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
>>>
>>>
>>>
>>>
>>>
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>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
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> 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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> rpy-list@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rpy-list
------------------------------------------------------------------------------
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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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