>>>> lipo: can't open input file: /var/tmp//ccFngK8H.out (No
>>>> such
>>>> file or directory)
>>>> error: command 'gcc-4.0' failed with exit status 1
>>>>
>>>>
>>>>
>>>> Edit:
>>>> tried Michael Dondrup's suggestions:
>>>>
>>>> sudo python setup.py build --r-home /Library/Frameworks/
>>>> R.framework/Versions/2.11/Resources install
>>>>
>>>> and got this Error:
>>>>
>>>> running build
>>>> running build_py
>>>> running build_ext
>>>> building 'rpy2.rinterface.rinterface' extension
>>>> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch i386 -
>>>> arch ppc -arch x86_64 -g -O2 -DNDEBUG -g -O3 -DR_INTERFACE_PTRS=1 -
>>>> DHAVE_POSIX_SIGJMP=1 -DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1 -Irpy/
>>>> rinterface -I/Library/Frameworks/Python.framework/Versions/2.7/
>>>> include/
>>>> python2.7 -I/Library/Frameworks/R.framework/Resources/include -I/
>>>> Library/Frameworks/R.framework/Resources/include/i386 -c rpy/
>>>> rinterface/rinterface.c -o build/temp.macosx-10.5-fat3-2.7/rpy/
>>>> rinterface/rinterface.o -F/Library/Frameworks/R.framework/.. -
>>>> framework R -L/Library/Frameworks/R.framework/Resources/lib/i386 -
>>>> lRlapack -L/Library/Frameworks/R.framework/Resources/lib/i386 -
>>>> lRblas
>>>> i686-apple-darwin9-gcc-4.0.1: -lRlapack: linker input file
>>>> unused
>>>> because linking not done
>>>> i686-apple-darwin9-gcc-4.0.1: -lRblas: linker input file
>>>> unused
>>>> because linking not done
>>>> i686-apple-darwin9-gcc-4.0.1: -lRlapack: linker input file
>>>> unused
>>>> because linking not done
>>>> i686-apple-darwin9-gcc-4.0.1: -lRblas: linker input file
>>>> unused
>>>> because linking not done
>>>> powerpc-apple-darwin9-gcc-4.0.1: -lRlapack: linker input file
>>>> unused because linking not done
>>>> powerpc-apple-darwin9-gcc-4.0.1: -lRblas: linker input file
>>>> unused because linking not done
>>>> gcc-4.0 -arch i386 -arch ppc -arch x86_64 -isysroot / -g -
>>>> bundle -
>>>> undefined dynamic_lookup build/temp.macosx-10.5-fat3-2.7/rpy/
>>>> rinterface/rinterface.o -L-F/Library/Frameworks/R.framework/.. -L-
>>>> framework -LR -L/Library/Frameworks/R.framework/Versions/2.11/
>>>> Resources/modules -L-F/Library/Frameworks/R.framework/.. -L-
>>>> framework -
>>>> LR -L/Library/Frameworks/R.framework/Versions/2.11/Resources/
>>>> modules -
>>>> lR -o build/lib.macosx-10.5-fat3-2.7/rpy2/rinterface/rinterface.so
>>>> ld: library not found for -lR
>>>> collect2: ld returned 1 exit statusld
>>>> : library not found for -lR
>>>> collect2: ld: library not found for -lR
>>>> ld returned 1 exit status
>>>> collect2: ld returned 1 exit status
>>>> lipo: can't open input file: /var/tmp//ccet5GLC.out (No such
>>>> file
>>>> or directory)
>>>> error: command 'gcc-4.0' failed with exit status 1
>>>>
>>>>
>>>> As Laurent Gautier suggested I tried installing rpy2 2.1.6 and
>>>> 2.2.0
>>>> future version.
