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Concave hull crashes program #59778

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2 tasks done
ninafogel opened this issue Dec 6, 2024 · 20 comments
Open
2 tasks done

Concave hull crashes program #59778

ninafogel opened this issue Dec 6, 2024 · 20 comments
Labels
Bug Either a bug report, or a bug fix. Let's hope for the latter! Crash/Data Corruption Processing Relating to QGIS Processing framework or individual Processing algorithms

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@ninafogel
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What is the bug or the crash?

When I try and run the "Concave Hull" algorithm (under Vector Geometry), it crashes QGIS.

Steps to reproduce the issue

  1. Open Concave Hull algorithm (Processing toolbox > Vector geometry > Concave Hull)
  2. Select point layer for input layer
  3. change no other settings
  4. Press run, watch program crash

Versions

3.40.1 Bratislava for Mac
3.34.13 Prizren LTR for Mac

Supported QGIS version

  • I'm running a supported QGIS version according to the roadmap.

New profile

Additional context

No response

@ninafogel ninafogel added the Bug Either a bug report, or a bug fix. Let's hope for the latter! label Dec 6, 2024
@agiudiceandrea
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@ninafogel, thanks for reporting. How did you install QGIS on macOS (via dmg installer, conda-forge, MacPorts, ...)? Please provide the QGIS full version info ("In the QGIS Help menu -> About, click in the table, Ctrl+A and then Ctrl+C. Finally paste here. Do not make a screenshot."). Please provide a sample layer with which the issue occurs.

@agiudiceandrea agiudiceandrea added the Feedback Waiting on the submitter for answers label Dec 7, 2024
@ninafogel
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Downloaded from the QGIS website:

<style type="text/css"> p, li { white-space: pre-wrap; } </style>
QGIS version 3.40.1-Bratislava
QGIS code revision 989853a
 
Libraries
Qt version 5.15.2
Python version 3.9.5
GDAL/OGR version 3.3.2
PROJ version 8.1.1
EPSG Registry database version v10.028 (2021-07-07)
GEOS version 3.9.1-CAPI-1.14.2
SQLite version 3.35.2
PDAL version 2.3.0
PostgreSQL client version unknown
SpatiaLite version 5.0.1
QWT version 6.1.6
QScintilla2 version 2.11.5
OS version macOS 14.6
 
Active Python plugins
processing_r 4.1.0
BoundingBox 2.2
Submission 0.10
concavehull 2.0
processing 2.12.99
grassprovider 2.12.99
db_manager 0.1.20
MetaSearch 0.3.6
QGIS version 3.40.1-Bratislava QGIS code revision [989853a](https://github.com/qgis/QGIS/commit/989853a7a31)

Libraries
Qt version
5.15.2
Python version
3.9.5
GDAL/OGR version
3.3.2
PROJ version
8.1.1
EPSG Registry database version
v10.028 (2021-07-07)
GEOS version
3.9.1-CAPI-1.14.2
SQLite version
3.35.2
PDAL version
2.3.0
PostgreSQL client version
unknown
SpatiaLite version
5.0.1
QWT version
6.1.6
QScintilla2 version
2.11.5
OS version
macOS 14.6

Active Python plugins
processing_r
4.1.0
BoundingBox
2.2
Submission
0.10
concavehull
2.0
processing
2.12.99
grassprovider
2.12.99
db_manager
0.1.20
MetaSearch
0.3.6

@ninafogel
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gbifclean.csv
Sample layer -- a bunch of records of bumblebees from GBIF -- uploaded as deliminated text layer with WGS 84

@agiudiceandrea
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agiudiceandrea commented Dec 7, 2024

I cannot replicate the described issue using QGIS 3.34.13 on Windows 10 (OSGeo4W) with the provided layer and instructions.
I guess the issue only occurs on macOS using QGIS installed via dmg installers from qgis.org, maybe due to outdated libraries versions shipped by such installer.
Alternative installers for macOS are available e.g. via Conda-forge https://aneto.pt/posts/tutorials/2019-05-29-using-qgis-from-conda/ and MacPorts https://www.qgis.org/resources/installation-guide/#macports which ship updated versions of some libraries.

