Erotemic / ibeis

image based ecological information system
Apache License 2.0
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ibeis run error #83

Open Meyerdk opened 1 year ago

Meyerdk commented 1 year ago

Hi, hope you can assist? Thanx!

opencv-python was un installed and opencv-python-headless installed.

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway. qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)

Erotemic commented 1 year ago

I recently wrote up a set of debugging instructions for this:

Check 1

Again run:

pip uninstall python-opencv 
pip uninstall python-opencv 
pip uninstall python-opencv-headless
pip uninstall python-opencv-headless

(As shown run each command twice to ensure there are not duplicates)

Now pip install python-opencv-headless. And check if that works.

If it breaks, rerun ibeis, but run:

export QT_DEBUG_PLUGINS=1

first to get more verbose output from PyQt and rerun ibeis.

Check 2

If that doesn't work let's dive deeper and debug it. I put together the following script that will provide me with more information I can use to help diagnose your problem.


#!/bin/bash
__doc__="
These are steps to help debug opencv / pyqt5 issues
"

# Where are your Python site packages?
PYTHON_SITE_PACKAGE_DPATH=$(python -c "import sysconfig; print(sysconfig.get_paths()['platlib'])")
echo "PYTHON_SITE_PACKAGE_DPATH = $PYTHON_SITE_PACKAGE_DPATH"

# Running X or Wayland?
echo "$XDG_SESSION_TYPE = $$XDG_SESSION_TYPE"

# Where is the cv2 library located
OPENCV_MODULE_DPATH=$(python -c "import cv2; print(cv2.__file__)")
echo "OPENCV_MODULE_DPATH = $OPENCV_MODULE_DPATH"

# What opencv packages do you have installed in site packages?
find "$PYTHON_SITE_PACKAGE_DPATH"  -maxdepth 1 -iname "*opencv*"

ls "$PYTHON_SITE_PACKAGE_DPATH"/opencv_python_headless.libs

# Where is PyQt5?
PYQT_MODULE_DPATH=$(python -c "import PyQt5; print(PyQt5.__file__)")
echo "PYQT_MODULE_DPATH = $PYQT_MODULE_DPATH"

Check 3

The above information should be enough, but if not there is additional information that might be useful:

#### If the above is still unclear, the kwimage / kwplot modules have useful
#### helpers for debugging pyqt issues.

# install kwimage / kwplot

pip install kwimage[headless] kwplot xdoctest

# Run the kwplot pyqt tests
export QT_DEBUG_PLUGINS=1
xdoctest -m kwplot.auto_backends autompl --check
KWPLOT_UNSAFE=1 xdoctest -m kwplot.auto_backends autompl --check
KWPLOT_UNSAFE=0 xdoctest -m kwplot.auto_backends autompl --check
Meyerdk commented 1 year ago

Dear Erotemic/ibeis (Jon Crall)

Thank you for the feedback.

First Numpy 1.24 have an issue with floats. I change the version to 1.23.4 solving the float issue

OpenCV was uninstalled and headless opencv reinstallled as pe the instruction.

Ibeis fail to start so I run the 2 x scrips to get more info in the debugging. Please see below

