Upgrade from NDK 19b to 23b causes problems with Pandas library

[deeprotype]

Checklist

• the issue is indeed a bug and not a support request
• issue doesn't already exist: https://github.com/kivy/python-for-android/issues
• I have a short, runnable example that reproduces the issue
• I reproduced the problem with the latest development version (p4a.branch = develop)
• I used the grave accent (aka backticks) to format code or logs when appropriated

Versions

• Python: v3.7 & v3.8.10
• OS: Android 11
• Kivy: v1.9.1
• Cython: v0.29.19
• OpenJDK: -
• Pandas: v1.0.3 (newer version unfortunately does not work)

Description

Hello everyone,

since the upgrade from NDK 19b to 23b the library Pandas cannot be used anymore. My current applied commit is: 654448b (Branch: Master). -> same thing on the develop brunch

Although the build process is done with buildozer without any problems, the app crashes after loading the library. Does anyone know why this is happening and how I can fix the problem?

Thanks a lot for your help!

Best regards,
Manuel

buildozer.spec

Command:

buildozer -v android debug

Used Code:

from kivy.app import App
from kivy.uix.button import Button
import pandas as pd

class TestApp(App):
    def build(self):
        return Button(text='Hello World')

TestApp().run()

Spec file:

[app]

# (str) Title of your application
title = My Application

# (str) Package name
package.name = myapp

# (str) Package domain (needed for android/ios packaging)
package.domain = org.test

# (str) Source code where the main.py live
source.dir = .

# (list) Source files to include (let empty to include all the files)
source.include_exts = py,png,jpg,kv,atlas

# (list) List of inclusions using pattern matching
#source.include_patterns = assets/*,images/*.png

# (list) Source files to exclude (let empty to not exclude anything)
#source.exclude_exts = spec

# (list) List of directory to exclude (let empty to not exclude anything)
#source.exclude_dirs = tests, bin, venv

# (list) List of exclusions using pattern matching
# Do not prefix with './'
#source.exclude_patterns = license,images/*/*.jpg

# (str) Application versioning (method 1)
version = 0.1

# (str) Application versioning (method 2)
# version.regex = __version__ = ['"](.*)['"]
# version.filename = %(source.dir)s/main.py

# (list) Application requirements
# comma separated e.g. requirements = sqlite3,kivy
requirements = python3,kivy, pandas

# (str) Custom source folders for requirements
# Sets custom source for any requirements with recipes
# requirements.source.kivy = ../../kivy

# (str) Presplash of the application
#presplash.filename = %(source.dir)s/data/presplash.png

# (str) Icon of the application
#icon.filename = %(source.dir)s/data/icon.png

# (str) Supported orientation (one of landscape, sensorLandscape, portrait or all)
orientation = portrait

# (list) List of service to declare
#services = NAME:ENTRYPOINT_TO_PY,NAME2:ENTRYPOINT2_TO_PY

#
# OSX Specific
#

#
# author = © Copyright Info

# change the major version of python used by the app
osx.python_version = 3

# Kivy version to use
osx.kivy_version = 1.9.1

#
# Android specific
#

# (bool) Indicate if the application should be fullscreen or not
fullscreen = 0

# (string) Presplash background color (for android toolchain)
# Supported formats are: #RRGGBB #AARRGGBB or one of the following names:
# red, blue, green, black, white, gray, cyan, magenta, yellow, lightgray,
# darkgray, grey, lightgrey, darkgrey, aqua, fuchsia, lime, maroon, navy,
# olive, purple, silver, teal.
#android.presplash_color = #FFFFFF

# (string) Presplash animation using Lottie format.
# see https://lottiefiles.com/ for examples and https://airbnb.design/lottie/
# for general documentation.
# Lottie files can be created using various tools, like Adobe After Effect or Synfig.
#android.presplash_lottie = "path/to/lottie/file.json"

# (str) Adaptive icon of the application (used if Android API level is 26+ at runtime)
#icon.adaptive_foreground.filename = %(source.dir)s/data/icon_fg.png
#icon.adaptive_background.filename = %(source.dir)s/data/icon_bg.png

# (list) Permissions
#android.permissions = INTERNET

# (list) features (adds uses-feature -tags to manifest)
#android.features = android.hardware.usb.host

# (int) Target Android API, should be as high as possible.
#android.api = 27

# (int) Minimum API your APK / AAB will support.
#android.minapi = 21

# (int) Android SDK version to use
#android.sdk = 20

# (str) Android NDK version to use
#android.ndk = 23b

# (int) Android NDK API to use. This is the minimum API your app will support, it should usually match android.minapi.
#android.ndk_api = 21