@agiudiceandrea agiudiceandrea added macOS and removed Feedback Waiting on the submitter for answers labels Dec 7, 2024
@juliepierson
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Hi, same problem here with QGIS 3.34 on Ubuntu 22.04, installed with repo https://qgis.org/ubuntu-ltr
Thanks for your help !

@agiudiceandrea
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agiudiceandrea commented Dec 20, 2024

@juliepierson, may you provide a sample layer and step-by-step instruction in order to replicate the issue and may you provide the crash report if available?

@agiudiceandrea agiudiceandrea added Processing Relating to QGIS Processing framework or individual Processing algorithms Crash/Data Corruption labels Dec 20, 2024
@juliepierson
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Thanks for your answer @agiudiceandrea . As far as I know, the tool crashes when using any point layer, but here is a test shapefile with a few random points : test.zip

To reproduce :

  • launch QGIS
  • load point layer
  • execute concave hull tool with test point layer and default parameters
  • QGIS crashes

I get this message when launching QGIS from terminal, don't know if it is useful :
Warning: Qt Concurrent has caught an exception thrown from a worker thread. This is not supported, exceptions thrown in worker threads must be caught before control returns to Qt Concurrent. terminate called after throwing an instance of 'QgsNotSupportedException' Abandon (core dumped)

@agiudiceandrea
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agiudiceandrea commented Dec 20, 2024

Thanks @juliepierson.
The issue doesn't occur using QGIS from OSGeo4W on Windows.
I guess the issue may be due to the the fact that QGIS installed from https://qgis.org/ubuntu-ltr on Ubuntu 22.04 uses GEOS 3.10, while QGIS on Windows from OSGeo4W uses GEOS 3.13.

You could try to install QGIS in alternative ways in order to let it use a more recent version of the GEOS library. For example, e.g.:

@juliepierson
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Thanks @agiudiceandrea ! I think I will wait until next LTR version, if anyone tests this in the meantime I'll be interested to know if the problem was solved.

@boardend
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boardend commented Dec 30, 2024

I had the same problem with QGIS Desktop running in a Docker container with version qgis/qgis:final-3_36_3 (Ubuntu 22.04.1 with GEOS 3.10.2), this is fixed with qgis/qgis:3.40.2 (Ubuntu 22.04.1 24.04.1, with GEOS 3.12.1)

@agiudiceandrea
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@boardend, you probably meant "this is fixed with qgis/qgis:3.40.2 (Ubuntu 24.04.1, with GEOS 3.12.1)" ("Ubuntu 24.04.1" instead of "Ubuntu 22.04.1"). Didn't you?

@boardend
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boardend commented Jan 1, 2025

@agiudiceandrea uname -a inside qgis/qgis:3.40.2 gives me 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 17:42:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

@boardend
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boardend commented Jan 1, 2025

Oh, no. Dumb me... Sorry @agiudiceandrea, Docker uses the hosts system kernel, so uname -a was the wrong command to get the Ubuntu version of the Docker image. lsb_release -a reports Ubuntu 24.04.1 LTS and libgeos3.12.1t64 comes from http://archive.ubuntu.com/ubuntu noble/universe amd64

@nirvn
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nirvn commented Jan 24, 2025

Can't replicate on Ubuntu 24.10 (geos 3.12.2).

@ninafogel , if this is an issue with an old version of geos, this could already be fixed in a new macos package built against vcpkg which has geos 3.13. You can try these builds a try: #60039 (comment) and confirm whether the issue is fixed there?

@agiudiceandrea
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agiudiceandrea commented Jan 24, 2025

@nirvn, it looks like the issue occurs only using QGIS built against GEOS < 3.11: in this case QGIS uses its own implementation (QgsConcaveHullAlgorithm::concaveHullQgis) of the concavehull algorithm instead of the one based on GEOS (QgsConcaveHullAlgorithm::concaveHullGeos).

