Can't update matplotlib using conda?! Breaks Qt...

Tobias Haeberle

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Jul 24, 2015, 4:35:15 AM7/24/15

to Pyzo

Hi,

was trying to update matplotlib using conda.

tobis-mac:bin tobias$ ./conda update matplotlib
Fetching package metadata: ......
Solving package specifications: .
Package plan for installation in environment /Volumes/Home/tobias/pyzo2015a:

The following packages will be downloaded:

package | build
---------------------------|-----------------
libpng-1.6.17 | 0 184 KB
openssl-1.0.1k | 1 2.5 MB
sqlite-3.8.4.1 | 1 824 KB
tk-8.5.18 | 0 1.9 MB
yaml-0.1.6 | 0 79 KB
freetype-2.5.2 | 2 692 KB
qt-4.8.6 | 3 39.0 MB
conda-env-2.3.0 | py34_0 24 KB
numpy-1.9.2 | py34_0 2.6 MB
pyparsing-2.0.3 | py34_0 66 KB
python-3.4.3 | 0 19.1 MB
pytz-2015.4 | py34_0 174 KB
pyyaml-3.11 | py34_1 144 KB
requests-2.7.0 | py34_0 623 KB
setuptools-18.0.1 | py34_0 345 KB
sip-4.16.5 | py34_0 209 KB
conda-3.15.1 | py34_0 175 KB
pip-7.1.0 | py34_0 1.4 MB
pyqt-4.11.3 | py34_0 4.0 MB
python-dateutil-2.4.2 | py34_0 221 KB
matplotlib-1.4.3 | np19py34_3 41.1 MB
------------------------------------------------------------
Total: 115.2 MB

The following NEW packages will be INSTALLED:

pyqt: 4.11.3-py34_0
python-dateutil: 2.4.2-py34_0
qt: 4.8.6-3
sip: 4.16.5-py34_0

The following packages will be UPDATED:

conda: 3.9.0-py34_0 --> 3.15.1-py34_0
conda-env: 2.1.3-py34_0 --> 2.3.0-py34_0
freetype: 2.4.10-1 --> 2.5.2-2
libpng: 1.5.13-1 --> 1.6.17-0
matplotlib: 1.4.2-np19py34_0 --> 1.4.3-np19py34_3
numpy: 1.9.1-py34_0 --> 1.9.2-py34_0
openssl: 1.0.1k-0 --> 1.0.1k-1
pip: 6.0.8-py34_0 --> 7.1.0-py34_0
pyparsing: 2.0.1-py34_0 --> 2.0.3-py34_0
python: 3.4.2-0 --> 3.4.3-0
pytz: 2014.9-py34_0 --> 2015.4-py34_0
pyyaml: 3.11-py34_0 --> 3.11-py34_1
requests: 2.5.1-py34_0 --> 2.7.0-py34_0
setuptools: 12.2-py34_0 --> 18.0.1-py34_0
sqlite: 3.8.4.1-0 --> 3.8.4.1-1
tk: 8.5.15-0 --> 8.5.18-0
yaml: 0.1.4-1 --> 0.1.6-0

I think it is a bit strange, that conda wants to install NEW packages pyqt and qt. Shouldn't they already be present on my system after a clean pyzo2015a install?!?!

Once this process had finished, IEP stopped working because it complained that - indeed - Qt was loaded twice...

objc[17409]: Class QNSImageView is implemented in both /Volumes/Home/tobias/pyzo2015a/lib/QtGui and /Volumes/Home/tobias/pyzo2015a/lib/libQtGui.4.8.6.dylib. One of the two will be used. Which one is undefined.
QObject::moveToThread: Current thread (0x1004a8f30) is not the object's thread (0x1006ca980).
Cannot move to target thread (0x1004a8f30)

On Mac OS X, you might be loading two sets of Qt binaries into the same process. Check that all plugins are compiled against the right Qt binaries. Export DYLD_PRINT_LIBRARIES=1 and check that only one set of binaries are being loaded.
QObject::moveToThread: Current thread (0x1004a8f30) is not the object's thread (0x1006ca980).
Cannot move to target thread (0x1004a8f30)

What can I do, I need to update matplotlib because there is bug in the current version, that is critical to me...

