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Foundry Spatial jkjAK: Untitled snippet

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foundry@postgres2:~/code$ 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]
     int R_gc_running();
     ^
    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']



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/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

running build_ext

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]

 int R_gc_running();

 ^

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

----------------------------------------
Cleaning up...
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)

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