#if GEOS_VERSION_MAJOR == 3 && GEOS_VERSION_MINOR < 11
concaveHullQgis( sink, parameters, context, feedback );
#else
concaveHullGeos( sink, parameters, feedback );
#endif

Since 3.9 <= GEOS versions < 3.11 are still accepted by the build requirements, I think the issue should be addressed since it very likely occurs due to a bug in the QGIS source code.

@nirvn
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nirvn commented Jan 26, 2025

I've tried forcing my build to go through concaveHullQgis(...) and I couldn't get QGIS to crash. Tried with both @juliepierson 's test.zip dataset and @ninafogel 's gbifclean.csv

@agiudiceandrea
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agiudiceandrea commented Jan 26, 2025

Thanks @nirvn. @juliepierson @ninafogel may you please check if the crash also occurs using the "Delaunay triangulation" processing algorithm (which is used by "Concave hull" when GEOS < 3.11) with the same input layer and default parameters?

@agiudiceandrea
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These are the latest debug messages before the crash on Ubuntu 20.04, QGIS 3.41.0-Master, GEOS 3.10.2 ("Dalaunay triangulation" doesn't crash):

Stacktrace (piped through c++filt):
/usr/bin/qgis.bin(+0x11892)[0x55b29184d892]
/usr/bin/qgis.bin(+0x122bd)[0x55b29184e2bd]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xc4530)[0x7ffb7541b530]
/lib/x86_64-linux-gnu/libQt5Core.so.5(qt_message_output(QtMsgType, QMessageLogContext const&, QString const&)+0xf)[0x7ffb7541cb3f]
/lib/x86_64-linux-gnu/libQt5Core.so.5(QDebug::~QDebug()+0x70)[0x7ffb755213f0]
/lib/libqgis_core.so.3.41.0(QgsMapLayer::crs() const+0x2e6)[0x7ffb72a4857c]
/lib/libqgis_core.so.3.41.0(QgsVectorLayerFeatureSource::QgsVectorLayerFeatureSource(QgsVectorLayer const*)+0x486)[0x7ffb735e3b98]
/lib/libqgis_core.so.3.41.0(QgsVectorLayer::getFeatures(QgsFeatureRequest const&) const+0x39d)[0x7ffb7354ea4f]
/lib/libqgis_core.so.3.41.0(QgsProcessingFeatureSource::getFeatures(QgsFeatureRequest const&, QFlags<Qgis::ProcessingFeatureSourceFlag>) const+0x220)[0x7ffb72380ebe]
/lib/libqgis_analysis.so.3.41.0(+0x340f1c)[0x7ffb7058df1c]
/lib/libqgis_analysis.so.3.41.0(+0x340bfd)[0x7ffb7058dbfd]
/lib/libqgis_core.so.3.41.0(QgsProcessingAlgorithm::runPrepared(QMap<QString, QVariant> const&, QgsProcessingContext&, QgsProcessingFeedback*)+0x3af)[0x7ffb7229ba99]
/lib/libqgis_core.so.3.41.0(QgsProcessingAlgRunnerTask::run()+0xf2)[0x7ffb722a921c]
/usr/lib/python3/dist-packages/qgis/_core.cpython-310-x86_64-linux-gnu.so(sipQgsProcessingAlgRunnerTask::run()+0x7a)[0x7ffabb6fcb76]
/lib/libqgis_core.so.3.41.0(QgsTask::start()+0x10f)[0x7ffb72c0ba6b]
/lib/libqgis_core.so.3.41.0(+0x181a219)[0x7ffb72c10219]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xcff92)[0x7ffb75426f92]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xccca1)[0x7ffb75423ca1]
/lib/x86_64-linux-gnu/libc.so.6(+0x94b43)[0x7ffb71004b43]
