Can not install RPy2
Question
While trying to install RPy2 I get the below output. What am I doing wrong? Which preconditions are not met?
username@usernameVB:~$ pip install rpy2
Collecting rpy2
Using cached https://files.pythonhosted.org/packages/f1/98/c7652cc9d7fc0afce74d2c30a52b9c9ac391713a63d037e4ab8feb56c530/rpy2-2.9.4.tar.gz
Requirement already satisfied: six in ./miniconda3/lib/python3.6/site-packages (from rpy2) (1.11.0)
Requirement already satisfied: jinja2 in ./miniconda3/lib/python3.6/site-packages (from rpy2) (2.10)
Requirement already satisfied: MarkupSafe>=0.23 in ./miniconda3/lib/python3.6/site-packages (from jinja2->rpy2) (1.0)
Building wheels for collected packages: rpy2
Running setup.py bdist_wheel for rpy2 ... error
Complete output from command /home/username/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-9d74vjq7/rpy2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-e0iufv00 --python-tag cp36:
R version 3.5.1 (2018-07-02) -- "Feather Spray"
/usr/lib/R/bin/R CMD config --ldflags
/usr/lib/R/bin/R CMD config --cppflags
Compilation parameters for rpy2's C components:
include_dirs = ['/usr/share/R/include']
library_dirs = ['/usr/lib/R/lib']
libraries = ['R', 'pcre', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm', 'icuuc', 'icui18n']
extra_link_args = ['-Wl,--export-dynamic', '-fopenmp', '-Wl,-Bsymbolic-functions', '-Wl,-z,relro']
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/situation.py -> build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/__init__.py -> build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/tests.py -> build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-3.6/rpy2
creating build/lib.linux-x86_64-3.6/rpy2/rlike
copying ./rpy/rlike/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/rlike
copying ./rpy/rlike/functional.py -> build/lib.linux-x86_64-3.6/rpy2/rlike
copying ./rpy/rlike/container.py -> build/lib.linux-x86_64-3.6/rpy2/rlike
copying ./rpy/rlike/indexing.py -> build/lib.linux-x86_64-3.6/rpy2/rlike
creating build/lib.linux-x86_64-3.6/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_functional.py -> build/lib.linux-x86_64-3.6/rpy2/rlike/tests
copying ./rpy/rlike/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_container.py -> build/lib.linux-x86_64-3.6/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_indexing.py -> build/lib.linux-x86_64-3.6/rpy2/rlike/tests
creating build/lib.linux-x86_64-3.6/rpy2/rinterface
copying ./rpy/rinterface/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface
creating build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Device.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpSymbol.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
creating build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/help.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/environments.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/methods.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/language.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/packages.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/functions.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/vectors.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/conversion.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/packages_utils.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/constants.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/pandas2ri.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/robject.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/numpy2ri.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
creating build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPackages.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFunction.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFormula.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testMethods.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRObject.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testArray.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testLanguage.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testVector.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testHelp.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRobjects.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
creating build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/ggplot2.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/tidyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/grid.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/dbplyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/dplyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/test_dplyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/grdevices.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
creating build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_grdevices.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_dplyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
creating build/lib.linux-x86_64-3.6/rpy2/interactive
copying ./rpy/interactive/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/interactive
copying ./rpy/interactive/process_revents.py -> build/lib.linux-x86_64-3.6/rpy2/interactive
copying ./rpy/interactive/packages.py -> build/lib.linux-x86_64-3.6/rpy2/interactive
creating build/lib.linux-x86_64-3.6/rpy2/interactive/tests
copying ./rpy/interactive/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/interactive/tests
creating build/lib.linux-x86_64-3.6/rpy2/ipython
copying ./rpy/ipython/ggplot.py -> build/lib.linux-x86_64-3.6/rpy2/ipython
copying ./rpy/ipython/html.py -> build/lib.linux-x86_64-3.6/rpy2/ipython
copying ./rpy/ipython/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/ipython
copying ./rpy/ipython/rmagic.py -> build/lib.linux-x86_64-3.6/rpy2/ipython
creating build/lib.linux-x86_64-3.6/rpy2/ipython/tests
copying ./rpy/ipython/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/ipython/tests
copying ./rpy/ipython/tests/test_rmagic.py -> build/lib.linux-x86_64-3.6/rpy2/ipython/tests
running build_clib
building 'r_utils' library
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/rpy
creating build/temp.linux-x86_64-3.6/rpy/rinterface
gcc -pthread -B /home/username/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./rpy/rinterface -I/usr/share/R/include -c ./rpy/rinterface/r_utils.c -o build/temp.linux-x86_64-3.6/./rpy/rinterface/r_utils.o
