Anyone out there who can help us with this? We really need to get rpy running.
On Sun, Jul 16, 2017 at 6:22 PM, Larry Martell <larry.mart...@gmail.com> wrote:
> 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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