Kind Regard Dr Meyer de KocK

[main!] WARNING: args.dbdir is None [main] _init_gui() [guitool_ibeis] Init new QApplication Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway. QFactoryLoader::QFactoryLoader() checking directory path "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms" ... QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqeglfs.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqeglfs.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "eglfs" ] }, "archreq": 0, "className": "QEglFSIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("eglfs") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqlinuxfb.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqlinuxfb.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "linuxfb" ] }, "archreq": 0, "className": "QLinuxFbIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("linuxfb") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimal.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimal.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "minimal" ] }, "archreq": 0, "className": "QMinimalIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("minimal") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimalegl.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimalegl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "minimalegl" ] }, "archreq": 0, "className": "QMinimalEglIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("minimalegl") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqoffscreen.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqoffscreen.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "offscreen" ] }, "archreq": 0, "className": "QOffscreenIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("offscreen") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqvnc.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqvnc.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "vnc" ] }, "archreq": 0, "className": "QVncIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("vnc") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-egl.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-egl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-egl" ] }, "archreq": 0, "className": "QWaylandEglPlatformIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("wayland-egl") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-generic.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-generic.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland" ] }, "archreq": 0, "className": "QWaylandIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("wayland") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-egl.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-egl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-xcomposite-egl" ] }, "archreq": 0, "className": "QWaylandXCompositeEglPlatformIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("wayland-xcomposite-egl") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-glx.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-glx.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-xcomposite-glx" ] }, "archreq": 0, "className": "QWaylandXCompositeGlxPlatformIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("wayland-xcomposite-glx") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwebgl.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwebgl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "webgl" ] }, "archreq": 0, "className": "QWebGLIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("webgl") QFactoryLoader::QFactoryLoader() looking at "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so" Found metadata in lib /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "xcb" ] }, "archreq": 0, "className": "QXcbIntegrationPlugin", "debug": false, "version": 331520 }

Got keys from plugin meta data ("xcb") QFactoryLoader::QFactoryLoader() checking directory path "/home/meyer/.local/conda/envs/py38/bin/platforms" ... Cannot load library /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so: (libxcb-xinerama.so.0: cannot open shared object file: No such file or directory) QLibraryPrivate::loadPlugin failed on "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so" : "Cannot load library /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so: (libxcb-xinerama.so.0: cannot open shared object file: No such file or directory)" qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)

(py38) @.***:~$ pip install kwimage[headless] kwplot

Run the kwplot pyqt tests

export QT_DEBUG_PLUGINS=1 xdoctest -m kwplot.auto_backends autompl --check KWPLOT_UNSAFE=1 xdoctest -m kwplot.auto_backends autompl --check KWPLOT_UNSAFE=0 xdoctest -m kwplot.auto_backends autompl --check Collecting kwimage[headless] Downloading kwimage-0.9.11-py3-none-any.whl (310 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 310.2/310.2 kB 2.8 MB/s eta 0:00:00 Collecting kwplot Downloading kwplot-0.4.13-py3-none-any.whl (55 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.6/55.6 kB 1.6 MB/s eta 0:00:00 Requirement already satisfied: numpy in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (1.23.4) Requirement already satisfied: scikit-image in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (0.19.3) Requirement already satisfied: scipy in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (1.10.0) Requirement already satisfied: Pillow in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (9.4.0) Collecting kwarray Downloading kwarray-0.6.9-py3-none-any.whl (101 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 101.5/101.5 kB 2.3 MB/s eta 0:00:00 Collecting distinctipy Downloading distinctipy-1.2.2-py3-none-any.whl (25 kB) Requirement already satisfied: parse in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (1.8.4) Requirement already satisfied: ubelt in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (1.2.3) Collecting shapely Using cached shapely-2.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.3 MB) Requirement already satisfied: opencv-python-headless in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (4.7.0.68) Requirement already satisfied: six in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwplot) (1.16.0) Requirement already satisfied: matplotlib in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwplot) (3.6.3) Requirement already satisfied: contourpy>=1.0.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (1.0.7) Requirement already satisfied: python-dateutil>=2.7 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (2.8.2) Requirement already satisfied: packaging>=20.0 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (23.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (1.4.4) Requirement already satisfied: fonttools>=4.22.0 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (4.38.0) Requirement already satisfied: pyparsing>=2.2.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (3.0.9) Requirement already satisfied: cycler>=0.10 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (0.11.0) Requirement already satisfied: imageio>=2.4.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from scikit-image->kwimage[headless]) (2.25.0) Requirement already satisfied: PyWavelets>=1.1.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from scikit-image->kwimage[headless]) (1.4.1) Requirement already satisfied: tifffile>=2019.7.26 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from scikit-image->kwimage[headless]) (2023.2.2) Requirement already satisfied: networkx>=2.2 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from scikit-image->kwimage[headless]) (3.0) Installing collected packages: shapely, distinctipy, kwarray, kwimage, kwplot Successfully installed distinctipy-1.2.2 kwarray-0.6.9 kwimage-0.9.11 kwplot-0.4.13 shapely-2.0.1 Command 'xdoctest' not found, did you mean: command 'doctest' from deb doctest (0.16.3-1build5.1) Try: sudo apt install Command 'xdoctest' not found, did you mean: command 'doctest' from deb doctest (0.16.3-1build5.1) Try: sudo apt install Command 'xdoctest' not found, did you mean: command 'doctest' from deb doctest (0.16.3-1build5.1) Try: sudo apt install

