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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