rpy-2.6.0:20150731-145031.log

rpy-2.6.0:20150731-145031.log (text/plain), 13.27 KB, created by Agostino Sarubbo on 2015-07-31 15:08:36 UTC

 * Package:    dev-python/rpy-2.6.0
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 python_targets_python3_4 userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
 * python3_4: running distutils-r1_run_phase python_compile
/usr/bin/python3.4 setup.py build
R version 3.0.1 (2013-05-16) -- "Good Sport"
/usr/lib64/R/bin/R CMD config --ldflags
/usr/lib64/R/bin/R CMD config --cppflags

    Compilation parameters for rpy2's C components:
        include_dirs    = ['/usr/lib64/R/include']
        library_dirs    = ['/usr/lib64/R/lib']
        libraries       = ['R']
        extra_link_args = []
    
running build
running build_py
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2
copying ./rpy/tests_rpy_classic.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2
copying ./rpy/tests.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2
copying ./rpy/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2
copying ./rpy/rpy_classic.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike
copying ./rpy/rlike/container.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike
copying ./rpy/rlike/indexing.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike
copying ./rpy/rlike/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike
copying ./rpy/rlike/functional.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_container.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_functional.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_indexing.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike/tests
copying ./rpy/rlike/tests/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rlike/tests
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface
copying ./rpy/rinterface/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpClosure.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_EmbeddedR.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVector.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Device.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpSymbol.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Sexp.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/rinterface/tests
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/help.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/numpy2ri.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/constants.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/environments.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/vectors.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/packages.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/packages_utils.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/functions.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/language.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/robject.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/methods.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/conversion.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
copying ./rpy/robjects/pandas2ri.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testLanguage.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRObject.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testHelp.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRobjects.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testEnvironment.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testMethods.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPandasConversions.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testDataFrame.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFunction.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFormula.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testArray.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testVector.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testNumpyConversions.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPackages.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/tests
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/lib
copying ./rpy/robjects/lib/grid.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/lib
copying ./rpy/robjects/lib/ggplot2.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/lib
copying ./rpy/robjects/lib/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/lib
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_ggplot2.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/robjects/lib/tests
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/interactive
copying ./rpy/interactive/packages.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/interactive
copying ./rpy/interactive/process_revents.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/interactive
copying ./rpy/interactive/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/interactive
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/interactive/tests
copying ./rpy/interactive/tests/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/interactive/tests
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/ipython
copying ./rpy/ipython/html.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/ipython
copying ./rpy/ipython/ggplot.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/ipython
copying ./rpy/ipython/rmagic.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/ipython
copying ./rpy/ipython/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/ipython
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/ipython/tests
copying ./rpy/ipython/tests/test_rmagic.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/ipython/tests
copying ./rpy/ipython/tests/__init__.py -> /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/lib/rpy2/ipython/tests
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
R version 3.0.1 (2013-05-16) -- "Good Sport"
building 'rpy2.rinterface._rinterface' extension
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/temp.linux-x86_64-3.4
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/temp.linux-x86_64-3.4/rpy
creating /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/temp.linux-x86_64-3.4/rpy/rinterface
x86_64-pc-linux-gnu-gcc -march=native -Wformat -Werror=format-security -g0 -O2 -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/usr/lib64/R/include -I/usr/include/python3.4 -c ./rpy/rinterface/_rinterface.c -o /var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0-python3_4/temp.linux-x86_64-3.4/./rpy/rinterface/_rinterface.o
In file included from ./rpy/rinterface/_rinterface.c:126:0:
./rpy/rinterface/r_utils.c:32:31: fatal error: R_ext/Rallocators.h: No such file or directory
 #include <R_ext/Rallocators.h>
                               ^
compilation terminated.
error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1
 * ERROR: dev-python/rpy-2.6.0::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line   93:  Called src_compile
 *   environment, line 3853:  Called distutils-r1_src_compile
 *   environment, line 1029:  Called _distutils-r1_run_foreach_impl 'python_compile'
 *   environment, line  328:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 3328:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2436:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2434:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
 *   environment, line  629:  Called distutils-r1_run_phase 'python_compile'
 *   environment, line 1022:  Called python_compile
 *   environment, line 2930:  Called distutils-r1_python_compile
 *   environment, line  902:  Called esetup.py 'build'
 *   environment, line 1510:  Called die
 * The specific snippet of code:
 *       "${@}" || die
 * 
 * If you need support, post the output of `emerge --info '=dev-python/rpy-2.6.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-python/rpy-2.6.0::gentoo'`.
 * The complete build log is located at '/var/log/log/build/dev-python/rpy-2.6.0:20150731-145031.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/dev-python/rpy-2.6.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-python/rpy-2.6.0/temp/environment'.
 * Working directory: '/var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0'
 * S: '/var/tmp/portage/dev-python/rpy-2.6.0/work/rpy2-2.6.0'