/lib/x86_64-linux-gnu/libc.so.6(+0x126a00)[0x7ffb71096a00]
./src/core/qgsmessagelog.cpp:40 : (logMessage) [130ms] [thread:0x55b29499aeb0] 2025-01-27T00:11:53 Qt[1] crs (./src/core/qgsmaplayer.cpp:1316) is run from a different thread than the object  lives in [0x55b29499aeb0 vs 0x55b29376c890]
Warning: customProperty (./src/core/qgsmaplayer.cpp:2667) is run from a different thread than the object  lives in [0x55b29499aeb0 vs 0x55b29376c890]
Stacktrace (piped through c++filt):
/usr/bin/qgis.bin(+0x11892)[0x55b29184d892]
/usr/bin/qgis.bin(+0x122bd)[0x55b29184e2bd]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xc4530)[0x7ffb7541b530]
/lib/x86_64-linux-gnu/libQt5Core.so.5(qt_message_output(QtMsgType, QMessageLogContext const&, QString const&)+0xf)[0x7ffb7541cb3f]
/lib/x86_64-linux-gnu/libQt5Core.so.5(QDebug::~QDebug()+0x70)[0x7ffb755213f0]
/lib/libqgis_core.so.3.41.0(QgsMapLayer::customProperty(QString const&, QVariant const&) const+0x2f4)[0x7ffb72a5edfe]
/lib/libqgis_core.so.3.41.0(QgsExpressionContextUtils::layerScope(QgsMapLayer const*)+0xca)[0x7ffb7211cb42]
/lib/libqgis_core.so.3.41.0(QgsVectorLayerFeatureSource::QgsVectorLayerFeatureSource(QgsVectorLayer const*)+0x6fd)[0x7ffb735e3e0f]
/lib/libqgis_core.so.3.41.0(QgsVectorLayer::getFeatures(QgsFeatureRequest const&) const+0x39d)[0x7ffb7354ea4f]
/lib/libqgis_core.so.3.41.0(QgsProcessingFeatureSource::getFeatures(QgsFeatureRequest const&, QFlags<Qgis::ProcessingFeatureSourceFlag>) const+0x220)[0x7ffb72380ebe]
/lib/libqgis_analysis.so.3.41.0(+0x340f1c)[0x7ffb7058df1c]
/lib/libqgis_analysis.so.3.41.0(+0x340bfd)[0x7ffb7058dbfd]
/lib/libqgis_core.so.3.41.0(QgsProcessingAlgorithm::runPrepared(QMap<QString, QVariant> const&, QgsProcessingContext&, QgsProcessingFeedback*)+0x3af)[0x7ffb7229ba99]
/lib/libqgis_core.so.3.41.0(QgsProcessingAlgRunnerTask::run()+0xf2)[0x7ffb722a921c]
/usr/lib/python3/dist-packages/qgis/_core.cpython-310-x86_64-linux-gnu.so(sipQgsProcessingAlgRunnerTask::run()+0x7a)[0x7ffabb6fcb76]
/lib/libqgis_core.so.3.41.0(QgsTask::start()+0x10f)[0x7ffb72c0ba6b]
/lib/libqgis_core.so.3.41.0(+0x181a219)[0x7ffb72c10219]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xcff92)[0x7ffb75426f92]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xccca1)[0x7ffb75423ca1]
/lib/x86_64-linux-gnu/libc.so.6(+0x94b43)[0x7ffb71004b43]
./src/core/qgsmessagelog.cpp:40 : (logMessage) [110ms] [thread:0x55b29499aeb0] 2025-01-27T00:11:53 Qt[1] customProperty (./src/core/qgsmaplayer.cpp:2667) is run from a different thread than the object  lives in [0x55b29499aeb0 vs 0x55b29376c890]
Warning: name (./src/core/qgsmaplayer.cpp:239) is run from a different thread than the object  lives in [0x55b29499aeb0 vs 0x55b29376c890]
Stacktrace (piped through c++filt):
/usr/bin/qgis.bin(+0x11892)[0x55b29184d892]
/usr/bin/qgis.bin(+0x122bd)[0x55b29184e2bd]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xc4530)[0x7ffb7541b530]