In file included from /usr/share/R/include/Rdefines.h:36:0,
from ./rpy/rinterface/r_utils.c:24:
/usr/share/R/include/R_ext/Memory.h:48:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
int R_gc_running();
^~~
In file included from /usr/share/R/include/Rinternals.h:51:0,
from /usr/share/R/include/Rdefines.h:40,
from ./rpy/rinterface/r_utils.c:24:
/usr/share/R/include/R_ext/Rdynload.h:38:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
typedef void * (*DL_FUNC)();
^~~~~~~
In file included from /usr/share/R/include/Rdefines.h:40:0,
from ./rpy/rinterface/r_utils.c:24:
/usr/share/R/include/Rinternals.h:1040:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
const char *R_curErrorBuf();
^~~~~
/usr/share/R/include/Rinternals.h:1115:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void R_init_altrep();
^~~~
/usr/share/R/include/Rinternals.h:1128:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SEXP R_MakeUnwindCont();
^~~~
ar rc build/temp.linux-x86_64-3.6/libr_utils.a build/temp.linux-x86_64-3.6/./rpy/rinterface/r_utils.o
running build_ext
R version 3.5.1 (2018-07-02) -- "Feather Spray"
building 'rpy2.rinterface._rinterface' extension
gcc -pthread -B /home/username/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -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/share/R/include -I/home/username/miniconda3/include/python3.6m -c ./rpy/rinterface/_rinterface.c -o build/temp.linux-x86_64-3.6/./rpy/rinterface/_rinterface.o
In file included from /usr/share/R/include/R.h:87:0,
from ./rpy/rinterface/_rinterface.h:8,
from ./rpy/rinterface/_rinterface.c:52:
/usr/share/R/include/R_ext/Memory.h:48:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
int R_gc_running();
^~~
In file included from /usr/share/R/include/Rinternals.h:51:0,
from ./rpy/rinterface/_rinterface.h:9,
from ./rpy/rinterface/_rinterface.c:52:
/usr/share/R/include/R_ext/Rdynload.h:38:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
typedef void * (*DL_FUNC)();
^~~~~~~
In file included from ./rpy/rinterface/_rinterface.h:9:0,
from ./rpy/rinterface/_rinterface.c:52:
/usr/share/R/include/Rinternals.h:1040:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
const char *R_curErrorBuf();
^~~~~
/usr/share/R/include/Rinternals.h:1115:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void R_init_altrep();
^~~~
/usr/share/R/include/Rinternals.h:1128:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SEXP R_MakeUnwindCont();
^~~~
In file included from ./rpy/rinterface/_rinterface.c:64:0:
/usr/share/R/include/Rinterface.h:157:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
extern void (*ptr_R_ProcessEvents)();
^~~~~~
./rpy/rinterface/_rinterface.c:80:10: fatal error: readline/readline.h: No such file or directory
#include <readline/readline.h>
^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Failed building wheel for rpy2
Running setup.py clean for rpy2
Failed to build rpy2
Installing collected packages: rpy2
Running setup.py install for rpy2 ... error
Complete output from command /home/username/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-9d74vjq7/rpy2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-hf8g7yqq/install-record.txt --single-version-externally-managed --compile:
R version 3.5.1 (2018-07-02) -- "Feather Spray"
/usr/lib/R/bin/R CMD config --ldflags
/usr/lib/R/bin/R CMD config --cppflags
Compilation parameters for rpy2's C components:
include_dirs = ['/usr/share/R/include']
library_dirs = ['/usr/lib/R/lib']
libraries = ['R', 'pcre', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm', 'icuuc', 'icui18n']
extra_link_args = ['-Wl,--export-dynamic', '-fopenmp', '-Wl,-Bsymbolic-functions', '-Wl,-z,relro']
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/situation.py -> build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/__init__.py -> build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/tests.py -> build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-3.6/rpy2
copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-3.6/rpy2
creating build/lib.linux-x86_64-3.6/rpy2/rlike
copying ./rpy/rlike/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/rlike
copying ./rpy/rlike/functional.py -> build/lib.linux-x86_64-3.6/rpy2/rlike
copying ./rpy/rlike/container.py -> build/lib.linux-x86_64-3.6/rpy2/rlike
copying ./rpy/rlike/indexing.py -> build/lib.linux-x86_64-3.6/rpy2/rlike
creating build/lib.linux-x86_64-3.6/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_functional.py -> build/lib.linux-x86_64-3.6/rpy2/rlike/tests
copying ./rpy/rlike/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_container.py -> build/lib.linux-x86_64-3.6/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_indexing.py -> build/lib.linux-x86_64-3.6/rpy2/rlike/tests
creating build/lib.linux-x86_64-3.6/rpy2/rinterface
copying ./rpy/rinterface/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface
creating build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Device.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpSymbol.py -> build/lib.linux-x86_64-3.6/rpy2/rinterface/tests
creating build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/help.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/environments.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/methods.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/language.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/packages.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/functions.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/vectors.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/conversion.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/packages_utils.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/constants.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/pandas2ri.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/robject.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
copying ./rpy/robjects/numpy2ri.py -> build/lib.linux-x86_64-3.6/rpy2/robjects
