Hey there. I am building a Boot2Qt image for my Jetson Nano. Yocto release is dunfell. Currently I am trying to build the scipy library release 1.5.3. This is the recipe I am using:

inherit pypi setuptools3

SUMMARY = "SciPy: Scientific Library for Python"
HOMEPAGE = "https://www.scipy.org"
LICENSE = "BSD"
LIC_FILES_CHKSUM = "file://LICENSE.txt;md5=8256119827cf2bbe63512d4868075867"

SRC_URI += " file://0001-Allow-passing-flags-via-FARCH-for-mach.patch"
SRC_URI[md5sum] = "ecf5c58e4df1d257abf1634d51cb9205"
SRC_URI[sha256sum] = "ddae76784574cc4c172f3d5edd7308be16078dd3b977e8746860c76c195fa707"

DEPENDS += "${PYTHON_PN}-numpy ${PYTHON_PN}-numpy-native ${PYTHON_PN}-pybind11-native lapack"
RDEPENDS_${PN} += "${PYTHON_PN}-numpy lapack"

CLEANBROKEN = "1"

export LAPACK = "${STAGING_LIBDIR}"
export BLAS = "${STAGING_LIBDIR}"

export F90 = "${TARGET_PREFIX}gfortran"
export FARCH = "${TUNE_CCARGS}"
# Numpy expects the LDSHARED env variable to point to a single
# executable, but OE sets it to include some flags as well. So we split
# the existing LDSHARED variable into the base executable and flags, and
# prepend the flags into LDFLAGS
LDFLAGS_prepend := "${@" ".join(d.getVar('LDSHARED', True).split()[1:])} "
export LDSHARED := "${@d.getVar('LDSHARED', True).split()[0]}"

# Tell Numpy to look in target sysroot site-packages directory for libraries
LDFLAGS_append = " -L${STAGING_LIBDIR}/${PYTHON_DIR}/site-packages/numpy/core/lib"

-package <packagename> contains bad RPATH <rpath> in file <file> [rpaths]The specified binary produced by the recipe contains dynamic library load paths (rpaths) that contain build system paths such as TMPDIR, which are incorrect for the target and could potentially be a security issue. Check for bad -rpathoptions being passed to the linker in your do_compile log. Depending on the build system used by the software being built, there might be a configure option to disable rpath usage completely within the build of the software.

I looked in the run.do_configure file. This is what the BUILD_LDFLAGS variable is set like:

export BUILD_LDFLAGS="-L/media/dell/ext4_volume/jetson-nano-build-files/tmp/work/aarch64-poky-linux/python3-scipy/1.5.3-r0/recipe-sysroot-native/usr/lib                         -L/media/dell/ext4_volume/jetson-nano-build-files/tmp/work/aarch64-poky-linux/python3-scipy/1.5.3-r0/recipe-sysroot-native/lib                         -Wl,--enable-new-dtags                         -Wl,-rpath-link,/media/dell/ext4_volume/jetson-nano-build-files/tmp/work/aarch64-poky-linux/python3-scipy/1.5.3-r0/recipe-sysroot-native/usr/lib                         -Wl,-rpath-link,/media/dell/ext4_volume/jetson-nano-build-files/tmp/work/aarch64-poky-linux/python3-scipy/1.5.3-r0/recipe-sysroot-native/lib                         -Wl,-rpath,/media/dell/ext4_volume/jetson-nano-build-files/tmp/work/aarch64-poky-linux/python3-scipy/1.5.3-r0/recipe-sysroot-native/usr/lib                         -Wl,-rpath,/media/dell/ext4_volume/jetson-nano-build-files/tmp/work/aarch64-poky-linux/python3-scipy/1.5.3-r0/recipe-sysroot-native/lib                         -Wl,-O1 -Wl,--allow-shlib-undefined -Wl,--dynamic-linker=/media/dell/ext4_volume/jetson-nano-build-files/tmp/sysroots-uninative/x86_64-linux/lib/ld-linux-x86-64.so.2"

So I created a copy of bitbake.conf in my custom layer and set the priority of the layer above the poky/meta/ layer. With this the -rpath and -rpath-link options are removed from the BUILD_LDFLAGS variable. Now if I build the package, the build still fails with the same error.
Running grep on the tmp/work/aarch64-poky-linux/python3-scipy/1.5.3-r0/temp/ showed that -rpath option is still being passed to gcc. Complete log.do_compile here.

Right now I am kind of clueless as to how I should approach debugging this. Would really appreciate any help. Thanks.