On Sat, Feb 4, 2023 at 9:42 PM Jon Crall @.***> wrote:

I recently wrote up a set of debugging instructions for this: Check 1

Again run:

pip uninstall python-opencv pip uninstall python-opencv pip uninstall python-opencv-headless pip uninstall python-opencv-headless

(As shown run each command twice to ensure there are not duplicates)

Now pip install python-opencv-headless. And check if that works.

If it breaks, rerun ibeis, but run:

export QT_DEBUG_PLUGINS=1

first to get more verbose output from PyQt and rerun ibeis. Check 2

If that doesn't work let's dive deeper and debug it. I put together the following script that will provide me with more information I can use to help diagnose your problem.

!/bin/bash

doc="These are steps to help debug opencv / pyqt5 issues"

Where are your Python site packages?

PYTHON_SITE_PACKAGE_DPATH=$(python -c "import sysconfig; print(sysconfig.get_paths()['platlib'])")echo "PYTHON_SITE_PACKAGE_DPATH = $PYTHON_SITE_PACKAGE_DPATH"

Running X or Wayland?echo "$XDG_SESSION_TYPE = $$XDG_SESSION_TYPE"

Where is the cv2 library located

OPENCV_MODULE_DPATH=$(python -c "import cv2; print(cv2.file)")echo "OPENCV_MODULE_DPATH = $OPENCV_MODULE_DPATH"

What opencv packages do you have installed in site packages?

find "$PYTHON_SITE_PACKAGE_DPATH" -maxdepth 1 -iname "opencv"

ls "$PYTHON_SITE_PACKAGE_DPATH"/opencv_python_headless.libs

Where is PyQt5?

PYQT_MODULE_DPATH=$(python -c "import PyQt5; print(PyQt5.file)")echo "PYQT_MODULE_DPATH = $PYQT_MODULE_DPATH"

Check 3

The above information should be enough, but if not there is additional information that might be useful:

If the above is still unclear, the kwimage / kwplot modules have useful#### helpers for debugging pyqt issues.

install kwimage / kwplot

pip install kwimage[headless] kwplot

Run the kwplot pyqt testsexport QT_DEBUG_PLUGINS=1

xdoctest -m kwplot.auto_backends autompl --check KWPLOT_UNSAFE=1 xdoctest -m kwplot.auto_backends autompl --check KWPLOT_UNSAFE=0 xdoctest -m kwplot.auto_backends autompl --check