# (bool) Use --private data storage (True) or --dir public storage (False)
#android.private_storage = True

# (str) Android NDK directory (if empty, it will be automatically downloaded.)
#android.ndk_path =

# (str) Android SDK directory (if empty, it will be automatically downloaded.)
#android.sdk_path =

# (str) ANT directory (if empty, it will be automatically downloaded.)
#android.ant_path =

# (bool) If True, then skip trying to update the Android sdk
# This can be useful to avoid excess Internet downloads or save time
# when an update is due and you just want to test/build your package
# android.skip_update = False

# (bool) If True, then automatically accept SDK license
# agreements. This is intended for automation only. If set to False,
# the default, you will be shown the license when first running
# buildozer.
# android.accept_sdk_license = False

# (str) Android entry point, default is ok for Kivy-based app
#android.entrypoint = org.kivy.android.PythonActivity

# (str) Full name including package path of the Java class that implements Android Activity
# use that parameter together with android.entrypoint to set custom Java class instead of PythonActivity
#android.activity_class_name = org.kivy.android.PythonActivity

# (str) Extra xml to write directly inside the <manifest> element of AndroidManifest.xml
# use that parameter to provide a filename from where to load your custom XML code
#android.extra_manifest_xml = ./src/android/extra_manifest.xml

# (str) Extra xml to write directly inside the <manifest><application> tag of AndroidManifest.xml
# use that parameter to provide a filename from where to load your custom XML arguments:
#android.extra_manifest_application_arguments = ./src/android/extra_manifest_application_arguments.xml

# (str) Full name including package path of the Java class that implements Python Service
# use that parameter to set custom Java class instead of PythonService
#android.service_class_name = org.kivy.android.PythonService

# (str) Android app theme, default is ok for Kivy-based app
# android.apptheme = "@android:style/Theme.NoTitleBar"

# (list) Pattern to whitelist for the whole project
#android.whitelist =

# (str) Path to a custom whitelist file
#android.whitelist_src =

# (str) Path to a custom blacklist file
#android.blacklist_src =

# (list) List of Java .jar files to add to the libs so that pyjnius can access
# their classes. Don't add jars that you do not need, since extra jars can slow
# down the build process. Allows wildcards matching, for example:
# OUYA-ODK/libs/*.jar
#android.add_jars = foo.jar,bar.jar,path/to/more/*.jar

# (list) List of Java files to add to the android project (can be java or a
# directory containing the files)
#android.add_src =

# (list) Android AAR archives to add
#android.add_aars =

# (list) Put these files or directories in the apk assets directory.
# Either form may be used, and assets need not be in 'source.include_exts'.
# 1) android.add_assets = source_asset_relative_path
# 2) android.add_assets = source_asset_path:destination_asset_relative_path
#android.add_assets =

# (list) Gradle dependencies to add
#android.gradle_dependencies =

# (bool) Enable AndroidX support. Enable when 'android.gradle_dependencies'
# contains an 'androidx' package, or any package from Kotlin source.
# android.enable_androidx requires android.api >= 28
#android.enable_androidx = False

# (list) add java compile options
# this can for example be necessary when importing certain java libraries using the 'android.gradle_dependencies' option
# see https://developer.android.com/studio/write/java8-support for further information
# android.add_compile_options = "sourceCompatibility = 1.8", "targetCompatibility = 1.8"

# (list) Gradle repositories to add {can be necessary for some android.gradle_dependencies}
# please enclose in double quotes 
# e.g. android.gradle_repositories = "maven { url 'https://kotlin.bintray.com/ktor' }"
#android.add_gradle_repositories =

# (list) packaging options to add 
# see https://google.github.io/android-gradle-dsl/current/com.android.build.gradle.internal.dsl.PackagingOptions.html
# can be necessary to solve conflicts in gradle_dependencies
# please enclose in double quotes 
# e.g. android.add_packaging_options = "exclude 'META-INF/common.kotlin_module'", "exclude 'META-INF/*.kotlin_module'"
#android.add_packaging_options =

# (list) Java classes to add as activities to the manifest.
#android.add_activities = com.example.ExampleActivity

# (str) OUYA Console category. Should be one of GAME or APP
# If you leave this blank, OUYA support will not be enabled
#android.ouya.category = GAME