/lib/x86_64-linux-gnu/libQt5Core.so.5(qt_message_output(QtMsgType, QMessageLogContext const&, QString const&)+0xf)[0x7ffb7541cb3f]
/lib/x86_64-linux-gnu/libQt5Core.so.5(QDebug::~QDebug()+0x70)[0x7ffb755213f0]
/lib/libqgis_core.so.3.41.0(QgsMapLayer::name() const+0x2ef)[0x7ffb72a2eca7]
/lib/libqgis_core.so.3.41.0(QgsExpressionContextUtils::layerScope(QgsMapLayer const*)+0x2a5)[0x7ffb7211cd1d]
/lib/libqgis_core.so.3.41.0(QgsVectorLayerFeatureSource::QgsVectorLayerFeatureSource(QgsVectorLayer const*)+0x6fd)[0x7ffb735e3e0f]
/lib/libqgis_core.so.3.41.0(QgsVectorLayer::getFeatures(QgsFeatureRequest const&) const+0x39d)[0x7ffb7354ea4f]
/lib/libqgis_core.so.3.41.0(QgsProcessingFeatureSource::getFeatures(QgsFeatureRequest const&, QFlags<Qgis::ProcessingFeatureSourceFlag>) const+0x220)[0x7ffb72380ebe]
/lib/libqgis_analysis.so.3.41.0(+0x340f1c)[0x7ffb7058df1c]
/lib/libqgis_analysis.so.3.41.0(+0x340bfd)[0x7ffb7058dbfd]
/lib/libqgis_core.so.3.41.0(QgsProcessingAlgorithm::runPrepared(QMap<QString, QVariant> const&, QgsProcessingContext&, QgsProcessingFeedback*)+0x3af)[0x7ffb7229ba99]
/lib/libqgis_core.so.3.41.0(QgsProcessingAlgRunnerTask::run()+0xf2)[0x7ffb722a921c]
/usr/lib/python3/dist-packages/qgis/_core.cpython-310-x86_64-linux-gnu.so(sipQgsProcessingAlgRunnerTask::run()+0x7a)[0x7ffabb6fcb76]
/lib/libqgis_core.so.3.41.0(QgsTask::start()+0x10f)[0x7ffb72c0ba6b]
/lib/libqgis_core.so.3.41.0(+0x181a219)[0x7ffb72c10219]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xcff92)[0x7ffb75426f92]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xccca1)[0x7ffb75423ca1]
/lib/x86_64-linux-gnu/libc.so.6(+0x94b43)[0x7ffb71004b43]
./src/core/qgsmessagelog.cpp:40 : (logMessage) [101ms] [thread:0x55b29499aeb0] 2025-01-27T00:11:53 Qt[1] name (./src/core/qgsmaplayer.cpp:239) is run from a different thread than the object  lives in [0x55b29499aeb0 vs 0x55b29376c890]
Warning: verticalCrs (./src/core/qgsmaplayer.cpp:1324) is run from a different thread than the object  lives in [0x55b29499aeb0 vs 0x55b29376c890]
Stacktrace (piped through c++filt):
/usr/bin/qgis.bin(+0x11892)[0x55b29184d892]
/usr/bin/qgis.bin(+0x122bd)[0x55b29184e2bd]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xc4530)[0x7ffb7541b530]
/lib/x86_64-linux-gnu/libQt5Core.so.5(qt_message_output(QtMsgType, QMessageLogContext const&, QString const&)+0xf)[0x7ffb7541cb3f]
/lib/x86_64-linux-gnu/libQt5Core.so.5(QDebug::~QDebug()+0x70)[0x7ffb755213f0]
/lib/libqgis_core.so.3.41.0(QgsMapLayer::verticalCrs() const+0x2e6)[0x7ffb72a48b06]
/lib/libqgis_core.so.3.41.0(QgsExpressionContextUtils::layerScope(QgsMapLayer const*)+0x7dd)[0x7ffb7211d255]
/lib/libqgis_core.so.3.41.0(QgsVectorLayerFeatureSource::QgsVectorLayerFeatureSource(QgsVectorLayer const*)+0x6fd)[0x7ffb735e3e0f]
/lib/libqgis_core.so.3.41.0(QgsVectorLayer::getFeatures(QgsFeatureRequest const&) const+0x39d)[0x7ffb7354ea4f]
/lib/libqgis_core.so.3.41.0(QgsProcessingFeatureSource::getFeatures(QgsFeatureRequest const&, QFlags<Qgis::ProcessingFeatureSourceFlag>) const+0x220)[0x7ffb72380ebe]
