+foundry@postgres2:~/code/routomator/pyroutomator$ sudo pip install rpy2
+Downloading/unpacking rpy2
+ Downloading rpy2-2.6.0.tar.gz (171kB): 171kB downloaded
+ Running setup.py (path:/tmp/pip_build_root/rpy2/setup.py) egg_info for package rpy2
+ R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+ /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']
+ extra_link_args = ['-Wl,--export-dynamic', '-fopenmp']
+ R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+ warning: no files found matching 'README' anywhere in distribution
+ warning: no previously-included files matching '*patch*' found anywhere in distribution
+ warning: no previously-included files matching '*diff*' found anywhere in distribution
+ warning: no previously-included files matching '.hg' found anywhere in distribution
+ warning: no files found matching 'MANIFEST'
+ warning: no files found matching 'README'
+ warning: no files found matching 'MPL_LICENSE'
+ warning: no files found matching 'GPL_LICENSE'
+ warning: no files found matching 'LGPL_LICENSE'
+ no previously-included directories found matching 'dist'
+ warning: no files found matching 'doc/source/rpy2_logo.png'
+Requirement already satisfied (use --upgrade to upgrade): six in /usr/lib/python2.7/dist-packages (from rpy2)
+Requirement already satisfied (use --upgrade to upgrade): singledispatch in /usr/local/lib/python2.7/dist-packages (from rpy2)
+Installing collected packages: rpy2
+ Running setup.py install for rpy2
+ R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+ /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']
+ extra_link_args = ['-Wl,--export-dynamic', '-fopenmp']
+ R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+ building 'rpy2.rinterface._rinterface' extension
+ x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -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/usr/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/share/R/include/R.h:46:0,
+ from ./rpy/rinterface/_rinterface.h:8,
+ from ./rpy/rinterface/_rinterface.c:58:
+ /usr/share/R/include/R_ext/Memory.h:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
+ In file included from ./rpy/rinterface/_rinterface.h:9:0,
+ from ./rpy/rinterface/_rinterface.c:58:
+ /usr/share/R/include/Rinternals.h:865:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
+ const char *R_curErrorBuf();
+ In file included from ./rpy/rinterface/_rinterface.c:70:0:
+ /usr/share/R/include/Rinterface.h:138:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
+ extern void (*ptr_R_ProcessEvents)();
+ In file included from ./rpy/rinterface/_rinterface.c:79:0:
+ /usr/share/R/include/R_ext/Rdynload.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
+ typedef void * (*DL_FUNC)();
+ In file included from ./rpy/rinterface/_rinterface.c:122:0:
+ ./rpy/rinterface/embeddedr.c: In function ‘SexpObject_clear’:
+ ./rpy/rinterface/embeddedr.c:48:12: warning: unused variable ‘res’ [-Wunused-variable]
+ SEXP res = rpy_remove(Rf_mkString(name_buf),
+ In file included from ./rpy/rinterface/_rinterface.c:125:0:
+ ./rpy/rinterface/sexp.c: In function ‘Sexp_init’:
+ ./rpy/rinterface/sexp.c:738:13: warning: unused variable ‘copy’ [-Wunused-variable]
+ PyObject *copy = Py_True;
+ In file included from ./rpy/rinterface/_rinterface.c:129:0:
+ ./rpy/rinterface/_rinterface.c: At top level:
+ ./rpy/rinterface/sequence.c:2174:1: warning: ‘ComplexVectorSexp_AsSexp’ defined but not used [-Wunused-function]
+ ComplexVectorSexp_AsSexp(PyObject *pyfloat) {
+ In file included from ./rpy/rinterface/_rinterface.c:58:0:
+ ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowFiles’:
+ ./rpy/rinterface/_rinterface.h:72:23: warning: ‘gstate’ may be used uninitialized in this function [-Wmaybe-uninitialized]
+ PyGILState_Release(gstate); \
+ ./rpy/rinterface/_rinterface.c:874:20: note: ‘gstate’ was declared here
+ PyGILState_STATE gstate;
+ ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_WriteConsoleEx’:
+ ./rpy/rinterface/_rinterface.c:420:10: warning: ‘consolecallback’ may be used uninitialized in this function [-Wmaybe-uninitialized]
+ result = PyEval_CallObject(consolecallback, arglist);
+ In file included from ./rpy/rinterface/_rinterface.c:58:0:
+ ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_CleanUp’:
+ ./rpy/rinterface/_rinterface.h:72:23: warning: ‘gstate’ may be used uninitialized in this function [-Wmaybe-uninitialized]
+ PyGILState_Release(gstate); \
+ ./rpy/rinterface/_rinterface.c:1022:20: note: ‘gstate’ was declared here
+ PyGILState_STATE gstate;
+ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o -L/usr/lib/R/lib -Wl,-R/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -o build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so -Wl,--export-dynamic -fopenmp
+ /usr/bin/ld: cannot find -llzma
+ collect2: error: ld returned 1 exit status
+ error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
+ Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-HXsFEK-record/install-record.txt --single-version-externally-managed --compile:
+ R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+/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']
+ extra_link_args = ['-Wl,--export-dynamic', '-fopenmp']
+creating build/lib.linux-x86_64-2.7
+creating 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
+copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
+copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2
+creating 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
+copying ./rpy/rlike/__init__.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/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/__init__.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_SexpVectorNumeric.py -> 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/test_SexpClosure.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_Device.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_Sexp.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_EmbeddedR.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
