Build issue with 2.6.1

Issue #294 resolved
Ralf Gommers created an issue

Python 2.7 on 32-bit Linux. Both current master and release 2.6.1 from PyPi fail to build:

$ python setup.py install --user
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
/usr/lib/R/bin/R CMD config --ldflags
/usr/lib/R/bin/R CMD config --cppflags

    Compilation parameters for rpy2's C components:
        include_dirs    = ['/usr/share/R/include']
        library_dirs    = ['/usr/lib/R/lib']
        libraries       = ['R']
        extra_link_args = []

/home/rgommers/.local/lib/python2.7/site-packages/setuptools/dist.py:285: UserWarning: Normalizing '2.7.0dev' to '2.7.0.dev0'
  normalized_version,
running install
running bdist_egg
running egg_info
creating rpy2.egg-info
writing requirements to rpy2.egg-info/requires.txt
writing rpy2.egg-info/PKG-INFO
writing top-level names to rpy2.egg-info/top_level.txt
writing dependency_links to rpy2.egg-info/dependency_links.txt
writing manifest file 'rpy2.egg-info/SOURCES.txt'
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
reading manifest file 'rpy2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'README' anywhere in distribution
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
warning: no files found matching 'MANIFEST'
warning: no files found matching 'README'
warning: no files found matching 'MPL_LICENSE'
warning: no files found matching 'GPL_LICENSE'
warning: no files found matching 'LGPL_LICENSE'
no previously-included directories found matching 'dist'
warning: no files found matching 'doc/source/rpy2_logo.png'
writing manifest file 'rpy2.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-i686/egg
running install_lib
running build_py
creating build
creating build/lib.linux-i686-2.7
creating build/lib.linux-i686-2.7/rpy2
copying ./rpy/__init__.py -> build/lib.linux-i686-2.7/rpy2
copying ./rpy/tests_rpy_classic.py -> build/lib.linux-i686-2.7/rpy2
copying ./rpy/rpy_classic.py -> build/lib.linux-i686-2.7/rpy2
copying ./rpy/tests.py -> build/lib.linux-i686-2.7/rpy2
creating build/lib.linux-i686-2.7/rpy2/rlike
copying ./rpy/rlike/__init__.py -> build/lib.linux-i686-2.7/rpy2/rlike
copying ./rpy/rlike/functional.py -> build/lib.linux-i686-2.7/rpy2/rlike
copying ./rpy/rlike/container.py -> build/lib.linux-i686-2.7/rpy2/rlike
copying ./rpy/rlike/indexing.py -> build/lib.linux-i686-2.7/rpy2/rlike
creating build/lib.linux-i686-2.7/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_container.py -> build/lib.linux-i686-2.7/rpy2/rlike/tests
copying ./rpy/rlike/tests/__init__.py -> build/lib.linux-i686-2.7/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_functional.py -> build/lib.linux-i686-2.7/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_indexing.py -> build/lib.linux-i686-2.7/rpy2/rlike/tests
creating build/lib.linux-i686-2.7/rpy2/rinterface
copying ./rpy/rinterface/__init__.py -> build/lib.linux-i686-2.7/rpy2/rinterface
creating build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Device.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/__init__.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpSymbol.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.linux-i686-2.7/rpy2/rinterface/tests
creating build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/language.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/__init__.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/vectors.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/packages.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/methods.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/conversion.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/functions.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/pandas2ri.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/numpy2ri.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/environments.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/packages_utils.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/help.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/constants.py -> build/lib.linux-i686-2.7/rpy2/robjects
copying ./rpy/robjects/robject.py -> build/lib.linux-i686-2.7/rpy2/robjects