/lib/libqgis_analysis.so.3.41.0(+0x340f1c)[0x7ffb7058df1c]
/lib/libqgis_analysis.so.3.41.0(+0x340bfd)[0x7ffb7058dbfd]
/lib/libqgis_core.so.3.41.0(QgsProcessingAlgorithm::runPrepared(QMap<QString, QVariant> const&, QgsProcessingContext&, QgsProcessingFeedback*)+0x3af)[0x7ffb7229ba99]
/lib/libqgis_core.so.3.41.0(QgsProcessingAlgRunnerTask::run()+0xf2)[0x7ffb722a921c]
/usr/lib/python3/dist-packages/qgis/_core.cpython-310-x86_64-linux-gnu.so(sipQgsProcessingAlgRunnerTask::run()+0x7a)[0x7ffabb6fcb76]
/lib/libqgis_core.so.3.41.0(QgsTask::start()+0x10f)[0x7ffb72c0ba6b]
/lib/libqgis_core.so.3.41.0(+0x181a219)[0x7ffb72c10219]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xcff92)[0x7ffb75426f92]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xccca1)[0x7ffb75423ca1]
/lib/x86_64-linux-gnu/libc.so.6(+0x94b43)[0x7ffb71004b43]
./src/core/qgsmessagelog.cpp:40 : (logMessage) [136ms] [thread:0x55b29499aeb0] 2025-01-27T00:11:54 Qt[1] verticalCrs (./src/core/qgsmaplayer.cpp:1324) is run from a different thread than the object  lives in [0x55b29499aeb0 vs 0x55b29376c890]
Warning: Qt Concurrent has caught an exception thrown from a worker thread.
This is not supported, exceptions thrown in worker threads must be
caught before control returns to Qt Concurrent.
Stacktrace (piped through c++filt):
/usr/bin/qgis.bin(+0x11892)[0x55b29184d892]
/usr/bin/qgis.bin(+0x122bd)[0x55b29184e2bd]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xc4530)[0x7ffb7541b530]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xc4649)[0x7ffb7541b649]
/lib/x86_64-linux-gnu/libQt5Core.so.5(QMessageLogger::warning(char const*, ...) const+0xba)[0x7ffb753e741c]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0x91d20)[0x7ffb753e8d20]
/lib/x86_64-linux-gnu/libQt5Core.so.5(+0xccca1)[0x7ffb75423ca1]
/lib/x86_64-linux-gnu/libc.so.6(+0x94b43)[0x7ffb71004b43]
/lib/x86_64-linux-gnu/libc.so.6(+0x126a00)[0x7ffb71096a00]
./src/core/qgsmessagelog.cpp:40 : (logMessage) [1215ms] [thread:0x55b29499aeb0] 2025-01-27T00:11:55 Qt[1] Qt Concurrent has caught an exception thrown from a worker thread.
This is not supported, exceptions thrown in worker threads must be
caught before control returns to Qt Concurrent.
terminate called after throwing an instance of 'QgsNotSupportedException'

@nyalldawson
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@agiudiceandrea do you get the crash if you set the processing default handling for invalid geometries to "ignore"?

@agiudiceandrea
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agiudiceandrea commented Jan 28, 2025

The test.zip input layer is a simple point layer (EPSG:4326) containing 6 valid points.
Anyway, on Ubuntu 20.04, "Concave hull" crashes even if the "Invalid features filtering" processing setting is set to "Skip (ignore) features with invalid geometries".

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