Chi Hsuan Yen added the comment:

Hmm things are quite complicated. Brief: the build is broken for out-of-source 
cross-compiling if the host Python is an in-source build.

(Below $build_dir refers to the directory that invokes $source_dir/configure)

In an out-of-source build, setup.py relies on 
sysconfig.get_config_var('srcdir') to get correct filenames. In _init_posix(), 
_get_sysconfigdata_name() still returns an incorrect name (for example, 
_sysconfigdata_m_linux_x86_64-linux-gnu, on Linux x86_64). There's no 
_sysconfigdata_m_linux_x86_64-linux-gnu.py in 
$build_dir/build/lib.linux-aarch64-3.6, so $PYTHON_FOR_BUILD imports the one 
from the host python, which has srcdir == '.' As a result, build_ext can't find 
source files:

building 'xxlimited' extension
/home/yen/Projects/python3-android/clang-bin/cc -fPIC -Wno-unused-result 
-Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -g -fwrapv -O3 -Wall 
-Wstrict-prototypes -march=x86-64 -mtune=generic -O2 -pipe 
-fstack-protector-strong -g -fvar-tracking-assignments -g 
-fvar-tracking-assignments -march=x86-64 -mtune=generic -O2 -pipe 
-fstack-protector-strong -g -fvar-tracking-assignments -g 
-fvar-tracking-assignments -std=c99 -DPy_LIMITED_API=0x03050000 -I./Include -I. 
-IInclude -I/usr/include -I/usr/local/include 
-I/home/yen/Projects/python3-android/src/cpython/build-target/Include 
-I/home/yen/Projects/python3-android/src/cpython/build-target -c xxlimited.c -o 
build/temp.linux-aarch64-3.6/xxlimited.o
clang: error: unknown argument: '-fvar-tracking-assignments'
clang: error: unknown argument: '-fvar-tracking-assignments'
clang: error: unknown argument: '-fvar-tracking-assignments'
clang: error: unknown argument: '-fvar-tracking-assignments'
clang: error: no such file or directory: 'xxlimited.c'
clang: error: no input files

Ironically, before 1d71ce4531ac, $build_dir/build/lib.linux-aarch64-3.6 has 
_sysconfigdata_m_linux_x86_64-linux-gnu.py, so building is OK.

Again, I don't know to fix it :(

[1] https://hg.python.org/cpython/file/1d71ce4531ac/setup.py#l218

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