Hello,
I am trying to install RPy2 in a Ubuntu Linux 32-bit 10.04 instance in
Amazon EC2.
The error message I get is as follows--
Command /usr/bin/python -c "import
setuptools;__file__='/home/ubuntu/build/rpy2/setup.py';exec(compile(open(__file__).read().replace('\r\n',
'\n'), __file__, 'exec'))" install --single-version-externally-managed
--record /tmp/pip-SgXfbr-record/install-record.txt failed with error code 1
Storing complete log in /home/ubuntu/.pip/pip.log
The file "pip.log" has the following info in it--
/usr/local/bin/pip run on Thu Nov 17 13:00:08 2011
Downloading/unpacking rpy2
Running setup.py egg_info for package rpy2
running egg_info
writing pip-egg-info/rpy2.egg-info/PKG-INFO
writing top-level names to pip-egg-info/rpy2.egg-info/top_level.txt
writing dependency_links to
pip-egg-info/rpy2.egg-info/dependency_links.txt
writing pip-egg-info/rpy2.egg-info/PKG-INFO
writing top-level names to pip-egg-info/rpy2.egg-info/top_level.txt
writing dependency_links to
pip-egg-info/rpy2.egg-info/dependency_links.txt
warning: manifest_maker: standard file '-c' not found
Configuration for R as a library:
include_dirs: ('/usr/share/R/include',)
libraries: ('lapack', 'blas', 'R')
library_dirs: ('/usr/lib/R/lib',)
extra_link_args: ()
# OSX-specific (included in extra_link_args)
framework_dirs: ()
frameworks: ()
reading manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*patch*' found
anywhere in distribution
warning: no previously-included files matching '*diff*' found
anywhere in distribution
warning: no previously-included files matching '.hg' found anywhere
in distribution
no previously-included directories found matching 'dist'
writing manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt'
Installing collected packages: rpy2
Found existing installation: rpy2 2.0.8
Uninstalling rpy2:
Removing file or directory /usr/share/pyshared/rpy2-2.0.8.egg-info
Successfully uninstalled rpy2
Running setup.py install for rpy2
Running command /usr/bin/python -c "import
setuptools;__file__='/home/ubuntu/build/rpy2/setup.py';exec(compile(open(__file__).read().replace('\r\n',
'\n'), __file__, 'exec'))" install --single-version-externally-managed
--record /tmp/pip-UuxJEQ-record/install-record.txt
running install
running build
running build_py
running build_ext
Configuration for R as a library:
include_dirs: ('/usr/share/R/include',)
libraries: ('lapack', 'blas', 'R')
library_dirs: ('/usr/lib/R/lib',)
extra_link_args: ()
# OSX-specific (included in extra_link_args)
framework_dirs: ()
frameworks: ()
building 'rpy2.rinterface._rinterface' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1
-DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1 -I./rpy/rinterface
-I/usr/include/python2.6 -I/usr/share/R/include
-c ./rpy/rinterface/_rinterface.c -o
build/temp.linux-i686-2.6/./rpy/rinterface/_rinterface.o
./rpy/rinterface/_rinterface.c:51:20: error: signal.h: No such file
or directory
./rpy/rinterface/_rinterface.c:52:20: error: setjmp.h: No such file
or directory
In file included
from /usr/lib/gcc/i486-linux-gnu/4.4.3/include-fixed/syslimits.h:7,
from /usr/lib/gcc/i486-linux-gnu/4.4.3/include-fixed/limits.h:11,
from /usr/include/python2.6/Python.h:19,
from ./rpy/rinterface/_rinterface.c:55:
/usr/lib/gcc/i486-linux-gnu/4.4.3/include-fixed/limits.h:122:61:
error: limits.h: No such file or directory
In file included from ./rpy/rinterface/_rinterface.c:55:
/usr/include/python2.6/Python.h:33:19: error: stdio.h: No such file
or directory
/usr/include/python2.6/Python.h:35:5: error: #error "Python.h
requires that stdio.h define NULL."