(py38) @.***:~$ pip install kwimage[headless] kwplot

Run the kwplot pyqt tests

export QT_DEBUG_PLUGINS=1 xdoctest -m kwplot.auto_backends autompl --check KWPLOT_UNSAFE=1 xdoctest -m kwplot.auto_backends autompl --check KWPLOT_UNSAFE=0 xdoctest -m kwplot.auto_backends autompl --check Collecting kwimage[headless] Downloading kwimage-0.9.11-py3-none-any.whl (310 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 310.2/310.2 kB 2.8 MB/s eta 0:00:00 Collecting kwplot Downloading kwplot-0.4.13-py3-none-any.whl (55 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.6/55.6 kB 1.6 MB/s eta 0:00:00 Requirement already satisfied: numpy in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (1.23.4) Requirement already satisfied: scikit-image in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (0.19.3) Requirement already satisfied: scipy in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (1.10.0) Requirement already satisfied: Pillow in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (9.4.0) Collecting kwarray Downloading kwarray-0.6.9-py3-none-any.whl (101 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 101.5/101.5 kB 2.3 MB/s eta 0:00:00 Collecting distinctipy Downloading distinctipy-1.2.2-py3-none-any.whl (25 kB) Requirement already satisfied: parse in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (1.8.4) Requirement already satisfied: ubelt in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (1.2.3) Collecting shapely Using cached shapely-2.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.3 MB) Requirement already satisfied: opencv-python-headless in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwimage[headless]) (4.7.0.68) Requirement already satisfied: six in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwplot) (1.16.0) Requirement already satisfied: matplotlib in ./.local/conda/envs/py38/lib/python3.8/site-packages (from kwplot) (3.6.3) Requirement already satisfied: contourpy>=1.0.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (1.0.7) Requirement already satisfied: python-dateutil>=2.7 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (2.8.2) Requirement already satisfied: packaging>=20.0 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (23.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (1.4.4) Requirement already satisfied: fonttools>=4.22.0 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (4.38.0) Requirement already satisfied: pyparsing>=2.2.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (3.0.9) Requirement already satisfied: cycler>=0.10 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from matplotlib->kwplot) (0.11.0) Requirement already satisfied: imageio>=2.4.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from scikit-image->kwimage[headless]) (2.25.0) Requirement already satisfied: PyWavelets>=1.1.1 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from scikit-image->kwimage[headless]) (1.4.1) Requirement already satisfied: tifffile>=2019.7.26 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from scikit-image->kwimage[headless]) (2023.2.2) Requirement already satisfied: networkx>=2.2 in ./.local/conda/envs/py38/lib/python3.8/site-packages (from scikit-image->kwimage[headless]) (3.0) Installing collected packages: shapely, distinctipy, kwarray, kwimage, kwplot Successfully installed distinctipy-1.2.2 kwarray-0.6.9 kwimage-0.9.11 kwplot-0.4.13 shapely-2.0.1 Command 'xdoctest' not found, did you mean: command 'doctest' from deb doctest (0.16.3-1build5.1) Try: sudo apt install Command 'xdoctest' not found, did you mean: command 'doctest' from deb doctest (0.16.3-1build5.1) Try: sudo apt install Command 'xdoctest' not found, did you mean: command 'doctest' from deb doctest (0.16.3-1build5.1) Try: sudo apt install

— Reply to this email directly, view it on GitHub https://github.com/Erotemic/ibeis/issues/83#issuecomment-1416834583, or unsubscribe https://github.com/notifications/unsubscribe-auth/APAUAN3XI4GTZXBDKCXXF3TWV2WMBANCNFSM6AAAAAAURHSMNU . You are receiving this because you authored the thread.Message ID: @.***>

-- Meyer de Kock

Erotemic commented 1 year ago

First Numpy 1.24 have an issue with floats. I change the version to 1.23.4 solving the float issue

That is a good workaround for now. I'm working on releasing a new version of IBEIS where that won't be a problem.

Command 'xdoctest' not found, did you mean

Looks like xdoctest isn't installed by default. pip install xdoctest and rerun the parts where it failed because xdoctest was not found. I've updated the instructions to fix that oversight.

QLibraryPrivate::loadPlugin failed on "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so": "Cannot load library /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so:(libxcb-xinerama.so.0: cannot open shared object file: No such file or directory)" qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.