+creating 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/conversion.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/environments.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
+copying ./rpy/robjects/constants.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/functions.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/robject.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/vectors.py -> 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/packages_utils.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
+copying ./rpy/robjects/language.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/testEnvironment.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/testVector.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/testFormula.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/testPackages.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/testMethods.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/testFunction.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/__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/testRobjects.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/ggplot2.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/__init__.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/test_ggplot2.py -> 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
+creating build/lib.linux-x86_64-2.7/rpy2/interactive
+copying ./rpy/interactive/process_revents.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/__init__.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/rmagic.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
+creating 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
+copying ./rpy/ipython/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/ipython/tests
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+building 'rpy2.rinterface._rinterface' extension
+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
+x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -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/usr/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/share/R/include/R.h:46:0,
+ from ./rpy/rinterface/_rinterface.h:8,
+ from ./rpy/rinterface/_rinterface.c:58:
+/usr/share/R/include/R_ext/Memory.h:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
+In file included from ./rpy/rinterface/_rinterface.h:9:0,
+ from ./rpy/rinterface/_rinterface.c:58:
+/usr/share/R/include/Rinternals.h:865:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
+ const char *R_curErrorBuf();
+In file included from ./rpy/rinterface/_rinterface.c:70:0:
+/usr/share/R/include/Rinterface.h:138:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
+ extern void (*ptr_R_ProcessEvents)();
+In file included from ./rpy/rinterface/_rinterface.c:79:0:
+/usr/share/R/include/R_ext/Rdynload.h:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
+ typedef void * (*DL_FUNC)();
+In file included from ./rpy/rinterface/_rinterface.c:122:0:
+./rpy/rinterface/embeddedr.c: In function ‘SexpObject_clear’:
+./rpy/rinterface/embeddedr.c:48:12: warning: unused variable ‘res’ [-Wunused-variable]
+ SEXP res = rpy_remove(Rf_mkString(name_buf),
+In file included from ./rpy/rinterface/_rinterface.c:125:0:
+./rpy/rinterface/sexp.c: In function ‘Sexp_init’:
+./rpy/rinterface/sexp.c:738:13: warning: unused variable ‘copy’ [-Wunused-variable]
+ PyObject *copy = Py_True;
+In file included from ./rpy/rinterface/_rinterface.c:129:0:
+./rpy/rinterface/_rinterface.c: At top level:
+./rpy/rinterface/sequence.c:2174:1: warning: ‘ComplexVectorSexp_AsSexp’ defined but not used [-Wunused-function]
+ ComplexVectorSexp_AsSexp(PyObject *pyfloat) {
+In file included from ./rpy/rinterface/_rinterface.c:58:0:
+./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowFiles’:
+./rpy/rinterface/_rinterface.h:72:23: warning: ‘gstate’ may be used uninitialized in this function [-Wmaybe-uninitialized]
+ PyGILState_Release(gstate); \
+./rpy/rinterface/_rinterface.c:874:20: note: ‘gstate’ was declared here
+ PyGILState_STATE gstate;
+./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_WriteConsoleEx’:
+./rpy/rinterface/_rinterface.c:420:10: warning: ‘consolecallback’ may be used uninitialized in this function [-Wmaybe-uninitialized]
+ result = PyEval_CallObject(consolecallback, arglist);
+In file included from ./rpy/rinterface/_rinterface.c:58:0:
+./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_CleanUp’:
+./rpy/rinterface/_rinterface.h:72:23: warning: ‘gstate’ may be used uninitialized in this function [-Wmaybe-uninitialized]
+ PyGILState_Release(gstate); \
+./rpy/rinterface/_rinterface.c:1022:20: note: ‘gstate’ was declared here
+ PyGILState_STATE gstate;
+x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o -L/usr/lib/R/lib -Wl,-R/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -o build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so -Wl,--export-dynamic -fopenmp
+/usr/bin/ld: cannot find -llzma
+collect2: error: ld returned 1 exit status
+error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
+----------------------------------------
+Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-HXsFEK-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/rpy2
+Traceback (most recent call last):
+ File "/usr/bin/pip", line 9, in <module>
+ load_entry_point('pip==1.5.4', 'console_scripts', 'pip')()
+ File "/usr/lib/python2.7/dist-packages/pip/__init__.py", line 235, in main
+ return command.main(cmd_args)
+ File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 161, in main
+ text = '\n'.join(complete_log)
+UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 79: ordinal not in range(128)
