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
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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