The QT_DEBUG_PLUGINS output is helpful. The next step is to take a closer look at the libraries that failed to load. Run:

ldd /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so

Or more generally (for other users that may be reading this) run:

PYQT_MODULE_DPATH=$(python -c "import PyQt5, pathlib; print(pathlib.Path(PyQt5.__file__).parent)")
echo "PYQT_MODULE_DPATH = $PYQT_MODULE_DPATH"

ldd "$PYQT_MODULE_DPATH"/Qt5/plugins/platforms/libqxcb.so

We want to check to see why libqxcb is failing to load. Using ldd to inspect the other modules it depends on may provide more information to continue debugging.

Meyerdk commented 1 year ago

Dear Jon

Thanks you for the quick response. I updated the xdoctest and tun the 2 x scripts, response below

(py38) @.:~$ ldd /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so linux-vdso.so.1 (0x00007ffc46dfd000) libQt5XcbQpa.so.5 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libQt5XcbQpa.so.5 (0x00007fb037600000) libfontconfig.so.1 => /lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007fb037d33000) libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007fb037c6b000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fb037c4f000) libQt5Gui.so.5 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libQt5Gui.so.5 (0x00007fb036c00000) libQt5DBus.so.5 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libQt5DBus.so.5 (0x00007fb036800000) libQt5Core.so.5 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libQt5Core.so.5 (0x00007fb036000000) libGL.so.1 => /lib/x86_64-linux-gnu/libGL.so.1 (0x00007fb037979000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fb037c48000) libX11-xcb.so.1 => /lib/x86_64-linux-gnu/libX11-xcb.so.1 (0x00007fb037c43000) libxcb-icccm.so.4 => /lib/x86_64-linux-gnu/libxcb-icccm.so.4 (0x00007fb037c3c000) libxcb-image.so.0 => /lib/x86_64-linux-gnu/libxcb-image.so.0 (0x00007fb037c34000) libxcb-shm.so.0 => /lib/x86_64-linux-gnu/libxcb-shm.so.0 (0x00007fb037c2f000) libxcb-util.so.1 => /lib/x86_64-linux-gnu/libxcb-util.so.1 (0x00007fb037c26000) libxcb-keysyms.so.1 => /lib/x86_64-linux-gnu/libxcb-keysyms.so.1 (0x00007fb037c21000) libxcb-randr.so.0 => /lib/x86_64-linux-gnu/libxcb-randr.so.0 (0x00007fb037c0e000) libxcb-render-util.so.0 => /lib/x86_64-linux-gnu/libxcb-render-util.so.0 (0x00007fb037c07000) libxcb-render.so.0 => /lib/x86_64-linux-gnu/libxcb-render.so.0 (0x00007fb03796a000) libxcb-shape.so.0 => /lib/x86_64-linux-gnu/libxcb-shape.so.0 (0x00007fb037965000) libxcb-sync.so.1 => /lib/x86_64-linux-gnu/libxcb-sync.so.1 (0x00007fb03795b000) libxcb-xfixes.so.0 => /lib/x86_64-linux-gnu/libxcb-xfixes.so.0 (0x00007fb0375f6000) libxcb-xinerama.so.0 => not found libxcb-xkb.so.1 => /lib/x86_64-linux-gnu/libxcb-xkb.so.1 (0x00007fb0375d8000) libxcb.so.1 => /lib/x86_64-linux-gnu/libxcb.so.1 (0x00007fb0375ae000) libXext.so.6 => /lib/x86_64-linux-gnu/libXext.so.6 (0x00007fb037599000) libX11.so.6 => /lib/x86_64-linux-gnu/libX11.so.6 (0x00007fb036ac0000) libxkbcommon-x11.so.0 => /lib/x86_64-linux-gnu/libxkbcommon-x11.so.0 (0x00007fb03758e000) libxkbcommon.so.0 => /lib/x86_64-linux-gnu/libxkbcommon.so.0 (0x00007fb037547000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fb037542000) libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fb035dd6000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fb035cef000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fb036aa0000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fb035ac7000) libxcb-xinerama.so.0 => not found libgthread-2.0.so.0 => /lib/x86_64-linux-gnu/libgthread-2.0.so.0 (0x00007fb03753b000) libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007fb03598d000) libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007fb03595c000) libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007fb036a97000) libpng16.so.16 => /lib/x86_64-linux-gnu/libpng16.so.16 (0x00007fb035921000) libbrotlidec.so.1 => /lib/x86_64-linux-gnu/libbrotlidec.so.1 (0x00007fb035913000) libdbus-1.so.3 => /lib/x86_64-linux-gnu/libdbus-1.so.3 (0x00007fb0358c5000) libicui18n.so.56 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libicui18n.so.56 (0x00007fb035400000) libicuuc.so.56 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libicuuc.so.56 (0x00007fb035000000) libicudata.so.56 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libicudata.so.56 (0x00007fb033600000) /lib64/ld-linux-x86-64.so.2 (0x00007fb037d8d000) libGLdispatch.so.0 => /lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007fb033548000) libGLX.so.0 => /lib/x86_64-linux-gnu/libGLX.so.0 (0x00007fb0353cc000) libXau.so.6 => /lib/x86_64-linux-gnu/libXau.so.6 (0x00007fb036a91000) libXdmcp.so.6 => /lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007fb0367f8000) libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007fb0334d2000) libbrotlicommon.so.1 => /lib/x86_64-linux-gnu/libbrotlicommon.so.1 (0x00007fb0358a2000) libsystemd.so.0 => /lib/x86_64-linux-gnu/libsystemd.so.0 (0x00007fb03340b000) libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007fb034fe8000) liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007fb0333e0000) libzstd.so.1 => /lib/x86_64-linux-gnu/libzstd.so.1 (0x00007fb033311000) liblz4.so.1 => /lib/x86_64-linux-gnu/liblz4.so.1 (0x00007fb0332f1000) libcap.so.2 => /lib/x86_64-linux-gnu/libcap.so.2 (0x00007fb0353c1000) libgcrypt.so.20 => /lib/x86_64-linux-gnu/libgcrypt.so.20 (0x00007fb0331b3000) libmd.so.0 => /lib/x86_64-linux-gnu/libmd.so.0 (0x00007fb0331a6000) libgpg-error.so.0 => /lib/x86_64-linux-gnu/libgpg-error.so.0 (0x00007fb033180000) (py38) @.:~$ PYQT_MODULE_DPATH=$(python -c "import PyQt5, pathlib; print(pathlib.Path(PyQt5.file).parent)") echo "PYQT_MODULE_DPATH = $PYQT_MODULE_DPATH"