# (str) Filename of OUYA Console icon. It must be a 732x412 png image.
#android.ouya.icon.filename = %(source.dir)s/data/ouya_icon.png

# (str) XML file to include as an intent filters in <activity> tag
#android.manifest.intent_filters =

# (str) launchMode to set for the main activity
#android.manifest.launch_mode = standard

# (list) Android additional libraries to copy into libs/armeabi
#android.add_libs_armeabi = libs/android/*.so
#android.add_libs_armeabi_v7a = libs/android-v7/*.so
#android.add_libs_arm64_v8a = libs/android-v8/*.so
#android.add_libs_x86 = libs/android-x86/*.so
#android.add_libs_mips = libs/android-mips/*.so

# (bool) Indicate whether the screen should stay on
# Don't forget to add the WAKE_LOCK permission if you set this to True
#android.wakelock = False

# (list) Android application meta-data to set (key=value format)
#android.meta_data =

# (list) Android library project to add (will be added in the
# project.properties automatically.)
#android.library_references =

# (list) Android shared libraries which will be added to AndroidManifest.xml using <uses-library> tag
#android.uses_library =

# (str) Android logcat filters to use
#android.logcat_filters = *:S python:D

# (bool) Android logcat only display log for activity's pid
#android.logcat_pid_only = False

# (str) Android additional adb arguments
#android.adb_args = -H host.docker.internal

# (bool) Copy library instead of making a libpymodules.so
#android.copy_libs = 1

# (list) The Android archs to build for, choices: armeabi-v7a, arm64-v8a, x86, x86_64
# In past, was `android.arch` as we weren't supporting builds for multiple archs at the same time.
android.archs = arm64-v8a, armeabi-v7a

# (int) overrides automatic versionCode computation (used in build.gradle)
# this is not the same as app version and should only be edited if you know what you're doing
# android.numeric_version = 1

# (bool) enables Android auto backup feature (Android API >=23)
android.allow_backup = True

# (str) XML file for custom backup rules (see official auto backup documentation)
# android.backup_rules =

# (str) If you need to insert variables into your AndroidManifest.xml file,
# you can do so with the manifestPlaceholders property.
# This property takes a map of key-value pairs. (via a string)
# Usage example : android.manifest_placeholders = [myCustomUrl:\"org.kivy.customurl\"]
# android.manifest_placeholders = [:]

# (bool) disables the compilation of py to pyc/pyo files when packaging
# android.no-compile-pyo = True

# (str) The format used to package the app for release mode (aab or apk or aar).
# android.release_artifact = aab

# (str) The format used to package the app for debug mode (apk or aar).
# android.debug_artifact = apk

#
# Python for android (p4a) specific
#

# (str) python-for-android URL to use for checkout
#p4a.url =

# (str) python-for-android fork to use in case if p4a.url is not specified, defaults to upstream (kivy)
#p4a.fork = kivy

# (str) python-for-android branch to use, defaults to master
#p4a.branch = master

# (str) python-for-android specific commit to use, defaults to HEAD, must be within p4a.branch
#p4a.commit = HEAD

# (str) python-for-android git clone directory (if empty, it will be automatically cloned from github)
#p4a.source_dir =

# (str) The directory in which python-for-android should look for your own build recipes (if any)
#p4a.local_recipes =

# (str) Filename to the hook for p4a
#p4a.hook =

# (str) Bootstrap to use for android builds
# p4a.bootstrap = sdl2

# (int) port number to specify an explicit --port= p4a argument (eg for bootstrap flask)
#p4a.port =

# Control passing the --use-setup-py vs --ignore-setup-py to p4a
# "in the future" --use-setup-py is going to be the default behaviour in p4a, right now it is not
# Setting this to false will pass --ignore-setup-py, true will pass --use-setup-py
# NOTE: this is general setuptools integration, having pyproject.toml is enough, no need to generate
# setup.py if you're using Poetry, but you need to add "toml" to source.include_exts.
#p4a.setup_py = false

# (str) extra command line arguments to pass when invoking pythonforandroid.toolchain
#p4a.extra_args =


#
# iOS specific
#

# (str) Path to a custom kivy-ios folder
#ios.kivy_ios_dir = ../kivy-ios
# Alternately, specify the URL and branch of a git checkout:
ios.kivy_ios_url = https://github.com/kivy/kivy-ios
ios.kivy_ios_branch = master