>>>> got a very long error list, an excerpt:
>>>>
>>>> unning build
>>>> running build_py
>>>> running build_ext
>>>> Configuration for R as a library:
>>>> include_dirs: ('/Library/Frameworks/R.framework/Resources/
>>>> include -I/Library/Frameworks/R.framework/Resources/include/i386',)
>>>> libraries: ('Rblas', 'Rlapack')
>>>> 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: ()
>>>> frameworks: ()
>>>> building 'rpy2.rinterface.rinterface' extension
>>>> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch i386 -
>>>> arch ppc -arch x86_64 -g -O2 -DNDEBUG -g -O3 -DR_INTERFACE_PTRS=1 -
>>>> DHAVE_POSIX_SIGJMP=1 -DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1 -I./rpy/
>>>> rinterface -I/Library/Frameworks/Python.framework/Versions/2.7/
>>>> include/
>>>> python2.7 -I/Library/Frameworks/R.framework/Resources/include -I/
>>>> Library/Frameworks/R.framework/Resources/include/i386 -c ./rpy/
>>>> rinterface/rinterface.c -o build/temp.macosx-10.5-fat3-2.7/./rpy/
>>>> rinterface/rinterface.o
>>>> ./rpy/rinterface/rinterface.c:61:15: error: R.h: No such
>>>> file or
>>>> directory
>>>> ./rpy/rinterface/rinterface.c:62:24: error: Rinternals.h: No
>>>> such
>>>> file or directory
>>>> ./rpy/rinterface/rinterface.c:63:22: error: Rdefines.h: No
>>>> such
>>>> file or directory
>>>> ./rpy/rinterface/rinterface.c:65:24: error: Rinterface.h: No
>>>> such
>>>> file or directory
>>>> ./rpy/rinterface/rinterface.c:66:27: error: R_ext/Complex.h:
>>>> No
>>>> such file or directory
>>>> ./rpy/rinterface/rinterface.c:67:23: error: Rembedded.h: No
>>>> such
>>>> file or directory
>>>> ./rpy/rinterface/rinterface.c:70:29: error: R_ext/eventloop.h:
>>>> No
>>>> such file or directory
>>>> ./rpy/rinterface/rinterface.c:74:28: error: R_ext/
>>>> Rdynload.h: No
>>>> such file or directory
>>>> ./rpy/rinterface/rinterface.c:75:28: error: R_ext/
>>>> RStartup.h: No
>>>> such file or directory
>>>> In file included from ./rpy/rinterface/rinterface.c:92:
>>>> ./rpy/rinterface/rpy_rinterface.h:36: error: syntax error
>>>> before
>>>> 'SEXP'
>>>> ./rpy/rinterface/rpy_rinterface.h:36: warning: no semicolon at
>>>> end of struct or union
>>>> ./rpy/rinterface/rpy_rinterface.h:37: warning: data definition
>>>> has no type or storage class
>>>> ./rpy/rinterface/rpy_rinterface.h:42: error: syntax error
>>>> before
>>>> 'SexpObject'
>>>> ./rpy/rinterface/rpy_rinterface.h:42: warning: no semicolon at
>>>> end of struct or union
>>>> ./rpy/rinterface/rpy_rinterface.h:44: warning: data definition
>>>> has no type or storage class
>>>> In file included from ./rpy/rinterface/rinterface.c:96:
>>>> ./rpy/rinterface/r_utils.h:6: error: syntax error before
>>>> 'rpy_findFun'
>>>> ./rpy/rinterface/r_utils.h:6: error: syntax error before
>>>> 'symbol'
>>>> ./rpy/rinterface/r_utils.h:6: warning: data definition has no
>>>> type or storage class
>>>> ./rpy/rinterface/r_utils.h:8: error: syntax error before
>>>> 'rpy_serialize'
>>>> ./rpy/rinterface/r_utils.h:8: error: syntax error before
>>>> 'object'
>>>> ./rpy/rinterface/r_utils.h:8: warning: data definition has no
>>>> type or storage class
>>>> ./rpy/rinterface/r_utils.h:9: error: syntax error before
>>>> 'rpy_unserialize'
>>>> ./rpy/rinterface/r_utils.h:9: error: syntax error before
>>>> 'connection'
>>>> ./rpy/rinterface/r_utils.h:9: warning: data definition has no
>>>> type or storage class
>>>> In file included from ./rpy/rinterface/rinterface.c:98:
>>>> ./rpy/rinterface/array.h:9: error: syntax error before '*'
>>>> token
>>>> In file included from ./rpy/rinterface/rinterface.c:100:
>>>> ./rpy/rinterface/rexternalptr.h:8: error: syntax error before
>>>> 'R_PyObject_decref'
>>>> ./rpy/rinterface/rexternalptr.h:8: error: syntax error before
>>>> 's'
>>>> ./rpy/rinterface/rexternalptr.h:8: warning: data definition
>>>> has
>>>> no type or storage class
>>>> ./rpy/rinterface/rinterface.c:102: error: syntax error before
>>>> '*'
>>>> token
>>>> ./rpy/rinterface/rinterface.c:102: error: syntax error before
>>>> 'sexp'
>>>> ./rpy/rinterface/rinterface.c:102: warning: data definition
>>>> has
>>>> no type or storage class
>>>> In file included from ./rpy/rinterface/rinterface.c:105:
>>>> ./rpy/rinterface/na_values.c: In function 'NAInteger_tp_new':
>>>> ./rpy/rinterface/na_values.c:232: error: 'NA_INTEGER'
>>>> undeclared
>>>> (first use in this function)
>>>> ./rpy/rinterface/na_values.c:232: error: (Each undeclared
>>>> identifier is reported only once
>>>> ./rpy/rinterface/na_values.c:232: error: for each function it
>>>> appears in.)
