I also tried building rpy2 from source and that failed with:
gcc -pthread -shared
build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o
-L/usr/local/lib64/R/lib -Lbuild/temp.linux-x86_64-2.7
-Wl,-R/usr/local/lib64/R/lib -lRblas -lgfortran -lm -lreadline -lpcre
-llzma -lbz2 -lz -lrt -ldl -lm -lr_utils -o
build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so
-Wl,--export-dynamic -fopenmp -Wl,--whole-archive
/usr/local/lib64/R/lib/libR.a -Wl,--no-whole-archive
/usr/bin/ld: cannot find -lr_utils
But I could not find how to get libr_utils.
On Sun, Jul 16, 2017 at 10:33 AM, Larry Martell <larry.mart...@gmail.com> wrote:
> I upgraded to R 3.3.3 and now the rpy2 install fails with this:
>
> Collecting rpy2
>
> Using cached rpy2-2.8.6.tar.gz
>
> Requirement already satisfied (use --upgrade to upgrade): six in
> /usr/local/lib/python2.7/site-packages (from rpy2)
>
> Requirement already satisfied (use --upgrade to upgrade):
> singledispatch in /usr/local/lib/python2.7/site-packages (from rpy2)
>
> Installing collected packages: rpy2
>
> Running setup.py install for rpy2 ... error
>
> Complete output from command /usr/local/bin/python2.7 -u -c
> "import setuptools,
> tokenize;__file__='/tmp/pip-build-eFwk3n/rpy2/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
> 'exec'))" install --record /tmp/pip-w5v7yg-record/install-record.txt
> --single-version-externally-managed --compile:
>
> R version 3.3.3 (2017-03-06) -- "Another Canoe"
>
> /usr/local/lib64/R/bin/R CMD config --ldflags
>
> /usr/local/lib64/R/bin/R CMD config --cppflags
>
>
>
> Compilation parameters for rpy2's C components:
>
> include_dirs = ['/usr/local/lib64/R/include']
>
> library_dirs = ['/usr/local/lib64/R/lib']
>
> libraries = ['Rblas', 'gfortran', 'm', 'readline',
> 'pcre', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm']
>
> extra_link_args = ['-Wl,--export-dynamic', '-fopenmp',
> '-Wl,--whole-archive', '/usr/local/lib64/R/lib/libR.a',
> '-Wl,--no-whole-archive']
>
>
>
> running install
>
> running build
>
> running build_py
>
> creating build
>
> creating build/lib.linux-x86_64-2.7
>
> creating build/lib.linux-x86_64-2.7/rpy2
>
> copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2
>
> copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
>
> copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
>
> copying ./rpy/tests.py -> build/lib.linux-x86_64-2.7/rpy2
>
> creating build/lib.linux-x86_64-2.7/rpy2/rlike
>
> copying ./rpy/rlike/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
>
> copying ./rpy/rlike/indexing.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
>
> copying ./rpy/rlike/container.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
>
> copying ./rpy/rlike/functional.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
>
> creating build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> copying ./rpy/rlike/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> copying ./rpy/rlike/tests/test_indexing.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> copying ./rpy/rlike/tests/test_functional.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> copying ./rpy/rlike/tests/test_container.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> creating build/lib.linux-x86_64-2.7/rpy2/rinterface
>
> copying ./rpy/rinterface/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface
>
> creating build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpSymbol.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpVector.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_Sexp.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpExtPtr.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpEnvironment.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_EmbeddedR.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpClosure.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_Device.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> creating build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/functions.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/vectors.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/environments.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/language.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/packages_utils.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/packages.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/pandas2ri.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/numpy2ri.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/conversion.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/methods.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/help.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/robject.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/constants.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> creating build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testMethods.