build.log of dev-python/rpy-2.2.6

build.log (text/plain), 13.81 KB, created by Linlin Yan on 2013-10-24 14:50:18 UTC

[32;01m * [39;49;00mPackage:    dev-python/rpy-2.2.6
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 elibc_glibc kernel_linux multilib test userland_GNU
[32;01m * [39;49;00mFEATURES:   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 <module>
    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 <module>
    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 <module>
    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
 [31;01m*[0m ERROR: dev-python/rpy-2.2.6::gentoo failed (test phase):
 [31;01m*[0m   Testing failed with CPython 2.7 in testing() function
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line   93:  Called src_test
 [31;01m*[0m   environment, line 3711:  Called python_execute_function 'testing'
 [31;01m*[0m   environment, line 2085:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m                       die "${failure_message}";
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=dev-python/rpy-2.2.6::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=dev-python/rpy-2.2.6::gentoo'`.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/dev-python/rpy-2.2.6/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/dev-python/rpy-2.2.6/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6'
 [31;01m*[0m S: '/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6'