>>>> ./rpy/rinterface/na_values.c: In function 'NALogical_tp_new':
>>>> ./rpy/rinterface/na_values.c:272: error: 'NA_LOGICAL'
>>>> undeclared
>>>> (first use in this function)
>>>> ./rpy/rinterface/na_values.c: In function 'NAReal_tp_new':./
>>>> rpy/
>>>> rinterface/rinterface.c:61:15: error: R.h: No such file or
>>>> directory
>>>> ./rpy/rinterface/rinterface.c:62:24: error: Rinternals.h: No
>>>> such
>>>> file or directory
>>>> ./rpy/rinterface/rinterface.c:63:22: error: Rdefines.h: No
>>>> such
>>>> file or directory
>>>> ./rpy/rinterface/rinterface.c:65:24: error: Rinterface.h: No
>>>> such
>>>> file or directory
>>>> ./rpy/rinterface/rinterface.c:66:27: error: R_ext/Complex.h:
>>>> No
>>>> such file or directory
>>>> ./rpy/rinterface/rinterface.c:67:23: error: Rembedded.h: No
>>>> such
>>>> file or directory
>>>> ./rpy/rinterface/rinterface.c:70:29: error: R_ext/eventloop.h:
>>>> No
>>>> such file or directory
>>>> ./rpy/rinterface/rinterface.c:74:28: error: R_ext/
>>>> Rdynload.h: No
>>>> such file or directory
>>>>
>>>> Edit:
>>>> tried new installation of R from source and rpy2 from MacPorts as
>>>> suggested.
>>>> now I'm getting this error (my mac is intel so I find it strange
>>>> the
>>>> arch parameter is i386):
>>>>
>>>> :info:build In file included from rpy/rinterface/rinterface.c:
>>>> 74:
>>>> :info:build /opt/local/lib/R/include/R_ext/Rdynload.h:26:
>>>> warning: function declaration isn't a prototype
>>>> :info:build In file included from rpy/rinterface/rinterface.c:
>>>> 105:
>>>> :info:build rpy/rinterface/sequence.c: In function
>>>> 'VectorSexp_ass_slice':
>>>> :info:build rpy/rinterface/sequence.c:447: warning: unused
>>>> variable 'sexp_item'
>>>> :info:build rpy/rinterface/sequence.c:447: warning: unused
>>>> variable 'tmp'
>>>> :info:build rpy/rinterface/sequence.c:446: warning: unused
>>>> variable 'vs'
>>>> :info:build rpy/rinterface/sequence.c:386: warning: unused
>>>> variable 'self_typeof'
>>>> :info:build rpy/rinterface/rinterface.c: In function
>>>> 'EmbeddedR_end':
>>>> :info:build rpy/rinterface/rinterface.c:1112: warning: unused
>>>> variable 'str'
>>>> :info:build rpy/rinterface/rinterface.c: In function
>>>> 'EmbeddedR_WriteConsole':
>>>> :info:build rpy/rinterface/rinterface.c:288: warning: 'gstate'
>>>> may be used uninitialized in this function
>>>> :info:build rpy/rinterface/rinterface.c: In function
>>>> 'EmbeddedR_ShowMessage':
>>>> :info:build rpy/rinterface/rinterface.c:356: warning: 'gstate'
>>>> may be used uninitialized in this function
>>>> :info:build rpy/rinterface/rinterface.c: In function
>>>> 'EmbeddedR_ReadConsole':
>>>> :info:build rpy/rinterface/rinterface.c:424: warning: 'gstate'
>>>> may be used uninitialized in this function
>>>> :info:build rpy/rinterface/rinterface.c: In function
>>>> 'EmbeddedR_FlushConsole':
>>>> :info:build rpy/rinterface/rinterface.c:524: warning: 'gstate'
>>>> may be used uninitialized in this function
>>>> :info:build rpy/rinterface/rinterface.c: In function
>>>> 'EmbeddedR_ChooseFile':
>>>> :info:build rpy/rinterface/rinterface.c:568: warning: 'gstate'
>>>> may be used uninitialized in this function
>>>> :info:build rpy/rinterface/rinterface.c: In function
>>>> 'EmbeddedR_ShowFiles':
>>>> :info:build rpy/rinterface/rinterface.c:654: warning: 'gstate'
>>>> may be used uninitialized in this function
