[yocto] aarch64-poky-linux-gcc error during compilation

vaishnavi tn send2meena at gmail.com
Fri Oct 13 08:07:09 PDT 2017 

Hello,

I am trying to include mlpack (with python bindings) to my yocto
build. I get the following error while building the python bindings:

===========================================
aarch64-poky-linux-gcc -march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb -DNDEBUG -g -O3 -Wall
-Wstrict-prototypes -O2 -pipe -g -feliminate-unused-debug-types -fPIC
-I/builds/build-h3/tmp/sysroots/x86_64-linux/usr/lib/python2.7/site-packages/numpy/core/include
-I/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/
-I/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/git/src
-I/builds/build-h3/tmp/sysroots/h3ulcb/usr/include
-I/builds/build-h3/tmp/sysroots/h3ulcb/usr/include
-I/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/..
-I/builds/build-h3/tmp/sysroots/h3ulcb/usr/include/python2.7 -c
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/sparse_coding.cpp
-o build/temp.linux-x86_64-2.7/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/sparse_coding.o
-DBINDING_TYPE=BINDING_TYPE_PYX -std=c++11 -march=armv8-a
-mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wall
-Wextra -ftemplate-depth=1000 -O3 -fopenmp
aarch64-poky-linux-gcc: error: : No such file or directory
aarch64-poky-linux-gcc: error: : No such file or directory
error: command 'aarch64-poky-linux-gcc' failed with exit status 1
src/mlpack/methods/sparse_coding/CMakeFiles/build_pyx_sparse_coding.dir/build.make:60:
recipe for target
'src/mlpack/methods/sparse_coding/CMakeFiles/build_pyx_sparse_coding'
failed
make[2]: *** [src/mlpack/methods/sparse_coding/CMakeFiles/build_pyx_sparse_coding]
Error 1
make[2]: Leaving directory
'/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build'
CMakeFiles/Makefile2:6651: recipe for target
'src/mlpack/methods/sparse_coding/CMakeFiles/build_pyx_sparse_coding.dir/all'
failed
make[1]: *** [src/mlpack/methods/sparse_coding/CMakeFiles/build_pyx_sparse_coding.dir/all]
Error 2
make[1]: *** Waiting for unfinished jobs....
/builds/build-h3/tmp/sysroots/x86_64-linux/usr/lib/python2.7/site-packages/setuptools-36.2.7-py2.7.egg/setuptools/dist.py:350:
UserWarning: The version specified ('3.0.x') is an invalid version,
this may not work as expected with newer versions of setuptools, pip,
and PyPI. Please see PEP 440 for more details.
running build_ext
cythoning /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/preprocess_split.pyx
to /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/preprocess_split.cpp
building 'mlpack.preprocess_split' extension
aarch64-poky-linux-gcc -march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb -DNDEBUG -g -O3 -Wall
-Wstrict-prototypes -O2 -pipe -g -feliminate-unused-debug-types -fPIC
-I/builds/build-h3/tmp/sysroots/x86_64-linux/usr/lib/python2.7/site-packages/numpy/core/include
-I/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/
-I/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/git/src
-I/builds/build-h3/tmp/sysroots/h3ulcb/usr/include
-I/builds/build-h3/tmp/sysroots/h3ulcb/usr/include
-I/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/..
-I/builds/build-h3/tmp/sysroots/h3ulcb/usr/include/python2.7 -c
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/preprocess_split.cpp
-o build/temp.linux-x86_64-2.7/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/preprocess_split.o
-DBINDING_TYPE=BINDING_TYPE_PYX -std=c++11 -march=armv8-a
-mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wall
-Wextra -ftemplate-depth=1000 -O3 -fopenmp
aarch64-poky-linux-gcc: error: : No such file or directory
aarch64-poky-linux-gcc: error: : No such file or directory
error: command 'aarch64-poky-linux-gcc' failed with exit status 1
src/mlpack/methods/preprocess/CMakeFiles/build_pyx_preprocess_split.dir/build.make:60:
recipe for target
'src/mlpack/methods/preprocess/CMakeFiles/build_pyx_preprocess_split'
failed
make[2]: *** [src/mlpack/methods/preprocess/CMakeFiles/build_pyx_preprocess_split]
Error 1
make[2]: Leaving directory
'/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build'
CMakeFiles/Makefile2:1387: recipe for target
'src/mlpack/methods/preprocess/CMakeFiles/build_pyx_preprocess_split.dir/all'
failed
make[1]: *** [src/mlpack/methods/preprocess/CMakeFiles/build_pyx_preprocess_split.dir/all]
Error 2
