matplotlib fails because of incomplatible qt versions

Deep Red

Hello,

After a recent qt update I have qt-related problem with different applications:
Cannot mix incompatible Qt library (5.15.7) with this library (5.15.8)

Among others there is matplotlib. Steps to reproduce:

Run gdb with python in type in prompt:

import matplotlib.pyplot as plt
subplots = plt.subplots()
[New Thread 0x7fffeeb7b6c0 (LWP 3332791)]
[New Thread 0x7fffecf586c0 (LWP 3332792)]
[New Thread 0x7fffe7fff6c0 (LWP 3332793)]
[New Thread 0x7fffe77fe6c0 (LWP 3332794)]
[New Thread 0x7fffe6ffd6c0 (LWP 3332795)]
Cannot mix incompatible Qt library (5.15.7) with this library (5.15.8)

Thread 6 "QDBusConnection" received signal SIGABRT, Aborted.

backtrace:
(gdb) bt
#0 0x00007ffff78b400c in () at /usr/lib64/libc.so.6
#1 0x00007ffff7866572 in raise () at /usr/lib64/libc.so.6
#2 0x00007ffff78504b2 in abort () at /usr/lib64/libc.so.6
#3 0x00007ffff2e91d6d in qt_message_output(QtMsgType, QMessageLogContext const&, QString const&) [clone .cold] () at /usr/lib64/libQt5Core.so.5
#4 0x00007ffff2ea838f in () at /usr/lib64/libQt5Core.so.5
#5 0x00007fffeec61773 in QDBusAbstractInterfacePrivate::QDBusAbstractInterfacePrivate(QString const&, QString const&, QString const&, QDBusConnection const&, bool) () at /usr/lib64/libQt5DBus.so.5
#6 0x00007fffeec62989 in QDBusAbstractInterface::QDBusAbstractInterface(QString const&, QString const&, char const*, QDBusConnection const&, QObject*) () at /usr/lib64/libQt5DBus.so.5
#7 0x00007fffeec49769 in QDBusConnectionInterface::QDBusConnectionInterface(QDBusConnection const&, QObject*) () at /usr/lib64/libQt5DBus.so.5
#8 0x00007fffeec4690a in QDBusConnectionPrivate::createBusService() () at /usr/lib64/libQt5DBus.so.5
#9 0x00007fffeec47ce1 in QDBusConnectionManager::executeConnectionRequest(QDBusConnectionManager::ConnectionRequestData*) ()
at /usr/lib64/libQt5DBus.so.5
#10 0x00007ffff30a4b14 in QObject::event(QEvent*) () at /usr/lib64/libQt5Core.so.5
#11 0x00007ffff307a2f5 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () at /usr/lib64/libQt5Core.so.5
#12 0x00007ffff307d6c3 in QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) () at /usr/lib64/libQt5Core.so.5
#13 0x00007ffff30ca8f3 in postEventSourceDispatch(_GSource*, int ()(void), void*) () at /usr/lib64/libQt5Core.so.5
#14 0x00007ffff46fb208 in g_main_context_dispatch () at /usr/lib64/libglib-2.0.so.0
#15 0x00007ffff46fb738 in g_main_context_iterate.constprop () at /usr/lib64/libglib-2.0.so.0
#16 0x00007ffff46fb7cc in g_main_context_iteration () at /usr/lib64/libglib-2.0.so.0
#17 0x00007ffff30ca3f6 in QEventDispatcherGlib::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () at /usr/lib64/libQt5Core.so.5
#18 0x00007ffff3078ddb in QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) () at /usr/lib64/libQt5Core.so.5
#19 0x00007ffff2eca022 in QThread::exec() () at /usr/lib64/libQt5Core.so.5
#20 0x00007fffeec454c7 in QDBusConnectionManager::run() () at /usr/lib64/libQt5DBus.so.5
#21 0x00007ffff2ecb267 in QThreadPrivate::start(void*) () at /usr/lib64/libQt5Core.so.5
#22 0x00007ffff78b232a in () at /usr/lib64/libc.so.6
#23 0x00007ffff7931d0c in () at /usr/lib64/libc.so.6

I use Gentoo Linux, current kernel version 6.1.13.