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testPandasConversions.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testRObject.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testFunction.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testNumpyConversions.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testArray.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testDataFrame.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testEnvironment.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testVector.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testPackages.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testHelp.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testLanguage.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testRobjects.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> copying ./rpy/robjects/tests/testFormula.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>
> creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>
> copying ./rpy/robjects/lib/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>
> copying ./rpy/robjects/lib/tidyr.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>
> copying ./rpy/robjects/lib/grid.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>
> copying ./rpy/robjects/lib/grdevices.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>
> copying ./rpy/robjects/lib/dplyr.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>
> copying ./rpy/robjects/lib/ggplot2.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>
> creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>
> copying ./rpy/robjects/lib/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>
> copying ./rpy/robjects/lib/tests/test_ggplot2.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>
> copying ./rpy/robjects/lib/tests/test_grdevices.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>
> copying ./rpy/robjects/lib/tests/test_dplyr.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>
> creating build/lib.linux-x86_64-2.7/rpy2/interactive
>
> copying ./rpy/interactive/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/interactive
>
> copying ./rpy/interactive/packages.py ->
> build/lib.linux-x86_64-2.7/rpy2/interactive
>
> copying ./rpy/interactive/process_revents.py ->
> build/lib.linux-x86_64-2.7/rpy2/interactive
>
> creating build/lib.linux-x86_64-2.7/rpy2/interactive/tests
>
> copying ./rpy/interactive/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/interactive/tests
>
> creating build/lib.linux-x86_64-2.7/rpy2/ipython
>
> copying ./rpy/ipython/html.py -> build/lib.linux-x86_64-2.7/rpy2/ipython
>
> copying ./rpy/ipython/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/ipython
>
> copying ./rpy/ipython/ggplot.py -> build/lib.linux-x86_64-2.7/rpy2/ipython
>
> copying ./rpy/ipython/rmagic.py -> build/lib.linux-x86_64-2.7/rpy2/ipython
>
> creating build/lib.linux-x86_64-2.7/rpy2/ipython/tests
>
> copying ./rpy/ipython/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/ipython/tests
>
> copying ./rpy/ipython/tests/test_rmagic.py ->
> build/lib.linux-x86_64-2.7/rpy2/ipython/tests
>
> running build_clib
>
> building 'r_utils' library
>
> creating build/temp.linux-x86_64-2.7
>
> creating build/temp.linux-x86_64-2.7/rpy
>
> creating build/temp.linux-x86_64-2.7/rpy/rinterface
>
> gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
> -Wall -Wstrict-prototypes -fPIC -I./rpy/rinterface
> -I/usr/local/lib64/R/include -c ./rpy/rinterface/r_utils.c -o
> build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o
>
> In file included from /usr/local/lib64/R/include/Rdefines.h:36,
>
> from ./rpy/rinterface/r_utils.c:23:
>
> /usr/local/lib64/R/include/R_ext/Memory.h:51: warning: function
> declaration isn’t a prototype
>
> In file included from /usr/local/lib64/R/include/Rdefines.h:40,
>
> from ./rpy/rinterface/r_utils.c:23:
>
> /usr/local/lib64/R/include/Rinternals.h:886: warning: function
> declaration isn’t a prototype
>
> ar rc build/temp.linux-x86_64-2.7/libr_utils.a
> build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o
>
> running build_ext
>
> R version 3.3.3 (2017-03-06) -- "Another Canoe"
>
> building 'rpy2.rinterface._rinterface' extension
>
> gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
> -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/local/lib64/R/include
> -I/usr/local/include/python2.7 -c ./rpy/rinterface/_rinterface.c -o
> build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o
>
> In file included from /usr/local/include/python2.7/Python.h:8,
>
> from ./rpy/rinterface/_rinterface.c:49:
>
> /usr/local/include/python2.7/pyconfig.h:1188:1: warning:
> "_POSIX_C_SOURCE" redefined
>
> In file included from /usr/include/signal.h:29,
>
> from ./rpy/rinterface/_rinterface.c:45:
>
> /usr/include/features.h:213:1: warning: this is the location of
