matplotlib fails because of incomplatible qt versions

Deep Red

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

gdb stellarium
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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.

Deep Red

The bug disappeared after qt upgrade to the version 5.15.9