I have R 2.13.0 installed via the CRAN Ubuntu lucid repo (installed packages r-base, r-base-dev, and liblapack-dev). When I tried out RPy2 (either 2.1 or 2.2) from ipython, I get a seg fault. Details below. Any ideas what's going on? Thanks in advance.
$ R --version R version 2.13.0 (2011-04-13) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/. $ pip install 'rpy2==2.1.9' /home/yang/env/lib/python2.6/site-packages/pip-0.8.1-py2.6.egg/pip/req.py:641: UserWarning: Unbuilt egg for mining [unknown version] (/home/yang/pod/mining) self.satisfied_by = pkg_resources.get_distribution(self.req) Downloading/unpacking rpy2==2.1.9 Downloading rpy2-2.1.9.tar.gz (129Kb): 129Kb downloaded Running setup.py egg_info for package rpy2 Configuration for R as a library: include_dirs: ('/usr/share/R/include',) libraries: ('lapack', 'blas', 'R') library_dirs: ('/usr/lib64/R/lib',) extra_link_args: () # OSX-specific (included in extra_link_args) framework_dirs: () frameworks: () Installing collected packages: rpy2 Running setup.py install for rpy2 Configuration for R as a library: include_dirs: ('/usr/share/R/include',) libraries: ('lapack', 'blas', 'R') library_dirs: ('/usr/lib64/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 -Irpy/rinterface -I/usr/include/python2.6 -I/usr/share/R/include -c rpy/rinterface/rinterface.c -o build/temp.linux-x86_64-2.6/rpy/rinterface/rinterface.o In file included from /usr/include/python2.6/Python.h:8, from rpy/rinterface/rinterface.c:55: /usr/include/python2.6/pyconfig.h:1031:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/signal.h:29, from rpy/rinterface/rinterface.c:51: /usr/include/features.h:210:1: warning: this is the location of the previous definition In file included from rpy/rinterface/rinterface.c:62: /usr/share/R/include/Rinternals.h:657: warning: function declaration isn’t a prototype In file included from rpy/rinterface/rinterface.c:74: /usr/share/R/include/R_ext/Rdynload.h:26: warning: function declaration isn’t a prototype In file included from rpy/rinterface/rinterface.c:105: rpy/rinterface/sequence.c: In function ‘VectorSexp_ass_slice’: rpy/rinterface/sequence.c:447: warning: unused variable ‘sexp_item’ rpy/rinterface/sequence.c:447: warning: unused variable ‘tmp’ rpy/rinterface/sequence.c:446: warning: unused variable ‘vs’ rpy/rinterface/sequence.c:386: warning: unused variable ‘self_typeof’ rpy/rinterface/rinterface.c: In function ‘EmbeddedR_end’: rpy/rinterface/rinterface.c:1112: warning: unused variable ‘str’ rpy/rinterface/rinterface.c: In function ‘EnvironmentSexp_ass_subscript’: rpy/rinterface/rinterface.c:2001: warning: unused variable ‘sexp_copy’ rpy/rinterface/rinterface.c: At top level: rpy/rinterface/rinterface.c:2775: warning: ‘externalMethods’ defined but not used rpy/rinterface/rinterface.c: In function ‘EmbeddedR_ShowFiles’: rpy/rinterface/rinterface.c:654: warning: ‘gstate’ may be used uninitialized in this function rpy/rinterface/rinterface.c: In function ‘EmbeddedR_FlushConsole’: rpy/rinterface/rinterface.c:524: warning: ‘gstate’ may be used uninitialized in this function rpy/rinterface/rinterface.c: In function ‘EmbeddedR_ChooseFile’: rpy/rinterface/rinterface.c:568: warning: ‘gstate’ may be used uninitialized in this function rpy/rinterface/rinterface.c: In function ‘EmbeddedR_ReadConsole’: rpy/rinterface/rinterface.c:424: warning: ‘gstate’ may be used uninitialized in this function rpy/rinterface/rinterface.c: In function ‘EmbeddedR_WriteConsole’: rpy/rinterface/rinterface.c:288: warning: ‘gstate’ may be used uninitialized in this function rpy/rinterface/rinterface.c: In function ‘EmbeddedR_ShowMessage’: rpy/rinterface/rinterface.c:356: warning: ‘gstate’ may be used uninitialized in this function rpy/rinterface/rinterface.c: In function ‘EmbeddedR_CleanUp’: rpy/rinterface/rinterface.c:787: warning: ‘gstate’ may be used uninitialized in this function gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/rpy/rinterface/rinterface.o -L/usr/lib64/R/lib -L/usr/lib64/R/modules -lR -llapack -lblas -lR -o build/lib.linux-x86_64-2.6/rpy2/rinterface/rinterface.so building 'rpy2.rinterface.rpy_device' 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 -Irpy/rinterface -I/usr/include/python2.6 -I/usr/share/R/include -c rpy/rinterface/rpy_device.c -o build/temp.linux-x86_64-2.6/rpy/rinterface/rpy_device.o In file included from rpy/rinterface/rpy_device.c:6: /usr/share/R/include/Rinternals.h:657: warning: function declaration isn’t a prototype rpy/rinterface/rpy_device.c:690: warning: ‘GrDev_clear’ defined but not used gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/rpy/rinterface/rpy_device.o -L/usr/lib64/R/lib -L/usr/lib64/R/modules -lR -llapack -lblas -lR -o build/lib.linux-x86_64-2.6/rpy2/rinterface/rpy_device.so Successfully installed rpy2 $ python Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC 4.4.3] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import rpy2.robjects >>> $ ipython Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) Type "copyright", "credits" or "license" for more information. IPython 0.10.