> the previous definition
>
> In file included from /usr/local/lib64/R/include/R.h:80,
>
> from ./rpy/rinterface/_rinterface.h:8,
>
> from ./rpy/rinterface/_rinterface.c:52:
>
> /usr/local/lib64/R/include/R_ext/Memory.h:51: warning: function
> declaration isn’t a prototype
>
> In file included from ./rpy/rinterface/_rinterface.h:9,
>
> from ./rpy/rinterface/_rinterface.c:52:
>
> /usr/local/lib64/R/include/Rinternals.h:886: warning: function
> declaration isn’t a prototype
>
> In file included from ./rpy/rinterface/_rinterface.c:64:
>
> /usr/local/lib64/R/include/Rinterface.h:149: warning: function
> declaration isn’t a prototype
>
> In file included from ./rpy/rinterface/_rinterface.c:73:
>
> /usr/local/lib64/R/include/R_ext/Rdynload.h:36: warning: function
> declaration isn’t a prototype
>
> In file included from ./rpy/rinterface/_rinterface.c:116:
>
> ./rpy/rinterface/embeddedr.c: In function ‘SexpObject_clear’:
>
> ./rpy/rinterface/embeddedr.c:48: warning: unused variable ‘res’
>
> In file included from ./rpy/rinterface/_rinterface.c:119:
>
> ./rpy/rinterface/sexp.c: In function ‘Sexp_init’:
>
> ./rpy/rinterface/sexp.c:742: warning: unused variable ‘copy’
>
> ./rpy/rinterface/_rinterface.c: At top level:
>
> ./rpy/rinterface/_rinterface.h:203: warning:
> ‘PyRinterface_IsInitialized’ declared ‘static’ but never defined
>
> ./rpy/rinterface/_rinterface.h:204: warning:
> ‘PyRinterface_FindFun’ declared ‘static’ but never defined
>
> ./rpy/rinterface/_rinterface.h:205: warning:
> ‘embeddedR_isInitialized’ defined but not used
>
> ./rpy/rinterface/sequence.c:2173: warning:
> ‘ComplexVectorSexp_AsSexp’ defined but not used
>
> ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowFiles’:
>
> ./rpy/rinterface/_rinterface.c:831: warning: ‘gstate’ may be used
> uninitialized in this function
>
> ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ResetConsole’:
>
> ./rpy/rinterface/_rinterface.c:677: warning: ‘gstate’ may be used
> uninitialized in this function
>
> ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_FlushConsole’:
>
> ./rpy/rinterface/_rinterface.c:643: warning: ‘gstate’ may be used
> uninitialized in this function
>
> ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ChooseFile’:
>
> ./rpy/rinterface/_rinterface.c:727: warning: ‘gstate’ may be used
> uninitialized in this function
>
> ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ReadConsole’:
>
> ./rpy/rinterface/_rinterface.c:498: warning: ‘gstate’ may be used
> uninitialized in this function
>
> ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_WriteConsoleEx’:
>
> ./rpy/rinterface/_rinterface.c:339: warning: ‘consolecallback’ may
> be used uninitialized in this function
>
> ./rpy/rinterface/_rinterface.c:354: warning: ‘gstate’ may be used
> uninitialized in this function
>
> ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowMessage’:
>
> ./rpy/rinterface/_rinterface.c:429: warning: ‘gstate’ may be used
> uninitialized in this function
>
> ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_CleanUp’:
>
> ./rpy/rinterface/_rinterface.c:979: warning: ‘gstate’ may be used
> uninitialized in this function
>
> gcc -pthread -shared
> build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o
> -L/usr/local/lib64/R/lib -Lbuild/temp.linux-x86_64-2.7
> -Wl,-R/usr/local/lib64/R/lib -lRblas -lgfortran -lm -lreadline -lpcre
> -llzma -lbz2 -lz -lrt -ldl -lm -lr_utils -o
> build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so
> -Wl,--export-dynamic -fopenmp -Wl,--whole-archive
> /usr/local/lib64/R/lib/libR.a -Wl,--no-whole-archive
>
> /usr/bin/ld: /usr/local/lib64/R/lib/libR.a(CommandLineArgs.o):
> relocation R_X86_64_32 against `.rodata' can not be used when making a
> shared object; recompile with -fPIC
>
> /usr/local/lib64/R/lib/libR.a(CommandLineArgs.o): could not read
> symbols: Bad value
>
> collect2: ld returned 1 exit status
>
> error: command 'gcc' failed with exit status 1
>
>
>
> ----------------------------------------
>
> Command "/usr/local/bin/python2.7 -u -c "import setuptools,
> tokenize;__file__='/tmp/pip-build-eFwk3n/rpy2/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
> 'exec'))" install --record /tmp/pip-w5v7yg-record/install-record.txt
> --single-version-externally-managed --compile" failed with error code
> 1 in /tmp/pip-build-eFwk3n/rpy2/
>
> On Mon, Jul 10, 2017 at 6:41 PM, Larry Martell <larry.mart...@gmail.com>
> wrote:
>> Yes, I see that warning, but I have R version 3.1.0 and the rpy2 docs
>> say it works with 3.1+
>>
>> How do I fix the 'R headers cannot be found' issue? I do have R-devel
>> installed.
>>
>> On Mon, Jul 10, 2017 at 6:34 PM, Laurent Gautier <lgaut...@gmail.com> wrote:
>>> R headers cannot be found.
>>>
>>> Note that there is a warning about the R version being too old for support
>>> with that version of rpy2 ( maybe it will work, maybe it won't).