# Another platform dependency: ios-deploy
# Uncomment to use a custom checkout
#ios.ios_deploy_dir = ../ios_deploy
# Or specify URL and branch
ios.ios_deploy_url = https://github.com/phonegap/ios-deploy
ios.ios_deploy_branch = 1.10.0

# (bool) Whether or not to sign the code
ios.codesign.allowed = false

# (str) Name of the certificate to use for signing the debug version
# Get a list of available identities: buildozer ios list_identities
#ios.codesign.debug = "iPhone Developer: <lastname> <firstname> (<hexstring>)"

# (str) The development team to use for signing the debug version
#ios.codesign.development_team.debug = <hexstring>

# (str) Name of the certificate to use for signing the release version
#ios.codesign.release = %(ios.codesign.debug)s

# (str) The development team to use for signing the release version
#ios.codesign.development_team.release = <hexstring>

# (str) URL pointing to .ipa file to be installed
# This option should be defined along with `display_image_url` and `full_size_image_url` options.
#ios.manifest.app_url =

# (str) URL pointing to an icon (57x57px) to be displayed during download
# This option should be defined along with `app_url` and `full_size_image_url` options.
#ios.manifest.display_image_url =

# (str) URL pointing to a large icon (512x512px) to be used by iTunes
# This option should be defined along with `app_url` and `display_image_url` options.
#ios.manifest.full_size_image_url =


[buildozer]

# (int) Log level (0 = error only, 1 = info, 2 = debug (with command output))
log_level = 2

# (int) Display warning if buildozer is run as root (0 = False, 1 = True)
warn_on_root = 1

# (str) Path to build artifact storage, absolute or relative to spec file
# build_dir = ./.buildozer

# (str) Path to build output (i.e. .apk, .aab, .ipa) storage
# bin_dir = ./bin

#    -----------------------------------------------------------------------------
#    List as sections
#
#    You can define all the "list" as [section:key].
#    Each line will be considered as a option to the list.
#    Let's take [app] / source.exclude_patterns.
#    Instead of doing:
#
#[app]
#source.exclude_patterns = license,data/audio/*.wav,data/images/original/*
#
#    This can be translated into:
#
#[app:source.exclude_patterns]
#license
#data/audio/*.wav
#data/images/original/*
#


#    -----------------------------------------------------------------------------
#    Profiles
#
#    You can extend section / key with a profile
#    For example, you want to deploy a demo version of your application without
#    HD content. You could first change the title to add "(demo)" in the name
#    and extend the excluded directories to remove the HD content.
#
#[app@demo]
#title = My Application (demo)
#
#[app:source.exclude_patterns@demo]
#images/hd/*
#
#    Then, invoke the command line with the "demo" profile:
#
#buildozer --profile demo android debug