Thanks

Tobias

Almar Klein

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Jul 24, 2015, 5:45:04 AM7/24/15

to py...@googlegroups.com

Apparently, PyQt is a dependency of the Matplotlib conda package. The
problem is that Pyzo comes with PySide, and things will indeed not work
when both are attemped to being loaded.

Two possible solutions:

- In the shell configurations, change the GUI integration from PySide to
PyQt4.
- update mpl with the -f flag, wich will not install dependencies.
However, it might be that the mpl config file will be overwritten on an
update, so you'd need to change it to make use of pyside again.

Hope this helps,
Almar

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Tobias Haeberle

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Feb 28, 2016, 9:55:52 AM2/28/16

to Pyzo

Hi Almar,

I had it working, but now I updated matplotlib again, and now have the same problem once again. I am using PyQt4 for the GUI, but still get the error. Any ideas?

In [2]: conda list

# packages in environment at /Applications/pyzo2015a:

#

conda 3.19.3 py34_0 defaults

conda-env 2.4.5 py34_0 defaults

cx_freeze 4.3.3 py34_4 file:///Users/almar/anaconda34/conda-bld/osx-64/cx_freeze-4.3.3-py34_4.tar.bz2

cycler 0.9.0 py34_0 defaults

dateutil 2.1 py34_2 http://repo.continuum.io/pkgs/free/osx-64/dateutil-2.1-py34_2.tar.bz2

fastcache 1.0.1 py34_0 http://repo.continuum.io/pkgs/free/osx-64/fastcache-1.0.1-py34_0.tar.bz2

freetype 2.5.5 0 defaults

iep 3.6.1 py34_0 https://conda.binstar.org/pyzo/osx-64/iep-3.6.1-py34_0.tar.bz2

imageio 1.1 py34_0 https://conda.binstar.org/pyzo/osx-64/imageio-1.1-py34_0.tar.bz2

ipython 2.4.1 py34_0 http://repo.continuum.io/pkgs/free/osx-64/ipython-2.4.1-py34_0.tar.bz2

jinja2 2.7.3 py34_1 http://repo.continuum.io/pkgs/free/osx-64/jinja2-2.7.3-py34_1.tar.bz2

libpng 1.6.17 0 defaults

libsodium 0.4.5 0 http://repo.continuum.io/pkgs/free/osx-64/libsodium-0.4.5-0.tar.bz2

markupsafe 0.23 py34_0 http://repo.continuum.io/pkgs/free/osx-64/markupsafe-0.23-py34_0.tar.bz2

matplotlib 1.5.1 np110py34_0 defaults

mkl 11.3.1 0 defaults

nose 1.3.4 py34_0 http://repo.continuum.io/pkgs/free/osx-64/nose-1.3.4-py34_0.tar.bz2

numpy 1.10.4 py34_0 defaults

openssl 1.0.2f 0 defaults

pandas 0.17.0 np110py34_0 http://repo.continuum.io/pkgs/free/osx-64/pandas-0.17.0-np110py34_0.tar.bz2

pip 8.0.3 py34_0 defaults

psutil 2.2.0 py34_0 http://repo.continuum.io/pkgs/free/osx-64/psutil-2.2.0-py34_0.tar.bz2

pycosat 0.6.1 py34_0 http://repo.continuum.io/pkgs/free/osx-64/pycosat-0.6.1-py34_0.tar.bz2

pygments 2.0.2 py34_0 http://repo.continuum.io/pkgs/free/osx-64/pygments-2.0.2-py34_0.tar.bz2

pyopengl 3.1.0b3 py34_0 file:///Users/almar/anaconda34/conda-bld/osx-64/pyopengl-3.1.0b3-py34_0.tar.bz2

pyparsing 2.0.3 py34_0 defaults

pyqt 4.11.4 py34_1 defaults

pyside-pyzo 1.2.1 py34_4 file:///Users/almar/anaconda34/conda-bld/osx-64/pyside-pyzo-1.2.1-py34_4.tar.bz2