ldd "$PYQT_MODULE_DPATH"/Qt5/plugins/platforms/libqxcb.so PYQT_MODULE_DPATH = /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5 linux-vdso.so.1 (0x00007ffe1293a000) libQt5XcbQpa.so.5 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libQt5XcbQpa.so.5 (0x00007fdac0a00000) libfontconfig.so.1 => /lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007fdac1199000) libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007fdac10d1000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fdac10b5000) libQt5Gui.so.5 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libQt5Gui.so.5 (0x00007fdac0000000) libQt5DBus.so.5 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libQt5DBus.so.5 (0x00007fdabfc00000) libQt5Core.so.5 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libQt5Core.so.5 (0x00007fdabf400000) libGL.so.1 => /lib/x86_64-linux-gnu/libGL.so.1 (0x00007fdac102c000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fdac1027000) libX11-xcb.so.1 => /lib/x86_64-linux-gnu/libX11-xcb.so.1 (0x00007fdac1022000) libxcb-icccm.so.4 => /lib/x86_64-linux-gnu/libxcb-icccm.so.4 (0x00007fdac101b000) libxcb-image.so.0 => /lib/x86_64-linux-gnu/libxcb-image.so.0 (0x00007fdac1013000) libxcb-shm.so.0 => /lib/x86_64-linux-gnu/libxcb-shm.so.0 (0x00007fdac100e000) libxcb-util.so.1 => /lib/x86_64-linux-gnu/libxcb-util.so.1 (0x00007fdac1005000) libxcb-keysyms.so.1 => /lib/x86_64-linux-gnu/libxcb-keysyms.so.1 (0x00007fdac0dfb000) libxcb-randr.so.0 => /lib/x86_64-linux-gnu/libxcb-randr.so.0 (0x00007fdac0de8000) libxcb-render-util.so.0 => /lib/x86_64-linux-gnu/libxcb-render-util.so.0 (0x00007fdac0de1000) libxcb-render.so.0 => /lib/x86_64-linux-gnu/libxcb-render.so.0 (0x00007fdac0dd0000) libxcb-shape.so.0 => /lib/x86_64-linux-gnu/libxcb-shape.so.0 (0x00007fdac0dcb000) libxcb-sync.so.1 => /lib/x86_64-linux-gnu/libxcb-sync.so.1 (0x00007fdac0dc1000) libxcb-xfixes.so.0 => /lib/x86_64-linux-gnu/libxcb-xfixes.so.0 (0x00007fdac0db7000) libxcb-xinerama.so.0 => not found libxcb-xkb.so.1 => /lib/x86_64-linux-gnu/libxcb-xkb.so.1 (0x00007fdac0d99000) libxcb.so.1 => /lib/x86_64-linux-gnu/libxcb.so.1 (0x00007fdac0d6d000) libXext.so.6 => /lib/x86_64-linux-gnu/libXext.so.6 (0x00007fdac09eb000) libX11.so.6 => /lib/x86_64-linux-gnu/libX11.so.6 (0x00007fdabfec0000) libxkbcommon-x11.so.0 => /lib/x86_64-linux-gnu/libxkbcommon-x11.so.0 (0x00007fdac0d62000) libxkbcommon.so.0 => /lib/x86_64-linux-gnu/libxkbcommon.so.0 (0x00007fdac09a4000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fdac0d5d000) libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fdabf1d6000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fdabf0ef000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fdac0984000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fdabeec7000) libxcb-xinerama.so.0 => not found libgthread-2.0.so.0 => /lib/x86_64-linux-gnu/libgthread-2.0.so.0 (0x00007fdac097f000) libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007fdabed8d000) libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007fdac094e000) libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007fdac0945000) libpng16.so.16 => /lib/x86_64-linux-gnu/libpng16.so.16 (0x00007fdabed52000) libbrotlidec.so.1 => /lib/x86_64-linux-gnu/libbrotlidec.so.1 (0x00007fdac0937000) libdbus-1.so.3 => /lib/x86_64-linux-gnu/libdbus-1.so.3 (0x00007fdabed04000) libicui18n.so.56 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libicui18n.so.56 (0x00007fdabe800000) libicuuc.so.56 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libicuuc.so.56 (0x00007fdabe400000) libicudata.so.56 => /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/../../lib/libicudata.so.56 (0x00007fdabca00000) /lib64/ld-linux-x86-64.so.2 (0x00007fdac11f3000) libGLdispatch.so.0 => /lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007fdabc948000) libGLX.so.0 => /lib/x86_64-linux-gnu/libGLX.so.0 (0x00007fdabfe8c000) libXau.so.6 => /lib/x86_64-linux-gnu/libXau.so.6 (0x00007fdabfbfa000) libXdmcp.so.6 => /lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007fdabecfc000) libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007fdabc8d2000) libbrotlicommon.so.1 => /lib/x86_64-linux-gnu/libbrotlicommon.so.1 (0x00007fdabecd9000) libsystemd.so.0 => /lib/x86_64-linux-gnu/libsystemd.so.0 (0x00007fdabc80b000) libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007fdabecc1000) liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007fdabe7d5000) libzstd.so.1 => /lib/x86_64-linux-gnu/libzstd.so.1 (0x00007fdabc73c000) liblz4.so.1 => /lib/x86_64-linux-gnu/liblz4.so.1 (0x00007fdabeca1000) libcap.so.2 => /lib/x86_64-linux-gnu/libcap.so.2 (0x00007fdabe7ca000) libgcrypt.so.20 => /lib/x86_64-linux-gnu/libgcrypt.so.20 (0x00007fdabc5fe000) libmd.so.0 => /lib/x86_64-linux-gnu/libmd.so.0 (0x00007fdabe7bd000) libgpg-error.so.0 => /lib/x86_64-linux-gnu/libgpg-error.so.0 (0x00007fdabc5d8000)

