* Package: dev-python/rpy-2.2.6  * Repository: gentoo  * Maintainer: python@gentoo.org sci@gentoo.org  * USE: abi_x86_64 amd64 elibc_glibc kernel_linux multilib test userland_GNU  * FEATURES: preserve-libs sandbox test userpriv usersandbox >>> Unpacking source... >>> Unpacking rpy2-2.2.6.tar.gz to /var/tmp/portage/dev-python/rpy-2.2.6/work >>> Source unpacked in /var/tmp/portage/dev-python/rpy-2.2.6/work >>> Preparing source in /var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6 ... * Building of dev-python/rpy-2.2.6 with CPython 2.7... python2.7 setup.py build -b build-2.7 running build running build_py creating build-2.7 creating build-2.7/lib.linux-x86_64-2.7 creating build-2.7/lib.linux-x86_64-2.7/rpy2 copying ./rpy/tests_rpy_classic.py -> build-2.7/lib.linux-x86_64-2.7/rpy2 copying ./rpy/rpy_classic.py -> build-2.7/lib.linux-x86_64-2.7/rpy2 copying ./rpy/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2 copying ./rpy/tests.py -> build-2.7/lib.linux-x86_64-2.7/rpy2 creating build-2.7/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/container.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/functional.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rlike copying ./rpy/rlike/indexing.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rlike creating build-2.7/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_container.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_functional.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rlike/tests copying ./rpy/rlike/tests/test_indexing.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rlike/tests creating build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface copying ./rpy/rinterface/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface creating build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpVector.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_Sexp.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_SexpClosure.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests copying ./rpy/rinterface/tests/test_Device.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/tests creating build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/vectors.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/constants.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/language.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/environments.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/methods.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/help.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/packages.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/conversion.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/robject.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/functions.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects copying ./rpy/robjects/numpy2ri.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects creating build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testArray.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testNumpyConversions.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testMethods.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testFunction.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testFormula.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testHelp.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testEnvironment.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testDataFrame.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testLanguage.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testRObject.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testVector.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testPackages.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests copying ./rpy/robjects/tests/testRobjects.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/tests creating build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/ggplot2.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/grid.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/lib copying ./rpy/robjects/lib/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/lib creating build-2.7/lib.linux-x86_64-2.7/rpy2/interactive copying ./rpy/interactive/process_revents.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/interactive copying ./rpy/interactive/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/interactive creating build-2.7/lib.linux-x86_64-2.7/rpy2/interactive/tests copying ./rpy/interactive/tests/__init__.py -> build-2.7/lib.linux-x86_64-2.7/rpy2/interactive/tests warning: build_py: byte-compiling is disabled, skipping. running build_ext Configuration for R as a library: include_dirs: ('/usr/lib64/R/include',) libraries: ('blas', 'R', 'Rlapack') library_dirs: ('/usr/lib64/R/lib',) extra_link_args: () # OSX-specific (included in extra_link_args) framework_dirs: () frameworks: () building 'rpy2.rinterface._rinterface' extension creating build-2.7/temp.linux-x86_64-2.7 creating build-2.7/temp.linux-x86_64-2.7/rpy creating build-2.7/temp.linux-x86_64-2.7/rpy/rinterface x86_64-pc-linux-gnu-gcc -pthread -O2 -Wall -pipe -fno-strict-aliasing -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -I./rpy/rinterface -I/usr/include/python2.7 -I/usr/lib64/R/include -c ./rpy/rinterface/_rinterface.c -o build-2.7/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o In file included from /usr/include/python2.7/Python.h:8:0, from ./rpy/rinterface/_rinterface.c:55: /usr/include/python2.7/pyconfig.h:1173:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default] In file included from /usr/include/signal.h:29:0, from ./rpy/rinterface/_rinterface.c:51: /usr/include/features.h:215:0: note: this is the location of the previous definition In file included from ./rpy/rinterface/_rinterface.c:110:0: ./rpy/rinterface/r_utils.h:14:10: warning: initialization makes pointer from integer without a cast [enabled by default] ./rpy/rinterface/r_utils.h:14:10: warning: (near initialization for ‘RPY_R_VERSION_LIST[3]’) [enabled by default] In file included from ./rpy/rinterface/_rinterface.c:130:0: ./rpy/rinterface/buffer.c: In function ‘VectorSexp_getreadbuf’: ./rpy/rinterface/buffer.c:189:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] In file included from ./rpy/rinterface/_rinterface.c:132:0: ./rpy/rinterface/sequence.c: In function ‘VectorSexp_ass_slice’: ./rpy/rinterface/sequence.c:542:15: warning: unused variable ‘sexp_item’ [-Wunused-variable] ./rpy/rinterface/sequence.c:542:10: warning: unused variable ‘tmp’ [-Wunused-variable] ./rpy/rinterface/sequence.c:541:17: warning: unused variable ‘vs’ [-Wunused-variable] ./rpy/rinterface/sequence.c:478:7: warning: unused variable ‘self_typeof’ [-Wunused-variable] ./rpy/rinterface/sequence.c: In function ‘IntVectorSexp_AsSexp’: ./rpy/rinterface/sequence.c:1290:7: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] ./rpy/rinterface/sequence.c: In function ‘FloatVectorSexp_AsSexp’: ./rpy/rinterface/sequence.c:1497:7: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] ./rpy/rinterface/sequence.c: In function ‘StrVectorSexp_AsSexp’: ./rpy/rinterface/sequence.c:1708:7: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] ./rpy/rinterface/sequence.c: In function ‘BoolVectorSexp_AsSexp’: ./rpy/rinterface/sequence.c:1872:7: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] ./rpy/rinterface/sequence.c: In function ‘ComplexVectorSexp_AsSexp’: ./rpy/rinterface/sequence.c:2174:7: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowMessage’: ./rpy/rinterface/_rinterface.c:397:21: warning: variable ‘old_int’ set but not used [-Wunused-but-set-variable] ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_FlushConsole’: ./rpy/rinterface/_rinterface.c:599:13: warning: variable ‘result’ set but not used [-Wunused-but-set-variable] ./rpy/rinterface/_rinterface.c: In function ‘newSEXP’: ./rpy/rinterface/_rinterface.c:2735:9: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] In file included from ./rpy/rinterface/_rinterface.c:132:0: ./rpy/rinterface/_rinterface.c: At top level: ./rpy/rinterface/sequence.c:2173:1: warning: ‘ComplexVectorSexp_AsSexp’ defined but not used [-Wunused-function] ./rpy/rinterface/_rinterface.c: In function ‘EmbeddedR_ShowFiles’: ./rpy/rinterface/_rinterface.c:856:3: warning: ‘gstate’ may be used uninitialized in this function [-Wmaybe-uninitialized] x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -L. -Wl,-O1 -Wl,--as-needed -O2 -Wall -pipe -fno-strict-aliasing build-2.7/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o -L/usr/lib64 -L/usr/lib64/R/lib -L/usr/lib64/R/modules -lR -lpython2.7 -lblas -lR -lRlapack -o build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so building 'rpy2.rinterface.rpy_device' extension x86_64-pc-linux-gnu-gcc -pthread -O2 -Wall -pipe -fno-strict-aliasing -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -Irpy/rinterface -I/usr/include/python2.7 -I/usr/lib64/R/include -c rpy/rinterface/rpy_device.c -o build-2.7/temp.linux-x86_64-2.7/rpy/rinterface/rpy_device.o rpy/rinterface/rpy_device.c: In function ‘initrpy_device’: rpy/rinterface/rpy_device.c:1220:17: warning: variable ‘d’ set but not used [-Wunused-but-set-variable] rpy/rinterface/rpy_device.c: At top level: rpy/rinterface/rpy_device.c:789:1: warning: ‘GrDev_clear’ defined but not used [-Wunused-function] x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -L. -Wl,-O1 -Wl,--as-needed -O2 -Wall -pipe -fno-strict-aliasing build-2.7/temp.linux-x86_64-2.7/rpy/rinterface/rpy_device.o -L/usr/lib64 -L/usr/lib64/R/lib -L/usr/lib64/R/modules -lR -lpython2.7 -lblas -lR -lRlapack -o build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/rpy_device.so >>> Source compiled. * Testing of dev-python/rpy-2.2.6 with CPython 2.7... Traceback (most recent call last): File "/usr/lib64/python2.7/runpy.py", line 162, in _run_module_as_main "__main__", fname, loader, pkg_name) File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6/build-2.7/lib.linux-x86_64-2.7/rpy2/tests.py", line 3, in import rpy2.robjects.tests File "/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6/build-2.7/lib.linux-x86_64-2.7/rpy2/robjects/__init__.py", line 14, in import rpy2.rinterface as rinterface File "/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6/build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/__init__.py", line 87, in from rpy2.rinterface._rinterface import * ImportError: /var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6/build-2.7/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so: undefined symbol: Rf_PrintWarnings * ERROR: dev-python/rpy-2.2.6::gentoo failed (test phase): * Testing failed with CPython 2.7 in testing() function * * Call stack: * ebuild.sh, line 93: Called src_test * environment, line 3711: Called python_execute_function 'testing' * environment, line 2085: Called die * The specific snippet of code: * die "${failure_message}"; * * If you need support, post the output of `emerge --info '=dev-python/rpy-2.2.6::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-python/rpy-2.2.6::gentoo'`. * The complete build log is located at '/var/tmp/portage/dev-python/rpy-2.2.6/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-python/rpy-2.2.6/temp/environment'. * Working directory: '/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6' * S: '/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6'