SGaist · I use Gentoo Linux, current kernel version 6.1.13.

Hi and welcome do devnet,

How did you install matplotlib ?

Deep Red

@SGaist Hello, in this case I first tried matplotlib installed with pip and later with the package manager (emerge). But this is not the only program refusing to work, I have a similar issue with telegram-desktop

SGaist

Did you use emerge to install all the packages ?

Did you also consider using a virtual environment ?

Deep Red

@SGaist Qt-related packages are installed with emerge as most of other programs. Python modules are kept within pip environment.

SGaist

@Deep-Red do you have PyQt or PySide installed in these environnement ?

Deep Red

@SGaist Pyqt only

SGaist

How did you build your pip environments ?

Usually PyQt and PySide should come with their own set of Qt libraries so updating your system should not influence that.

Deep Red

Now I activated pip with venv module and matplotlib is running inside the environment. But the telegram=desktop problem remains.

In Gentoo repository there are two packages:
dev-python/pyside2 (Python bindings for the Qt framework)
dev-python/pyside2-tools PySide development tools (pyside2-lupdate with support for Python)

But they were never present on my system as I can see from the package installation/removal history

SGaist

That's the goal of the python virtual environments, you isolate from the system for all the python dependencies.

As for Telegram, did you try to re-install it ?
Even if it's Gentoo, is it built from sources or a binary install ? If the latter, does it come with its own set of Qt libraries ?

Deep Red

@SGaist Neither telegram nor other programs work outside the virtual environment. Below I paste backtrace for stellarium (astronomy program).

gdb stellarium
GNU gdb (Gentoo 13.1 vanilla) 13.1
Copyright (C) 2023 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
https://bugs.gentoo.org/.
Find the GDB manual and other documentation resources online at:
http://www.gnu.org/software/gdb/documentation/.

For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from stellarium...
Reading symbols from /usr/lib/debug//usr/bin/stellarium.debug...
(No debugging symbols found in /usr/lib/debug//usr/bin/stellarium.debug)
(gdb) run
Starting program: /usr/bin/stellarium
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/usr/lib64/libthread_db.so.1".
[New Thread 0x7ffff28916c0 (LWP 1102513)]
[New Thread 0x7ffff13586c0 (LWP 1102534)]
[New Thread 0x7ffff0b576c0 (LWP 1102535)]
Cannot mix incompatible Qt library (5.15.7) with this library (5.15.8)

