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 <[email protected]> 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 <[email protected]> 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 <[email protected]>
>> 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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