initializing rtree.index.Index directly causes QGIS 3.34 and 3.36 to crash and exit.

[Fanchengyan]

What is the bug or the crash?

Initializing rtree.index.Index directly causes QGIS 3.34 and 3.36 to crash and exit.

Steps to reproduce the issue

1. Open Python Console
2. run the following script:

from rtree.index import Index, Property
index = Index(interleaved=False, properties=Property(dimension=3))

Then, QGIS will crash and exit directly.

Versions

<style type="text/css"> p, li { white-space: pre-wrap; } </style>

QGIS version	3.34.6-Prizren	QGIS code revision	623828f
Qt version	5.15.3
Python version	3.10.12
GDAL/OGR version	3.4.1
PROJ version	8.2.1
EPSG Registry database version	v10.041 (2021-12-03)
GEOS version	3.10.2-CAPI-1.16.0
SQLite version	3.37.2
PDAL version	2.3.0
PostgreSQL client version	14.11 (Ubuntu 14.11-0ubuntu0.22.04.1)
SpatiaLite version	5.0.1
QWT version	6.1.4
QScintilla2 version	2.11.6
OS version	Ubuntu 22.04.4 LTS
Active Python plugins
Geo-SAM	1.0
plugin_reloader	0.9.4
MetaSearch	0.3.6
db_manager	0.1.20
grassprovider	2.12.99
processing	2.12.99

QGIS version 3.34.6-Prizren QGIS code revision [623828f](https://github.com/qgis/QGIS/commit/623828f58c2) Qt version 5.15.3 Python version 3.10.12 GDAL/OGR version 3.4.1 PROJ version 8.2.1 EPSG Registry database version v10.041 (2021-12-03) GEOS version 3.10.2-CAPI-1.16.0 SQLite version 3.37.2 PDAL version 2.3.0 PostgreSQL client version 14.11 (Ubuntu 14.11-0ubuntu0.22.04.1) SpatiaLite version 5.0.1 QWT version 6.1.4 QScintilla2 version 2.11.6 OS version Ubuntu 22.04.4 LTS

Active Python plugins
Geo-SAM
1.0
plugin_reloader
0.9.4
MetaSearch
0.3.6
db_manager
0.1.20
grassprovider
2.12.99
processing
2.12.99

Supported QGIS version

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

New profile

• I tried with a new QGIS profile

Additional context

No response

[nyalldawson]

It's safer to use the inbuilt PyQgis spatial index classes (eg QgsSpatialIndex)

[Fanchengyan]

Hi @nyalldawson ,

Thank you for your prompt response. Do the officials have any plans to fix this issue in future versions of QGIS or rtree? Since the torchgeo library heavily relies on rtree, if this issue persists, the cost of developing deep-learning-related plugins for QGIS will increase dramatically.

[nyalldawson]

Did you install rtree via pip? Or system package? You've likely got a library mismatch which is clashing with one of the system libraries qgis is using.

[Fanchengyan]

Hi @nyalldawson ,

TorchGeo depends on rtree>=1, and I'm not sure if the version installed by default in QGIS is lower than this and being forcibly updated. But when we were developing the Geo-SAM plugin last year, the torchgeo at that time should have already had this dependency requirement, but the QGIS 3.30 at that time did not have this problem. This issue was only recently reported to us by our users (coolzhao/Geo-SAM#43), and it seems to have occurred around QGIS 3.34/3.36. I have tried to reinstall all versions of rtree between [1.0, 1.2], but QGIS still crashes. Is there any way to resolve this issue?

[nyalldawson]

Is there any way to resolve this issue?

Not from the qgis side, no.

By installing rtree via pip you're installing and using a different version of libspatialindex vs the system installed version of the library coming from the Ubuntu repository (which qgis uses). This library conflict results in the crash.

The solution would be to ensure you never install rtree via pip, and instead install it only from the Ubuntu repositories (python3-rtree).

Given that this isn't a qgis bug, I'm closing the ticket. But feel free to reply if you have further questions

[Fanchengyan]

Thanks, this solves the problem.