Thread 4 "QDBusConnection" received signal SIGABRT, Aborted.
[Switching to Thread 0x7ffff0b576c0 (LWP 1102535)]
0x00007ffff60b400c in ?? () from /usr/lib64/libc.so.6
(gdb) bt
#0 0x00007ffff60b400c in ?? () from /usr/lib64/libc.so.6
#1 0x00007ffff6066572 in raise () from /usr/lib64/libc.so.6
#2 0x00007ffff60504b2 in abort () from /usr/lib64/libc.so.6
#3 0x00007ffff6291d6d in QMessageLogger::fatal(char const*, ...) const () from /usr/lib64/libQt5Core.so.5
#4 0x00007ffff62a838f in QObjectPrivate::QObjectPrivate(int) [clone .cold] () from /usr/lib64/libQt5Core.so.5
#5 0x00007ffff29a2773 in QDBusAbstractInterfacePrivate::QDBusAbstractInterfacePrivate(QString const&, QString const&, QString const&, QDBusConnection const&, bool) () from /usr/lib64/libQt5DBus.so.5
#6 0x00007ffff29a3989 in QDBusAbstractInterface::QDBusAbstractInterface(QString const&, QString const&, char const*, QDBusConnection const&, QObject*) () from /usr/lib64/libQt5DBus.so.5
#7 0x00007ffff298a769 in QDBusConnectionInterface::QDBusConnectionInterface(QDBusConnection const&, QObject*) () from /usr/lib64/libQt5DBus.so.5
#8 0x00007ffff298790a in QDBusConnectionPrivate::createBusService() () from /usr/lib64/libQt5DBus.so.5
#9 0x00007ffff2988ce1 in QDBusConnectionManager::executeConnectionRequest(QDBusConnectionManager::ConnectionRequestData*) ()
from /usr/lib64/libQt5DBus.so.5
#10 0x00007ffff64a4b14 in QObject::event(QEvent*) () from /usr/lib64/libQt5Core.so.5
#11 0x00007ffff647a2f5 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () from /usr/lib64/libQt5Core.so.5
#12 0x00007ffff647d6c3 in QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) () from /usr/lib64/libQt5Core.so.5
#13 0x00007ffff64ca8f3 in postEventSourceDispatch(_GSource*, int ()(void), void*) () from /usr/lib64/libQt5Core.so.5
#14 0x00007ffff58221e8 in g_main_context_dispatch () from /usr/lib64/libglib-2.0.so.0
#15 0x00007ffff5822718 in g_main_context_iterate.constprop () from /usr/lib64/libglib-2.0.so.0
#16 0x00007ffff58227ac in g_main_context_iteration () from /usr/lib64/libglib-2.0.so.0
#17 0x00007ffff64ca3f6 in QEventDispatcherGlib::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib64/libQt5Core.so.5
#18 0x00007ffff6478ddb in QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib64/libQt5Core.so.5
#19 0x00007ffff62ca022 in QThread::exec() () from /usr/lib64/libQt5Core.so.5
#20 0x00007ffff29864c7 in QDBusConnectionManager::run() () from /usr/lib64/libQt5DBus.so.5
#21 0x00007ffff62cb267 in QThreadPrivate::start(void*) () from /usr/lib64/libQt5Core.so.5
#22 0x00007ffff60b232a in ?? () from /usr/lib64/libc.so.6
#23 0x00007ffff6131d0c in ?? () from /usr/lib64/libc.so.6

SGaist

Might be a silly question but did you check whether all Qt packages were updated ?

Deep Red

@SGaist I believe yes. At least all packages containing qt string are at their latest versions (available at the repository)

$ qlist -Iv  | grep -i qt
dev-python/PyQt-builder-1.14.1
dev-python/PyQt5-5.15.9
dev-python/PyQt5-sip-12.11.1
dev-python/qtconsole-5.4.1
dev-python/QtPy-2.3.0
dev-qt/linguist-tools-5.15.8
dev-qt/qdbus-5.15.8
dev-qt/qtbluetooth-5.15.8-r1
dev-qt/qtcharts-5.15.8
dev-qt/qtconcurrent-5.15.8
dev-qt/qtcore-5.15.8-r3
dev-qt/qtdbus-5.15.8
dev-qt/qtdeclarative-5.15.8-r2
dev-qt/qtgui-5.15.8-r3
dev-qt/qtimageformats-5.15.8-r2
dev-qt/qtmultimedia-5.15.8
dev-qt/qtnetwork-5.15.8-r1
dev-qt/qtopengl-5.15.8
dev-qt/qtprintsupport-5.15.8
dev-qt/qtscript-5.15.8
dev-qt/qtsql-5.15.8-r1
dev-qt/qtstyleplugins-5.0.0_p20170311-r1
dev-qt/qtsvg-5.15.8
dev-qt/qttest-5.15.8
dev-qt/qttranslations-5.15.8
dev-qt/qtwayland-5.15.8-r3
dev-qt/qtwidgets-5.15.8-r3
dev-qt/qtx11extras-5.15.8
dev-qt/qtxml-5.15.8
x11-themes/adwaita-qt-1.4.2

I also checked libraries that appear in the backtrace, all of them belong to 5.15.8 version

SGaist

I am having a doubt: does your issue happen only with the applications you installed in your virtual environments ?

Deep Red

@SGaist It happens on the system only in the virtual environment it works fine.

SGaist

But your original matplotlib issue, was it happening because you installed matplotlib system wide ?

Deep Red

@SGaist Yes, it happenned because of system wide installation, both with package manager and pip.

The same bug affects not only matplotlib, but also telegram-desktop, Stellarium, VLC and several other applications.

SGaist

You shouldn't need to do that but did you try to re-emerge these packages ?