>>>
>>> On Mon, Jul 10, 2017, 11:18 AM Larry Martell <larry.mart...@gmail.com>
>>> wrote:
>>>>
>>>> Trying to install rpy2 on redhat 6.7. I have R version 3.1.0:
>>>>
>>>> $ R --version
>>>>
>>>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>>>
>>>> Here is what I get from pip2.7 install rpy2:
>>>>
>>>> $ pip install rpy2
>>>>
>>>> Collecting rpy2
>>>> Downloading rpy2-2.8.6.tar.gz (191kB)
>>>> 100% |████████████████████████████████| 194kB 1.3MB/s
>>>> Requirement already satisfied (use --upgrade to upgrade): six in
>>>> /usr/local/lib/python2.7/site-packages (from rpy2)
>>>> Collecting singledispatch (from rpy2)
>>>> Downloading singledispatch-3.4.0.3-py2.py3-none-any.whl
>>>> Installing collected packages: singledispatch, rpy2
>>>> Running setup.py install for rpy2 ... error
>>>> Complete output from command /usr/local/bin/python2.7 -u -c
>>>> "import setuptools,
>>>>
>>>> tokenize;__file__='/tmp/pip-build-cM5dhd/rpy2/setup.py';exec(compile(getattr(tokenize,
>>>> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
>>>> 'exec'))" install --record /tmp/pip-zyalf5-record/install-record.txt
>>>> --single-version-externally-managed --compile:
>>>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>>> /tmp/pip-build-cM5dhd/rpy2/setup.py:236: UserWarning: R did not
>>>> seem to have the minimum required version number
>>>> warnings.warn("R did not seem to have the minimum required
>>>> version number")
>>>> /usr/local/lib64/R/bin/R CMD config --ldflags
>>>> R was not built as a library
>>>> /usr/local/lib64/R/bin/R CMD config --cppflags
>>>> R was not built as a library
>>>> /tmp/pip-build-cM5dhd/rpy2/setup.py:251: UserWarning: No include
>>>> specified
>>>> warnings.warn('No include specified')
>>>> /tmp/pip-build-cM5dhd/rpy2/setup.py:262: UserWarning: No libraries
>>>> as -l arguments to the compiler.
>>>> warnings.warn('No libraries as -l arguments to the compiler.')
>>>>
>>>> Compilation parameters for rpy2's C components:
>>>> include_dirs = []
>>>> library_dirs = []
>>>> libraries = []
>>>> extra_link_args = []
>>>>
>>>> running install
>>>> running build
>>>> running build_py
>>>> creating build
>>>> creating build/lib.linux-x86_64-2.7
>>>> creating build/lib.linux-x86_64-2.7/rpy2
>>>> copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2
>>>> copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy
>>>> copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
>>>> copying ./rpy/tests.py -> build/lib.linux-x86_64-2.7/rpy2
>>>> creating build/lib.linux-x86_64-2.7/rpy2/rlike
>>>> copying ./rpy/rlike/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rlike
>>>> copying ./rpy/rlike/indexing.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rlike
>>>> copying ./rpy/rlike/container.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rlike
>>>> copying ./rpy/rlike/functional.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rlike
>>>> creating build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>>>> copying ./rpy/rlike/tests/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>>>> copying ./rpy/rlike/tests/test_indexing.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>>>> copying ./rpy/rlike/tests/test_functional.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>>>> copying ./rpy/rlike/tests/test_container.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>>>> creating build/lib.linux-x86_64-2.7/rpy2/rinterface
>>>> copying ./rpy/rinterface/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface
>>>> creating build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_SexpSymbol.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_SexpVector.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_Sexp.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_SexpExtPtr.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_SexpEnvironment.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_EmbeddedR.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_SexpClosure.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> copying ./rpy/rinterface/tests/test_Device.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>>>> creating build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/functions.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/vectors.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/environments.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/language.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/packages_utils.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/packages.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/pandas2ri.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/numpy2ri.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/conversion.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/methods.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/help.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/robject.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> copying ./rpy/robjects/constants.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects
>>>> creating build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testMethods.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testPandasConversions.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testRObject.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testFunction.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testNumpyConversions.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testArray.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testDataFrame.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testEnvironment.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testVector.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testPackages.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testHelp.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testLanguage.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testRobjects.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> copying ./rpy/robjects/tests/testFormula.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