[ 89%] Linking CXX executable ../../../../bin/generate_pyx_softmax_regression
cd /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/methods/softmax_regression
&& /builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/cmake -E
cmake_link_script
CMakeFiles/generate_pyx_softmax_regression.dir/link.txt --verbose=1
/builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/aarch64-poky-linux/aarch64-poky-linux-g++
   -march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wall
-Wextra -ftemplate-depth=1000 -O3 -fopenmp -O2 -pipe -g
-feliminate-unused-debug-types  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -DNDEBUG
-march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wl,-O1
-Wl,--hash-style=gnu -Wl,--as-needed  -Wl,-O1 -Wl,--hash-style=gnu
-Wl,--as-needed
CMakeFiles/generate_pyx_softmax_regression.dir/__/__/bindings/python/generate_pyx_softmax_regression.cpp.o
CMakeFiles/generate_pyx_softmax_regression.dir/__/__/bindings/python/print_pyx.cpp.o
 -o ../../../../bin/generate_pyx_softmax_regression -rdynamic
../../../../lib/libmlpack.so.2.0 -lrt -larmadillo
-lboost_program_options-mt -lboost_unit_test_framework
-lboost_serialization-mt
cd /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/methods/softmax_regression
&& /builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/cmake
-DGENERATE_PYX_PROGRAM=/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_softmax_regression
-DPYX_OUTPUT_FILE=/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/softmax_regression.pyx
-P /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/git/CMake/GeneratePYX.cmake
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_softmax_regression:
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_softmax_regression:
cannot execute binary file
make[2]: Leaving directory
'/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build'
[ 89%] Built target generate_pyx_softmax_regression
[ 89%] Linking CXX executable ../../../../bin/generate_pyx_knn
cd /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/methods/neighbor_search
&& /builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/cmake -E
cmake_link_script CMakeFiles/generate_pyx_knn.dir/link.txt --verbose=1
/builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/aarch64-poky-linux/aarch64-poky-linux-g++
   -march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wall
-Wextra -ftemplate-depth=1000 -O3 -fopenmp -O2 -pipe -g
-feliminate-unused-debug-types  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -DNDEBUG
-march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wl,-O1
-Wl,--hash-style=gnu -Wl,--as-needed  -Wl,-O1 -Wl,--hash-style=gnu
-Wl,--as-needed
CMakeFiles/generate_pyx_knn.dir/__/__/bindings/python/generate_pyx_knn.cpp.o
CMakeFiles/generate_pyx_knn.dir/__/__/bindings/python/print_pyx.cpp.o
-o ../../../../bin/generate_pyx_knn -rdynamic
../../../../lib/libmlpack.so.2.0 -lrt -larmadillo
-lboost_program_options-mt -lboost_unit_test_framework
-lboost_serialization-mt
cd /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/methods/neighbor_search
&& /builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/cmake
-DGENERATE_PYX_PROGRAM=/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_knn
-DPYX_OUTPUT_FILE=/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/knn.pyx
-P /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/git/CMake/GeneratePYX.cmake
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_knn:
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_knn:
cannot execute binary file
make[2]: Leaving directory
'/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build'
[ 89%] Built target generate_pyx_knn
[ 89%] Linking CXX executable ../../../../bin/generate_pyx_kfn
cd /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/methods/neighbor_search
&& /builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/cmake -E
cmake_link_script CMakeFiles/generate_pyx_kfn.dir/link.txt --verbose=1
/builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/aarch64-poky-linux/aarch64-poky-linux-g++
   -march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wall
-Wextra -ftemplate-depth=1000 -O3 -fopenmp -O2 -pipe -g
-feliminate-unused-debug-types  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -DNDEBUG
-march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wl,-O1
-Wl,--hash-style=gnu -Wl,--as-needed  -Wl,-O1 -Wl,--hash-style=gnu
-Wl,--as-needed