creating build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testLanguage.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFunction.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testMethods.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/__init__.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testArray.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPackages.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRObject.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testVector.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testHelp.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFormula.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRobjects.py -> build/lib.linux-i686-2.7/rpy2/robjects/tests
creating build/lib.linux-i686-2.7/rpy2/robjects/lib
copying ./rpy/robjects/lib/grid.py -> build/lib.linux-i686-2.7/rpy2/robjects/lib
copying ./rpy/robjects/lib/__init__.py -> build/lib.linux-i686-2.7/rpy2/robjects/lib
copying ./rpy/robjects/lib/ggplot2.py -> build/lib.linux-i686-2.7/rpy2/robjects/lib
creating build/lib.linux-i686-2.7/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.linux-i686-2.7/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.linux-i686-2.7/rpy2/robjects/lib/tests
creating build/lib.linux-i686-2.7/rpy2/interactive
copying ./rpy/interactive/__init__.py -> build/lib.linux-i686-2.7/rpy2/interactive
copying ./rpy/interactive/packages.py -> build/lib.linux-i686-2.7/rpy2/interactive
copying ./rpy/interactive/process_revents.py -> build/lib.linux-i686-2.7/rpy2/interactive
creating build/lib.linux-i686-2.7/rpy2/interactive/tests
copying ./rpy/interactive/tests/__init__.py -> build/lib.linux-i686-2.7/rpy2/interactive/tests
creating build/lib.linux-i686-2.7/rpy2/ipython
copying ./rpy/ipython/rmagic.py -> build/lib.linux-i686-2.7/rpy2/ipython
copying ./rpy/ipython/__init__.py -> build/lib.linux-i686-2.7/rpy2/ipython
copying ./rpy/ipython/ggplot.py -> build/lib.linux-i686-2.7/rpy2/ipython
copying ./rpy/ipython/html.py -> build/lib.linux-i686-2.7/rpy2/ipython
creating build/lib.linux-i686-2.7/rpy2/ipython/tests
copying ./rpy/ipython/tests/__init__.py -> build/lib.linux-i686-2.7/rpy2/ipython/tests
copying ./rpy/ipython/tests/test_rmagic.py -> build/lib.linux-i686-2.7/rpy2/ipython/tests
running build_ext
building 'rpy2.rinterface._rinterface' extension
creating build/temp.linux-i686-2.7
creating build/temp.linux-i686-2.7/rpy
creating build/temp.linux-i686-2.7/rpy/rinterface
i686-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/usr/share/R/include -I/usr/include/python2.7 -c ./rpy/rinterface/_rinterface.c -o build/temp.linux-i686-2.7/./rpy/rinterface/_rinterface.o
In file included from /usr/share/R/include/R.h:40:0,
                 from ./rpy/rinterface/_rinterface.h:8,
                 from ./rpy/rinterface/_rinterface.c:58:
/usr/share/R/include/R_ext/Memory.h:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int R_gc_running();
 ^
In file included from ./rpy/rinterface/_rinterface.h:9:0,
                 from ./rpy/rinterface/_rinterface.c:58:
/usr/share/R/include/Rinternals.h:719:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 const char *R_curErrorBuf();
 ^
In file included from ./rpy/rinterface/_rinterface.c:70:0:
/usr/share/R/include/Rinterface.h:129:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 extern void (*ptr_R_ProcessEvents)();
 ^
In file included from ./rpy/rinterface/_rinterface.c:79:0:
/usr/share/R/include/R_ext/Rdynload.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 typedef void * (*DL_FUNC)();
 ^
In file included from ./rpy/rinterface/_rinterface.c:122:0:
./rpy/rinterface/embeddedr.c: In function ‘SexpObject_clear’:
./rpy/rinterface/embeddedr.c:48:12: warning: unused variable ‘res’ [-Wunused-variable]
       SEXP res = rpy_remove(Rf_mkString(name_buf), 
            ^
In file included from ./rpy/rinterface/_rinterface.c:125:0:
./rpy/rinterface/sexp.c: In function ‘Sexp_init’:
./rpy/rinterface/sexp.c:738:13: warning: unused variable ‘copy’ [-Wunused-variable]
   PyObject *copy = Py_True;
             ^
In file included from ./rpy/rinterface/_rinterface.c:126:0:
./rpy/rinterface/r_utils.c: At top level:
./rpy/rinterface/r_utils.c:32:31: fatal error: R_ext/Rallocators.h: No such file or directory
 #include <R_ext/Rallocators.h>
                               ^
compilation terminated.
error: command 'i686-linux-gnu-gcc' failed with exit status 1

Comments (2)

  1. Ralf Gommers reporter

    Thanks Laurent, that helps. I just used the R packaged by Ubuntu in its latest LTS release, will try to upgrade it.

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