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: import rpy2.robjects Segmentation fault $ pip install --upgrade 'rpy2' Downloading/unpacking rpy2 Downloading rpy2-2.2.0beta3.tar.gz (164Kb): 164Kb downloaded Running setup.py egg_info for package rpy2 Configuration for R as a library: include_dirs: ('/usr/share/R/include',) libraries: ('lapack', 'blas', 'R') library_dirs: ('/usr/lib64/R/lib',) extra_link_args: () # OSX-specific (included in extra_link_args) framework_dirs: () frameworks: () Installing collected packages: rpy2 Found existing installation: rpy2 2.1.9-20110510 Uninstalling rpy2: Successfully uninstalled rpy2 Running setup.py install for rpy2 Configuration for R as a library: include_dirs: ('/usr/share/R/include',) libraries: ('lapack', 'blas', 'R') library_dirs: ('/usr/lib64/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-x86_64-2.6/./rpy/rinterface/_rinterface.o In file included from /usr/include/python2.6/Python.h:8, from ./rpy/rinterface/_rinterface.c:55: /usr/include/python2.6/pyconfig.h:1031:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/signal.h:29, from ./rpy/rinterface/_rinterface.c:51: /usr/include/features.h:210:1: warning: this is the location of the previous definition In file included from ./rpy/rinterface/_rinterface.c:63: /usr/share/R/include/Rinternals.h:657: warning: function declaration isn’t a prototype In file included from ./rpy/rinterface/_rinterface.c:74: /usr/share/R/include/R_ext/Rdynload.h:26: warning: function declaration isn’t a prototype In file included from ./rpy/rinterface/_rinterface.c:122: ./rpy/rinterface/sequence.c: In function ‘VectorSexp_ass_slice’: ./rpy/rinterface/sequence.c:542: warning: unused variable ‘sexp_item’ ./rpy/rinterface/sequence.c:542: warning: unused variable ‘tmp’ ./rpy/rinterface/sequence.c:541: warning: unused variable ‘vs’ ./rpy/rinterface/sequence.c:478: warning: unused variable ‘self_typeof’ ./rpy/rinterface/sequence.c: In function ‘RPy_SeqToINTSXP’: ./rpy/rinterface/sequence.c:1193: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c:1202: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c: In function ‘RPy_IterToINTSXP’: ./rpy/rinterface/sequence.c:1241: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c:1261: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c:1270: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c: In function ‘RPy_SeqToREALSXP’: ./rpy/rinterface/sequence.c:1425: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c: In function ‘RPy_IterToREALSXP’: ./rpy/rinterface/sequence.c:1461: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c:1474: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c: In function ‘RPy_SeqToSTRSXP’: ./rpy/rinterface/sequence.c:1631: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c:1661: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c: In function ‘RPy_SeqToLGLSXP’: ./rpy/rinterface/sequence.c:1838: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c: In function ‘RPy_SeqToRAWSXP’: ./rpy/rinterface/sequence.c:1991: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c:1997: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c: In function ‘RPy_SeqToCPLXSXP’: ./rpy/rinterface/sequence.c:2133: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/sequence.c: In function ‘RPy_SeqToVECSXP’: ./rpy/rinterface/sequence.c:2330: warning: format ‘%i’ expects type ‘int’, but argument 3 has type ‘Py_ssize_t’ ./rpy/rinterface/_rinterface.c:2172:11: warning: extra tokens at end of #endif directive ./rpy/rinterface/_rinterface.c: At top level: ./rpy/rinterface/sequence.c:2144: warning: ‘ComplexVectorSexp_AsSexp’ defined but not used ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowFiles’: ./rpy/rinterface/_rinterface.c:738: warning: ‘gstate’ may be used uninitialized in this function ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_FlushConsole’: ./rpy/rinterface/_rinterface.c:592: warning: ‘gstate’ may be used uninitialized in this function ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ChooseFile’: ./rpy/rinterface/_rinterface.c:636: warning: ‘gstate’ may be used uninitialized in this function ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ReadConsole’: ./rpy/rinterface/_rinterface.c:460: warning: ‘gstate’ may be used uninitialized in this function ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_WriteConsole’: ./rpy/rinterface/_rinterface.c:318: warning: ‘gstate’ may be used uninitialized in this function ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowMessage’: ./rpy/rinterface/_rinterface.c:392: warning: ‘gstate’ may be used uninitialized in this function ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_CleanUp’: ./rpy/rinterface/_rinterface.c:886: warning: ‘gstate’ may be used uninitialized in this function gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/./rpy/rinterface/_rinterface.o -L/usr/lib64/R/lib -L/usr/lib64/R/modules -lR -llapack -lblas -lR -o build/lib.linux-x86_64-2.6/rpy2/rinterface/_rinterface.so building 'rpy2.rinterface.rpy_device' 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 -Irpy/rinterface -I/usr/include/python2.6 -I/usr/share/R/include -c rpy/rinterface/rpy_device.c -o build/temp.linux-x86_64-2.6/rpy/rinterface/rpy_device.o In file included from rpy/rinterface/rpy_device.c:33: /usr/share/R/include/Rinternals.h:657: warning: function declaration isn’t a prototype rpy/rinterface/rpy_device.c:789: warning: ‘GrDev_clear’ defined but not used gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/rpy/rinterface/rpy_device.o -L/usr/lib64/R/lib -L/usr/lib64/R/modules -lR -llapack -lblas -lR -o build/lib.linux-x86_64-2.6/rpy2/rinterface/rpy_device.so Successfully installed rpy2 Cleaning up... yang@partycat Tue May 10 16:20:42 ~/pod/sales git(master) $ ipython Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) Type "copyright", "credits" or "license" for more information. IPython 0.10.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: import rpy2.robjects Segmentation fault -- Yang Zhang http://yz.mit.edu/ ------------------------------------------------------------------------------ Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