>>>> :info:build rpy/rinterface/rinterface.c: In function
>>>> 'EmbeddedR_CleanUp':
>>>> :info:build rpy/rinterface/rinterface.c:787: warning: 'gstate'
>>>> may be used uninitialized in this function
>>>> :info:build rpy/rinterface/rinterface.c: At top level:
>>>> :info:build rpy/rinterface/rinterface.c:2774: warning:
>>>> 'externalMethods' defined but not used
>>>> :info:build i686-apple-darwin9-gcc-4.0.1: -lR: linker input
>>>> file
>>>> unused because linking not done
>>>> :info:build i686-apple-darwin9-gcc-4.0.1: -lRlapack: linker
>>>> input
>>>> file unused because linking not done
>>>> :info:build i686-apple-darwin9-gcc-4.0.1: -lRblas: linker
>>>> input
>>>> file unused because linking not done
>>>> :info:build /usr/bin/gcc-4.0 -L/opt/local/lib -bundle -
>>>> undefined
>>>> dynamic_lookup -arch i386 -arch i386 build/temp.macosx-10.5-
>>>> i386-2.6/
>>>> rpy/rinterface/rinterface.o -L/opt/local/lib/R/lib -L/opt/local/
>>>> lib/
>>>> R/
>>>> modules -lR -o build/lib.macosx-10.5-i386-2.6/rpy2/rinterface/
>>>> rinterface.so
>>>> :info:build ld: library not found for -lR
>>>> :info:build collect2: ld returned 1 exit status
>>>> :info:build error: command '/usr/bin/gcc-4.0' failed with exit
>>>> status 1
>>>> :info:build shell command " cd "/opt/local/var/macports/build/
>>>> _opt_local_var_macports_sources_rsync
>>>> .macports.org_release_ports_python_py26-rpy2/work/rpy2-2.1.4"&& /
>>>> opt/
>>>> local/Library/Frameworks/Python.framework/Versions/2.6/bin/
>>>> python2.6
>>>> setup.py --no-user-cfg build " returned error 1
>>>> :error:build Target org.macports.build returned: shell command
>>>> failed
>>>> :debug:build Backtrace: shell command failed
>>>> while executing
>>>> "command_exec build"
>>>> (procedure "portbuild::build_main" line 8)
>>>> invoked from within
>>>> "$procedure $targetname"
>>>> :info:build Warning: the following items did not execute (for
>>>> py26-rpy2): org.macports.activate org.macports.build
>>>> org.macports.destroot org.macports.install
>>>> :notice:build Log for py26-rpy2 is at: /opt/local/var/
>>>> macports/
>>>> logs/
>>>> _opt_local_var_macports_sources_rsync
>>>> .macports.org_release_ports_python_py26-rpy2/main.lo
>>>>
>>>>
>>>>
>>>> sorry for the long post and mess...
>>>> any help would be greatly appreciated.
>>>>
>>>> Alon philosof,
>>>> philo...@tx.tchnion.ac.il
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Beautiful is writing same markup. Internet Explorer 9 supports
>>>> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3.
>>>> Spend less time writing and rewriting code and more time creating
>>>> great
>>>> experiences on the web. Be a part of the beta today.
>>>> http://p.sf.net/sfu/beautyoftheweb
>>>> _______________________________________________
>>>> rpy-list mailing list
>>>> rpy-list@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/rpy-list
>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3.
>> Spend less time writing and rewriting code and more time creating
>> great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> rpy-list mailing list
>> rpy-list@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rpy-list
>
Alon philosof,
PhD student
Prof. Beja's lab,
Technion - Israel Institute of Technology
philo...@tx.tchnion.ac.il
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
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