Deep Red

@SGaist All packages were reemerged and even updated but still the same. I put here the information about stellarium:

genlop -i stellarium
 * sci-astronomy/stellarium


   Total builds: 10
   Global build time: 4 hours, 24 minutes and 35 seconds.
   Average merge time: 26 minutes and 27 seconds.

   Info about currently installed ebuild:

   * sci-astronomy/stellarium-1.2
   Install date: Wed Mar 29 17:22:44 2023
   USE="nls -debug -deep-sky -doc -gps -media -qt6 -+scripting -+show-my-sky -stars -telescope -test -webengine -+xlsx"
   CFLAGS="-march=native -O2 -pipe"   CXXFLAGS="-march=native -O2 -pipe"   LDFLAGS="-Wl,-O1 -Wl,--as-needed"

backtrace:

#0  0x00007ffff60b400c in ?? () from /usr/lib64/libc.so.6
#1  0x00007ffff6066572 in raise () from /usr/lib64/libc.so.6
#2  0x00007ffff60504b2 in abort () from /usr/lib64/libc.so.6
#3  0x00007ffff6291d6d in QMessageLogger::fatal(char const*, ...) const () from /usr/lib64/libQt5Core.so.5
#4  0x00007ffff62a838f in QObjectPrivate::QObjectPrivate(int) [clone .cold] () from /usr/lib64/libQt5Core.so.5
#5  0x00007ffff29a2773 in QDBusAbstractInterfacePrivate::QDBusAbstractInterfacePrivate(QString const&, QString const&, QString const&, QDBusConnection const&, bool) () from /usr/lib64/libQt5DBus.so.5
#6  0x00007ffff29a3989 in QDBusAbstractInterface::QDBusAbstractInterface(QString const&, QString const&, char const*, QDBusConnection const&, QObject*) () from /usr/lib64/libQt5DBus.so.5
#7  0x00007ffff298a769 in QDBusConnectionInterface::QDBusConnectionInterface(QDBusConnection const&, QObject*) () from /usr/lib64/libQt5DBus.so.5
#8  0x00007ffff298790a in QDBusConnectionPrivate::createBusService() () from /usr/lib64/libQt5DBus.so.5
#9  0x00007ffff2988ce1 in QDBusConnectionManager::executeConnectionRequest(QDBusConnectionManager::ConnectionRequestData*) ()
   from /usr/lib64/libQt5DBus.so.5
#10 0x00007ffff64a4b14 in QObject::event(QEvent*) () from /usr/lib64/libQt5Core.so.5
#11 0x00007ffff647a2f5 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () from /usr/lib64/libQt5Core.so.5
#12 0x00007ffff647d6c3 in QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) () from /usr/lib64/libQt5Core.so.5
#13 0x00007ffff64ca8f3 in postEventSourceDispatch(_GSource*, int (*)(void*), void*) () from /usr/lib64/libQt5Core.so.5
#14 0x00007ffff58221e8 in g_main_context_dispatch () from /usr/lib64/libglib-2.0.so.0
#15 0x00007ffff5822718 in g_main_context_iterate.constprop () from /usr/lib64/libglib-2.0.so.0
#16 0x00007ffff58227ac in g_main_context_iteration () from /usr/lib64/libglib-2.0.so.0
#17 0x00007ffff64ca3f6 in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib64/libQt5Core.so.5
#18 0x00007ffff6478ddb in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib64/libQt5Core.so.5
#19 0x00007ffff62ca022 in QThread::exec() () from /usr/lib64/libQt5Core.so.5
#20 0x00007ffff29864c7 in QDBusConnectionManager::run() () from /usr/lib64/libQt5DBus.so.5
#21 0x00007ffff62cb267 in QThreadPrivate::start(void*) () from /usr/lib64/libQt5Core.so.5
#22 0x00007ffff60b232a in ?? () from /usr/lib64/libc.so.6
#23 0x00007ffff6131d0c in ?? () from /usr/lib64/libc.so.6

SGaist

I don't think that it is that but what about the -qt6 USE option ?

I am currently wondering whether it's something specific to QtDBus since it seems to always stop there.