python3-protobuf yocto receipe, getting compiler error - python

I have been trying to compile python3-protobuf package from Yocto dunfell release, but I am getting compiler error.
I am below recipe from Yocto without any change:
python3-protobuf_3.11.3.bb
inherit setuptools3
require python-protobuf.inc
BBCLASSEXTEND = "native nativesdk"
DEPENDS += "protobuf"
DISTUTILS_BUILD_ARGS += "--cpp_implementation"
DISTUTILS_INSTALL_ARGS += "--cpp_implementation"
do_compile_prepend_class-native () {
export KOKORO_BUILD_NUMBER="1"
}
I am getting below error
aarch64-oe-linux-gcc -march=armv8-a+crc -fstack-protector-strong -pie -fPIE -D_FORTIFY_SOURCE=2 -Wa,--noexecstack -Wformat -Wformat-security -Werror=format-security --sysroot=/home/admin/build/distro-debug/tmp-glibc/work/aarch64-oe-linux/python3-protobuf/3.11.3-r0/recipe-sysroot -Wno-unused-result -Wsign-compare -DNDEBUG -g -O3 -Wall -O2 -g -Wa,--noexecstack -fexpensive-optimizations -frename-registers -ftree-vectorize -finline-functions -finline-limit=64 -Wno-error=maybe-uninitialized -Wno-error=unused-result -O2 -g -Wa,--noexecstack -fexpensive-optimizations -frename-registers -ftree-vectorize -finline-functions -finline-limit=64 -Wno-error=maybe-uninitialized -Wno-error=unused-result -O2 -g -Wa,--noexecstack -fexpensive-optimizations -frename-registers -ftree-vectorize -finline-functions -finline-limit=64 -Wno-error=maybe-uninitialized -Wno-error=unused-result -fPIC -I. -I../src -I/home/admin/build/distro-debug/tmp-glibc/work/aarch64-oe-linux/python3-protobuf/3.11.3-r0/recipe-sysroot/usr/include/python3.8 -c google/protobuf/pyext/message.cc -o /home/admin/build/distro-debug/tmp-glibc/work/aarch64-oe-linux/python3-protobuf/3.11.3-r0/build/temp.linux-x86_64-3.8/google/protobuf/pyext/message.o -Wno-write-strings -Wno-invalid-offsetof -Wno-sign-compare -Wno-unused-variable -std=c++11
google/protobuf/pyext/message.cc:70:10: fatal error: google/protobuf/stubs/map_util.h: No such file or directory
70 | #include <google/protobuf/stubs/map_util.h>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command 'aarch64-oe-linux-gcc' failed with exit status 1
ERROR: 'python3 setup.py build --cpp_implementation' execution failed.
WARNING: /home/admin/build/distro-debug/tmp-glibc/work/aarch64-oe-linux/python3-protobuf/3.11.3-r0/temp/run.do_compile.15287:1 exit 1 from 'exit 1'
If I remove below from recipe
DISTUTILS_BUILD_ARGS += "--cpp_implementation"
DISTUTILS_INSTALL_ARGS += "--cpp_implementation"
from the recipe, then I do not get any error.
Thanks

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-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?
Any pointers would really help.

mlpack builds the Python bindings in multiple steps:
build a generate_pyx_<name> program to generate the Cython .pyx file that will be compiled
run the generate_pyx_<name> program and save the output .pyx file
use Cython and setuptools to generate a .cpp file from the .pyx file then compile it
It's a bit of a roundabout process, but I believe what is happening here is that the generate_pyx_<name> programs are being compiled for the device instead of the host, and therefore can't be run to generate the .pyx files. There won't be a particularly easy way to fix this, unfortunately, because CMake will be compiling the generate_pyx_<name> target with the same options you are compiling the rest of the library with (which in your case targets the device).
In order to make this work, you'll need to modify src/mlpack/bindings/python/CMakeLists.txt, specifically the line
add_executable(generate_pyx_${name}
${CMAKE_BINARY_DIR}/src/mlpack/bindings/python/generate_pyx_${name}.cpp
${CMAKE_SOURCE_DIR}/src/mlpack/bindings/python/print_pyx.hpp
${CMAKE_SOURCE_DIR}/src/mlpack/bindings/python/print_pyx.cpp)
and related lines. In essence you will need to make sure that the CXXFLAGS like -march=armv8-a -mtune=cortex-a57.cortex-a53 do not get used for that particular target.

Run "ldd aarch64-poky-linux-gcc" first, check if all the libraries it linked with were existed in your machine, if not the system will tell you "No such file or directory".

Makefile:107: recipe for target '_shtns.so' failed

I am having a problem while trying to compile the shtns library with python support. I do:
./configure --prefix=$HOME/local --enable-python
make
and I get:
(...)
building '_shtns' extension
gcc -march=native -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-lMBuS3/python2.7-2.7.12=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/david/.local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c shtns_numpy_wrap.c -o build/temp.linux-x86_64-2.7/shtns_numpy_wrap.o -fopenmp
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-lMBuS3/python2.7-2.7.12=. -fstack-protector-strong -Wformat -Werror=format-security -L/home/david/local/lib -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-lMBuS3/python2.7-2.7.12=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/shtns_numpy_wrap.o sht_init.o sht_fly.o sht_omp.o -L/home/david/local/lib -lfftw3_omp -lfftw3 -lm -o build/lib.linux-x86_64-2.7/_shtns.so -L/home/david/local/lib
/usr/bin/ld: /home/david/local/lib/libfftw3.a(assert.o): relocation R_X86_64_PC32 against symbol `stdout##GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
Makefile:107: recipe for target '_shtns.so' failed
make: *** [_shtns.so] Error 1
I think those are the relevant lines. It suggests to compile using the -fpic flag, but that is already in my CFLAGS environment variable, as you can see in the first gcc line. The problem is with the 'x86_64-linux-gnu-gcc' bit. Any suggestions?

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