Kind regards Meyer

On Sun, Feb 5, 2023 at 8:51 PM Jon Crall @.***> wrote:

First Numpy 1.24 have an issue with floats. I change the version to 1.23.4 solving the float issue

That is a good workaround for now. I'm working on releasing a new version of IBEIS where that won't be a problem.

Command 'xdoctest' not found, did you mean

Looks like xdoctest isn't installed by default. pip install xdoctest and rerun the parts where it failed because xdoctest was not found. I've updated the instructions to fix that oversight.

QLibraryPrivate::loadPlugin failed on "/home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so": "Cannot load library /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so:(libxcb-xinerama.so.0: cannot open shared object file: No such file or directory)" qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.

The QT_DEBUG_PLUGINS output is helpful. The next step is to take a closer look at the libraries that failed to load. Run:

ldd /home/meyer/.local/conda/envs/py38/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so

Or more generally (for other users that may be reading this) run:

PYQT_MODULE_DPATH=$(python -c "import PyQt5, pathlib; print(pathlib.Path(PyQt5.file).parent)") echo "PYQT_MODULE_DPATH = $PYQT_MODULE_DPATH"

ldd "$PYQT_MODULE_DPATH"/Qt5/plugins/platforms/libqxcb.so

We want to check to see why libqxcb is failing to load. Using ldd to inspect the other modules it depends on may provide more information to continue debugging.

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Erotemic commented 1 year ago

Ok, I see libxcb-xinerama.so.0 => not found as the main culprit. You should be able to solve this by simply installing it:

sudo apt install libxcb-xinerama0
Meyerdk commented 1 year ago

Dear Jon

Work 100%

Thanks!

On Mon, 06 Feb 2023, 16:09 Jon Crall, @.***> wrote:

Ok, I see libxcb-xinerama.so.0 => not found as the main culprit. You should be able to solve this by simply installing it:

sudo apt install libxcb-xinerama0

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Meyerdk commented 1 year ago

Dear Jon

Please see the issue below regarding the creation of the database or open one

[image: image.png] Kind Regards Meyer

On Mon, Feb 6, 2023 at 4:34 PM M dk @.***> wrote:

Dear Jon

Work 100%

Thanks!

On Mon, 06 Feb 2023, 16:09 Jon Crall, @.***> wrote:

Ok, I see libxcb-xinerama.so.0 => not found as the main culprit. You should be able to solve this by simply installing it:

sudo apt install libxcb-xinerama0

— Reply to this email directly, view it on GitHub https://github.com/Erotemic/ibeis/issues/83#issuecomment-1419140960, or unsubscribe https://github.com/notifications/unsubscribe-auth/APAUAN2TOMNOYVI2ONIDHILWWEA27ANCNFSM6AAAAAAURHSMNU . You are receiving this because you authored the thread.Message ID: @.***>

-- Meyer de Kock

Erotemic commented 1 year ago

You haven't posted any image. Try using github directly.

Meyerdk commented 1 year ago

image

Erotemic commented 1 year ago

Ah, I recently fixed this issue and the fix should be released. Simply upgrade ibeis. pip install ibeis -U