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I rpy2 auf Red Hat 6. zu installieren versuche ich habe R 3.3.3 aufgerüstet hier folgen Sie den Anweisungen: https://oguya.ch/posts/2017-03-18-building-R-on-rhel-6/Fehler Installation ryp2 auf RHEL6 mit R 3.3.3
Wenn ich die rpy2 installieren schlägt fehl mit folgendem:
$ sudo /usr/local/bin/pip2.7 install rpy2
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/
Wer weiß, was das Problem ist und wie kann ich rpy2 hier installieren?
auch versucht, Gebäude rpy2 von der Quelle und das scheiterte mit:
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: cannot find -lr_utils
ich gesucht und gesucht, aber ich libr_utils von nicht einen Platz finden, bekommen.
Wenn die Installation von Pip funktioniert, hätte ich nicht nach anderen Wegen suchen müssen. Der letzte Fehler (die fehlende lib) kam von "python setup.py install". Ich habe das Problem gefunden - meine Installation von Epel-Release war durcheinander. Ich habe das neu installiert und dann konnte ich R von den Repos installieren und dann rpy2 mit pip installieren. Aber jetzt bekomme ich diesen Fehler, wenn ich es benutze: 'ImportError: 'Kein Modul namens rpy2.robjects''. Also muss ich mich darauf konzentrieren und sehen, was vor sich geht. –