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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