>>>> creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>>>> copying ./rpy/robjects/lib/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>>>> copying ./rpy/robjects/lib/tidyr.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>>>> copying ./rpy/robjects/lib/grid.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>>>> copying ./rpy/robjects/lib/grdevices.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>>>> copying ./rpy/robjects/lib/dplyr.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>>>> copying ./rpy/robjects/lib/ggplot2.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
>>>> creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>>>> copying ./rpy/robjects/lib/tests/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>>>> copying ./rpy/robjects/lib/tests/test_ggplot2.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>>>> copying ./rpy/robjects/lib/tests/test_grdevices.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>>>> copying ./rpy/robjects/lib/tests/test_dplyr.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
>>>> creating build/lib.linux-x86_64-2.7/rpy2/interactive
>>>> copying ./rpy/interactive/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/interactive
>>>> copying ./rpy/interactive/packages.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/interactive
>>>> copying ./rpy/interactive/process_revents.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/interactive
>>>> creating build/lib.linux-x86_64-2.7/rpy2/interactive/tests
>>>> copying ./rpy/interactive/tests/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/interactive/tests
>>>> creating build/lib.linux-x86_64-2.7/rpy2/ipython
>>>> copying ./rpy/ipython/html.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/ipython
>>>> copying ./rpy/ipython/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/ipython
>>>> copying ./rpy/ipython/ggplot.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/ipython
>>>> copying ./rpy/ipython/rmagic.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/ipython
>>>> creating build/lib.linux-x86_64-2.7/rpy2/ipython/tests
>>>> copying ./rpy/ipython/tests/__init__.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/ipython/tests
>>>> copying ./rpy/ipython/tests/test_rmagic.py ->
>>>> build/lib.linux-x86_64-2.7/rpy2/ipython/tests
>>>> running build_clib
>>>> building 'r_utils' library
>>>> creating build/temp.linux-x86_64-2.7
>>>> creating build/temp.linux-x86_64-2.7/rp
>>>> creating build/temp.linux-x86_64-2.7/rpy/rinterface
>>>> gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
>>>> -Wall -Wstrict-prototypes -fPIC -I./rpy/rinterface -c
>>>> ./rpy/rinterface/r_utils.c -o
>>>> build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o
>>>> ./rpy/rinterface/r_utils.c:23:22: error: Rdefines.h: No such file
>>>> or directory
>>>> ./rpy/rinterface/r_utils.c:24:31: error: R_ext/Rallocators.h: No
>>>> such file or directory
>>>> In file included from ./rpy/rinterface/r_utils.c:25:
>>>> ./rpy/rinterface/r_utils.h:5:22: error: Rversion.h: No such file
>>>> or directory
>>>> In file included from ./rpy/rinterface/r_utils.c:25:
>>>> ./rpy/rinterface/r_utils.h:7: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
>>>> or ‘__attribute__’ before ‘rpy2_serialize’
>>>> ./rpy/rinterface/r_utils.h:8: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
>>>> or ‘__attribute__’ before ‘rpy2_unserialize’
>>>> ./rpy/rinterface/r_utils.h:9: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
>>>> or ‘__attribute__’ before ‘rpy2_remove’
>>>> ./rpy/rinterface/r_utils.h:11: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_list_attr’
>>>> ./rpy/rinterface/r_utils.h:13: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_lang2str’
>>>> ./rpy/rinterface/r_utils.h:15: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘externallymanaged_vector’
>>>> ./rpy/rinterface/r_utils.h:17: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_newenv’
>>>> ./rpy/rinterface/r_utils.h:27: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_findfun’
>>>> ./rpy/rinterface/r_utils.c:53: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_findfun’
>>>> ./rpy/rinterface/r_utils.c:80: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_serialize’
>>>> ./rpy/rinterface/r_utils.c:104: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_unserialize’
>>>> ./rpy/rinterface/r_utils.c:124: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_list_attr’
>>>> ./rpy/rinterface/r_utils.c:147: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_remove’
>>>> ./rpy/rinterface/r_utils.c:163: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_newenv’
>>>> ./rpy/rinterface/r_utils.c:180: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘rpy2_lang2str’
>>>> ./rpy/rinterface/r_utils.c:213: error: expected ‘)’ before ‘*’ token
>>>> ./rpy/rinterface/r_utils.c:219: error: expected ‘)’ before ‘*’ token
>>>> ./rpy/rinterface/r_utils.c:225: error: expected ‘=’, ‘,’, ‘;’,
>>>> ‘asm’ or ‘__attribute__’ before ‘externallymanaged_vector’
>>>> error: command 'gcc' failed with exit status 1
>>>>
>>>> ----------------------------------------
>>>>
>>>> Command "/usr/local/bin/python2.7 -u -c "import setuptools,
>>>>
>>>> tokenize;__file__='/tmp/pip-build-cM5dhd/rpy2/setup.py';exec(compile(getattr(tokenize,
>>>> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
>>>> 'exec'))" install --record /tmp/pip-zyalf5-record/install-record.txt
>>>> --single-version-externally-managed --compile" failed with error code
>>>> 1 in /tmp/pip-build-cM5dhd/rpy2/
------------------------------------------------------------------------------
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