/usr/include/python2.6/Python.h:38:20: error: string.h: No such file
or directory
/usr/include/python2.6/Python.h:40:19: error: errno.h: No such file
or directory
/usr/include/python2.6/Python.h:42:20: error: stdlib.h: No such file
or directory
/usr/include/python2.6/Python.h:44:20: error: unistd.h: No such file
or directory
/usr/include/python2.6/Python.h:56:20: error: assert.h: No such file
or directory
In file included from /usr/include/python2.6/Python.h:58,
from ./rpy/rinterface/_rinterface.c:55:
/usr/include/python2.6/pyport.h:7:20: error: stdint.h: No such file
or directory
In file included from /usr/include/python2.6/Python.h:58,
from ./rpy/rinterface/_rinterface.c:55:
/usr/include/python2.6/pyport.h:89: error: expected ‘=’, ‘,’, ‘;’,
‘asm’ or ‘__attribute__’ before ‘Py_uintptr_t’
/usr/include/python2.6/pyport.h:90: error: expected ‘=’, ‘,’, ‘;’,
‘asm’ or ‘__attribute__’ before ‘Py_intptr_t’
/usr/include/python2.6/pyport.h:113: error: expected ‘=’, ‘,’, ‘;’,
‘asm’ or ‘__attribute__’ before ‘Py_ssize_t’
/usr/include/python2.6/pyport.h:235:76: error: math.h: No such file
or directory
/usr/include/python2.6/pyport.h:242:22: error: sys/time.h: No such
file or directory
/usr/include/python2.6/pyport.h:243:18: error: time.h: No such file
or directory
/usr/include/python2.6/pyport.h:261:24: error: sys/select.h: No such
file or directory
/usr/include/python2.6/pyport.h:300:22: error: sys/stat.h: No such
file or directory
In file included from /usr/include/python2.6/Python.h:78,
from ./rpy/rinterface/_rinterface.c:55:
/usr/include/python2.6/pymem.h:52: warning: parameter names (without
types) in function declaration
/usr/include/python2.6/pymem.h:53: error: expected declaration
specifiers or ‘...’ before ‘size_t’
In file included from /usr/include/python2.6/Python.h:80,
from ./rpy/rinterface/_rinterface.c:55:
/usr/include/python2.6/object.h:107: error: expected
specifier-qualifier-list before ‘Py_ssize_t’
/usr/include/python2.6/object.h:111: error: expected
specifier-qualifier-list before ‘Py_ssize_t’
/usr/include/python2.6/object.h:137: error: expected declaration
specifiers or ‘...’ before ‘*’ token
/usr/include/python2.6/object.h:137: warning: type defaults to ‘int’
in declaration of ‘Py_ssize_t’
/usr/include/python2.6/object.h:137: error: ‘Py_ssize_t’ declared as
function returning a function
/usr/include/python2.6/object.h:137: warning: function declaration
isn’t a prototype
/usr/include/python2.6/object.h:157: error: ‘readbufferproc’
declared as function returning a function
/usr/include/python2.6/object.h:158: error: ‘writebufferproc’
declared as function returning a function
/usr/include/python2.6/object.h:159: error: ‘segcountproc’ declared
as function returning a function
/usr/include/python2.6/object.h:160: error: ‘charbufferproc’
declared as function returning a function
/usr/include/python2.6/object.h:167: error: field ‘len’ declared as
a function
/usr/include/python2.6/object.h:168: error: field ‘itemsize’
declared as a function
/usr/include/python2.6/object.h:274: error: expected
specifier-qualifier-list before ‘lenfunc’
/usr/include/python2.6/object.h:288: error: expected
specifier-qualifier-list before ‘lenfunc’
/usr/include/python2.6/object.h:305: error: expected declaration
specifiers or ‘...’ before ‘FILE’
/usr/include/python2.6/object.h:319: warning: ‘struct _typeobject’
declared inside parameter list
/usr/include/python2.6/object.h:319: warning: its scope is only this
definition or declaration, which is probably not what you want
/usr/include/python2.6/object.h:320: warning: ‘struct _typeobject’
declared inside parameter list
/usr/include/python2.6/object.h:323: error: field ‘ob_refcnt’
declared as a function
/usr/include/python2.6/object.h:323: error: field ‘ob_size’ declared
as a function
/usr/include/python2.6/object.h:325: error: field ‘tp_basicsize’
declared as a function
/usr/include/python2.6/object.h:325: error: field ‘tp_itemsize’
declared as a function
/usr/include/python2.6/object.h:370: error: field
‘tp_weaklistoffset’ declared as a function
/usr/include/python2.6/object.h:385: error: field ‘tp_dictoffset’
declared as a function
/usr/include/python2.6/object.h:456: error: expected declaration
specifiers or ‘...’ before ‘FILE’
In file included from /usr/include/python2.6/Python.h:81,
from ./rpy/rinterface/_rinterface.c:55:
...MORE LINES IN LOG...
...MORE LINES IN LOG...
...MORE LINES IN LOG...
I have installed python2.6-dev and python v 2.6 correctly...As I am not
a python developer, and have little experience with rpy2, I dont know
how to resolve this problem. Any help would be appreciated.
Regards,
Arvind.
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