creating build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPackages.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFunction.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFormula.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testMethods.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRObject.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testArray.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testLanguage.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testVector.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testHelp.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRobjects.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/tests
creating build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/ggplot2.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/tidyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/grid.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/dbplyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/dplyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/test_dplyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
copying ./rpy/robjects/lib/grdevices.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib
creating build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_grdevices.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_dplyr.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.linux-x86_64-3.6/rpy2/robjects/lib/tests
creating build/lib.linux-x86_64-3.6/rpy2/interactive
copying ./rpy/interactive/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/interactive
copying ./rpy/interactive/process_revents.py -> build/lib.linux-x86_64-3.6/rpy2/interactive
copying ./rpy/interactive/packages.py -> build/lib.linux-x86_64-3.6/rpy2/interactive
creating build/lib.linux-x86_64-3.6/rpy2/interactive/tests
copying ./rpy/interactive/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/interactive/tests
creating build/lib.linux-x86_64-3.6/rpy2/ipython
copying ./rpy/ipython/ggplot.py -> build/lib.linux-x86_64-3.6/rpy2/ipython
copying ./rpy/ipython/html.py -> build/lib.linux-x86_64-3.6/rpy2/ipython
copying ./rpy/ipython/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/ipython
copying ./rpy/ipython/rmagic.py -> build/lib.linux-x86_64-3.6/rpy2/ipython
creating build/lib.linux-x86_64-3.6/rpy2/ipython/tests
copying ./rpy/ipython/tests/__init__.py -> build/lib.linux-x86_64-3.6/rpy2/ipython/tests
copying ./rpy/ipython/tests/test_rmagic.py -> build/lib.linux-x86_64-3.6/rpy2/ipython/tests
running build_clib
building 'r_utils' library
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/rpy
creating build/temp.linux-x86_64-3.6/rpy/rinterface
gcc -pthread -B /home/username/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./rpy/rinterface -I/usr/share/R/include -c ./rpy/rinterface/r_utils.c -o build/temp.linux-x86_64-3.6/./rpy/rinterface/r_utils.o
In file included from /usr/share/R/include/Rdefines.h:36:0,
from ./rpy/rinterface/r_utils.c:24:
/usr/share/R/include/R_ext/Memory.h:48:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
int R_gc_running();
^~~
In file included from /usr/share/R/include/Rinternals.h:51:0,
from /usr/share/R/include/Rdefines.h:40,
from ./rpy/rinterface/r_utils.c:24:
/usr/share/R/include/R_ext/Rdynload.h:38:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
typedef void * (*DL_FUNC)();
^~~~~~~
In file included from /usr/share/R/include/Rdefines.h:40:0,
from ./rpy/rinterface/r_utils.c:24:
/usr/share/R/include/Rinternals.h:1040:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
const char *R_curErrorBuf();
^~~~~
/usr/share/R/include/Rinternals.h:1115:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void R_init_altrep();
^~~~
/usr/share/R/include/Rinternals.h:1128:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SEXP R_MakeUnwindCont();
^~~~
ar rc build/temp.linux-x86_64-3.6/libr_utils.a build/temp.linux-x86_64-3.6/./rpy/rinterface/r_utils.o
running build_ext
R version 3.5.1 (2018-07-02) -- "Feather Spray"
building 'rpy2.rinterface._rinterface' extension
gcc -pthread -B /home/username/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -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/share/R/include -I/home/username/miniconda3/include/python3.6m -c ./rpy/rinterface/_rinterface.c -o build/temp.linux-x86_64-3.6/./rpy/rinterface/_rinterface.o
In file included from /usr/share/R/include/R.h:87:0,
from ./rpy/rinterface/_rinterface.h:8,
from ./rpy/rinterface/_rinterface.c:52:
/usr/share/R/include/R_ext/Memory.h:48:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
int R_gc_running();
^~~
In file included from /usr/share/R/include/Rinternals.h:51:0,
from ./rpy/rinterface/_rinterface.h:9,
from ./rpy/rinterface/_rinterface.c:52:
/usr/share/R/include/R_ext/Rdynload.h:38:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
typedef void * (*DL_FUNC)();
^~~~~~~
In file included from ./rpy/rinterface/_rinterface.h:9:0,
from ./rpy/rinterface/_rinterface.c:52:
/usr/share/R/include/Rinternals.h:1040:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
const char *R_curErrorBuf();
^~~~~
/usr/share/R/include/Rinternals.h:1115:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void R_init_altrep();
^~~~
/usr/share/R/include/Rinternals.h:1128:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SEXP R_MakeUnwindCont();
^~~~
In file included from ./rpy/rinterface/_rinterface.c:64:0:
/usr/share/R/include/Rinterface.h:157:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
extern void (*ptr_R_ProcessEvents)();
^~~~~~
./rpy/rinterface/_rinterface.c:80:10: fatal error: readline/readline.h: No such file or directory
#include <readline/readline.h>
^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/home/username/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-9d74vjq7/rpy2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-hf8g7yqq/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-9d74vjq7/rpy2/
Is there an issue in my R installation (it is a default R installed on Ubuntu)?
I need to add "more details" since my post can not be submitted since it appears to include only code. So here are more details: blah blah, detail 1, detail 2, detail 3, ...
1 answers
solution1
0 2018-08-06 21:41:50
You need to install the library readline and its headers.
The hint was near the end of the terminal output:
./rpy/rinterface/_rinterface.c:80:10: fatal error: readline/readline.h: No such file or directory
#include <readline/readline.h>
^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
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