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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