CMakeFiles/generate_pyx_kfn.dir/__/__/bindings/python/generate_pyx_kfn.cpp.o
CMakeFiles/generate_pyx_kfn.dir/__/__/bindings/python/print_pyx.cpp.o
-o ../../../../bin/generate_pyx_kfn -rdynamic
../../../../lib/libmlpack.so.2.0 -lrt -larmadillo
-lboost_program_options-mt -lboost_unit_test_framework
-lboost_serialization-mt
cd /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/methods/neighbor_search
&& /builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/cmake
-DGENERATE_PYX_PROGRAM=/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_kfn
-DPYX_OUTPUT_FILE=/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/kfn.pyx
-P /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/git/CMake/GeneratePYX.cmake
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_kfn:
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_kfn:
cannot execute binary file
make[2]: Leaving directory
'/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build'
[ 89%] Built target generate_pyx_kfn
[ 89%] Linking CXX executable ../../../../bin/generate_pyx_krann
cd /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/methods/rann
&& /builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/cmake -E
cmake_link_script CMakeFiles/generate_pyx_krann.dir/link.txt
--verbose=1
/builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/aarch64-poky-linux/aarch64-poky-linux-g++
   -march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wall
-Wextra -ftemplate-depth=1000 -O3 -fopenmp -O2 -pipe -g
-feliminate-unused-debug-types  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -DNDEBUG
-march=armv8-a -mtune=cortex-a57.cortex-a53
--sysroot=/builds/build-h3/tmp/sysroots/h3ulcb  -O2 -pipe -g
-feliminate-unused-debug-types -fvisibility-inlines-hidden -Wl,-O1
-Wl,--hash-style=gnu -Wl,--as-needed  -Wl,-O1 -Wl,--hash-style=gnu
-Wl,--as-needed
CMakeFiles/generate_pyx_krann.dir/__/__/bindings/python/generate_pyx_krann.cpp.o
CMakeFiles/generate_pyx_krann.dir/__/__/bindings/python/print_pyx.cpp.o
 -o ../../../../bin/generate_pyx_krann -rdynamic
../../../../lib/libmlpack.so.2.0 -lrt -larmadillo
-lboost_program_options-mt -lboost_unit_test_framework
-lboost_serialization-mt
cd /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/methods/rann
&& /builds/build-h3/tmp/sysroots/x86_64-linux/usr/bin/cmake
-DGENERATE_PYX_PROGRAM=/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_krann
-DPYX_OUTPUT_FILE=/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/src/mlpack/bindings/python/mlpack/krann.pyx
-P /builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/git/CMake/GeneratePYX.cmake
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_krann:
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build/bin/generate_pyx_krann:
cannot execute binary file
make[2]: Leaving directory
'/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build'
[ 89%] Built target generate_pyx_krann
make[1]: Leaving directory
'/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/build'
Makefile:141: recipe for target 'all' failed
make: *** [all] Error 2
ERROR: oe_runmake failed
ERROR: Function failed: do_compile (log file is located at
/builds/build-h3/tmp/work/aarch64-poky-linux/mlpack/git-r0/temp/log.do_compile.17361)
===========================================

My recipe looks like this:

===========================================
DEPENDS = "boost armadillo python-native python-setuptools-native
python-pandas-native python-numpy-native python-cython-native
python-pytest-runner-native doxygen-native"

LIC_FILES_CHKSUM = "file://LICENSE.txt;md5=3cee6555b8c975c14d29687fe7e78038"

SRC_URI = "git://github.com/mlpack/mlpack.git;protocol=https \
"
SRCREV = "b8ee319818e6213da4b92cb69dab94b956795401"

S = "${WORKDIR}/git"

inherit cmake pythonnative

EXTRA_OECMAKE = "-DDEBUG:BOOL=OFF \
-DPROFILE:BOOL=OFF \
-DBUILD_TESTS:BOOL=OFF \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \
-DCMAKE_SKIP_RPATH:BOOL=YES \
-DPY_PANDAS:PATH=${STAGING_LIBDIR_NATIVE}/python2.7/site-packages/pandas \
"

do_compile_prepend() {
export STAGING_LIBDIR="${STAGING_LIBDIR}"
export STAGING_INCDIR="${STAGING_INCDIR}"
}
===========================================

Is there something else that needs to be included in my recipe?
Or is the build environment missing something?

I'm a novice. So any pointers would really help.

Thanks!

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