Logs

08-09 16:52:35.660 30409 14008 I python  : Android kivy bootstrap done. __name__ is __main__
08-09 16:52:35.660 30409 14008 I python  : AND: Ran string
08-09 16:52:35.660 30409 14008 I python  : Run user program, change dir and execute entrypoint
08-09 16:52:35.741 30409 14008 I python  : [INFO   ] [Logger      ] Record log in /data/user/0/org.test.myapp/files/app/.kivy/logs/kivy_22-08-09_1.txt
08-09 16:52:35.741 30409 14008 I python  : [INFO   ] [Kivy        ] v2.1.0
08-09 16:52:35.741 30409 14008 I python  : [INFO   ] [Kivy        ] Installed at "/data/user/0/org.test.myapp/files/app/_python_bundle/site-packages/kivy/__init__.pyc"
08-09 16:52:35.741 30409 14008 I python  : [INFO   ] [Python      ] v3.9.9 (main, Aug  9 2022, 15:52:42)
08-09 16:52:35.741 30409 14008 I python  : [Clang 12.0.8 (https://android.googlesource.com/toolchain/llvm-project c935d99d
08-09 16:52:35.741 30409 14008 I python  : [INFO   ] [Python      ] Interpreter at ""
08-09 16:52:35.741 30409 14008 I python  : [INFO   ] [Logger      ] Purge log fired. Processing...
08-09 16:52:35.742 30409 14008 I python  : [INFO   ] [Logger      ] Purge finished!
08-09 16:52:36.212 30409 14008 I python  : [INFO   ] [Factory     ] 189 symbols loaded
08-09 16:52:36.340 30409 14008 I python  : [INFO   ] [Image       ] Providers: img_tex, img_dds, img_sdl2 (img_pil, img_ffpyplayer ignored)
08-09 16:52:36.355 30409 14008 I python  : [INFO   ] [Text        ] Provider: sdl2
08-09 16:52:36.450 30409 14008 I python  :  Traceback (most recent call last):
08-09 16:52:36.450 30409 14008 I python  :    File "/home/deeprotype/project/.buildozer/android/platform/build-arm64-v8a_armeabi-v7a/build/python-installs/myapp/arm64-v8a/pandas/__init__.py", line 32, in <module>
08-09 16:52:36.451 30409 14008 I python  :    File "/home/deeprotype/project/.buildozer/android/platform/build-arm64-v8a_armeabi-v7a/build/python-installs/myapp/arm64-v8a/pandas/_libs/__init__.py", line 3, in <module>
08-09 16:52:36.451 30409 14008 I python  :    File "/home/deeprotype/project/.buildozer/android/platform/build-arm64-v8a_armeabi-v7a/build/python-installs/myapp/arm64-v8a/pandas/_libs/tslibs/__init__.py", line 3, in <module>
08-09 16:52:36.451 30409 14008 I python  :  ImportError: dlopen failed: TLS symbol "_ZZN8gwp_asan15getThreadLocalsEvE6Locals" in dlopened "/data/user/0/org.test.myapp/files/app/_python_bundle/site-packages/pandas/_libs/tslibs/conversion.so" referenced from "/data/user/0/org.test.myapp/files/app/_python_bundle/site-packages/pandas/_libs/tslibs/conversion.so" using IE access model
08-09 16:52:36.451 30409 14008 I python  :
08-09 16:52:36.451 30409 14008 I python  :  During handling of the above exception, another exception occurred:
08-09 16:52:36.451 30409 14008 I python  :
08-09 16:52:36.451 30409 14008 I python  :  Traceback (most recent call last):
08-09 16:52:36.451 30409 14008 I python  :    File "/home/deeprotype/project/.buildozer/android/app/main.py", line 3, in <module>
08-09 16:52:36.451 30409 14008 I python  :    File "/home/deeprotype/project/.buildozer/android/platform/build-arm64-v8a_armeabi-v7a/build/python-installs/myapp/arm64-v8a/pandas/__init__.py", line 36, in <module>
08-09 16:52:36.451 30409 14008 I python  :  ImportError: C extension: dlopen failed: TLS symbol "_ZZN8gwp_asan15getThreadLocalsEvE6Locals" in dlopened "/data/user/0/org.test.myapp/files/app/_python_bundle/site-packages/pandas/_libs/tslibs/conversion.so" referenced from "/data/user/0/org.test.myapp/files/app/_python_bundle/site-packages/pandas/_libs/tslibs/conversion.so" using IE access model not built. If you want to import pandas from the source directory, you may need to run 'python setup.py build_ext --inplace --force' to build the C extensions first.
08-09 16:52:36.451 30409 14008 I python  : Python for android ended.

[mzakharo]

Confirming the issue with the latest pandas recipe.

For me, commenting out this line: env['LDFLAGS'] += ' -L{}'.format(arch.ndk_lib_dir) from recipe.py fixes the problem.

This functionality is used for any need_stl_shared recipe, and not sure exactly what the impact would be removing it on other recipes. Someone with more knowledge may please weigh in? Is this line a relic of a previous NDK and no longer needed? Somehow compilation and runtime works without the above mentioned line.

[misl6]

Hi @mzakharo, happy to see you back!

I guess that #2645 also fixes the issue on pandas, as looks like to be pretty the same.

Into the PR, I've added an extract from the "Build System Maintainers Guide (Android)" which explains why we need to avoid to manually link libc++ and its dependencies.

And @deeprotype, you you also try to use PR #2645 as explained here: #2643 (comment) ?

Having another confirmation may help the testing process, and speed up the merge (real-world use cases are way better than minimum reproducible examples).

[deeprotype]

Hi @mzakharo and @misl6,

thank you very much for your quick reply. The suggestions look promising! :) I'll test the approaches and get back to you with the results.

[deeprotype]

Thanks guys! The solution of @misl6 works for me.

I will now close the issue! :)

[misl6]

@deeprotype , please consider that just after the PR is merged (it may happen today), I will remove the related branch, and you will need to target the develop branch from kivy fork.

[aki-k]

Changing p4a.branch from master to develop helped me get a simple Pandas apk working.
I was getting the same error "ImportError: dlopen failed: TLS symbol "_ZZN8gwp_asan15getThreadLocalsEvE6Locals""