python 3.4.4 0 defaults

python-dateutil 2.4.2 py34_0 http://repo.continuum.io/pkgs/free/osx-64/python-dateutil-2.4.2-py34_0.tar.bz2

python.app 1.2 py34_3 http://repo.continuum.io/pkgs/free/osx-64/python.app-1.2-py34_3.tar.bz2

pytz 2015.7 py34_0 http://repo.continuum.io/pkgs/free/osx-64/pytz-2015.7-py34_0.tar.bz2

pyyaml 3.11 py34_1 http://repo.continuum.io/pkgs/free/osx-64/pyyaml-3.11-py34_1.tar.bz2

pyzmq 14.5.0 py34_0 http://repo.continuum.io/pkgs/free/osx-64/pyzmq-14.5.0-py34_0.tar.bz2

pyzo_files 0.0 0 <unknown>

pyzolib 0.3.3 py34_0 file:///Users/almar/anaconda34/conda-bld/osx-64/pyzolib-0.3.3-py34_0.tar.bz2

qt 4.8.7 1 defaults

readline 6.2 2 http://repo.continuum.io/pkgs/free/osx-64/readline-6.2-2.tar.bz2

requests 2.9.1 py34_0 defaults

scikit-image 0.10.1 np19py34_0 http://repo.continuum.io/pkgs/free/osx-64/scikit-image-0.10.1-np19py34_0.tar.bz2

scikit-learn 0.15.2 np19py34_0 http://repo.continuum.io/pkgs/free/osx-64/scikit-learn-0.15.2-np19py34_0.tar.bz2

scipy 0.15.1 np19py34_0 http://repo.continuum.io/pkgs/free/osx-64/scipy-0.15.1-np19py34_0.tar.bz2

setuptools 20.1.1 py34_0 defaults

sip 4.16.9 py34_0 defaults

six 1.10.0 py34_0 http://repo.continuum.io/pkgs/free/osx-64/six-1.10.0-py34_0.tar.bz2

sqlite 3.9.2 0 defaults

sympy 0.7.6 py34_0 http://repo.continuum.io/pkgs/free/osx-64/sympy-0.7.6-py34_0.tar.bz2

tk 8.5.18 0 http://repo.continuum.io/pkgs/free/osx-64/tk-8.5.18-0.tar.bz2

tornado 4.1 py34_0 http://repo.continuum.io/pkgs/free/osx-64/tornado-4.1-py34_0.tar.bz2

visvis 1.9.1 py34_1 https://conda.binstar.org/pyzo/osx-64/visvis-1.9.1-py34_1.tar.bz2

wheel 0.29.0 py34_0 defaults

xz 5.0.5 1 defaults

yaml 0.1.6 0 http://repo.continuum.io/pkgs/free/osx-64/yaml-0.1.6-0.tar.bz2

zeromq 4.0.4 0 http://repo.continuum.io/pkgs/free/osx-64/zeromq-4.0.4-0.tar.bz2

zlib 1.2.8 0 http://repo.continuum.io/pkgs/free/osx-64/zlib-1.2.8-0.tar.bz2

Tobias Haeberle

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Feb 28, 2016, 10:00:59 AM2/28/16

to Pyzo

That's the error:

objc[23015]: Class QCocoaColorPanelDelegate is implemented in both /Applications/pyzo2015a/lib/libQtGui.4.8.7.dylib and /Applications/pyzo2015a/lib/QtGui. One of the two will be used. Which one is undefined.

Tobias Haeberle

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Feb 28, 2016, 10:22:22 AM2/28/16

to Pyzo

Ok, found the following workaround:

conda update matplotlib

conda remove qt

And then use PySide for the shell in IEP.

Seems quite fragile...

Almar Klein

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Feb 29, 2016, 5:54:02 AM2/29/16

to Tobias Haeberle, Pyzo

Oh that’s a good point that I think I missed previous time; you’d need to get rid of qt because pyside-pyzo includes qt. In the future, Pyzo will be more like regular (an)conda, and using PyQt4. So any of this stuff should disappear :)

Regards,

Almar

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