Incompatible Qt lib?!

[jag...@gmail.com]

Hi,

After successfully launching klusta and klustaviewa on my mac, I tried to install it on our Linux server version 3.2.0-75-generic (buildd@kissel), running on
NAME="Ubuntu"
VERSION="12.04.5 LTS, Precise Pangolin"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu precise (12.04.5 LTS)"
VERSION_ID="12.04"
(gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) )

After error free installation process, when I try to run klustaviewa on Linux I'm getting the following error:

xxx/yyy/anaconda3/envs/klusta/lib/python2.7/site-packages/IPython/qt.py:13: ShimWarning: The `IPython.qt` package has been deprecated. You should import from qtconsole instead.
"You should import from qtconsole instead.", ShimWarning)
Cannot mix incompatible Qt library (version 0x40801) with this library (version 0x40805)
Aborted (core dumped)

I havent been using any desktop environment but simply through xterm. I tried to get tips from online by googling the error message but it seems no one has/had this specific case of incompatibility of Qt lib ver 40801 with Qt lib ver 40805 (I did find solutions when different Qt lib versions were incompatible, but since those were with different ver numbers I wasnt sure if I should try those solutions). Do you have any idea why I may be getting this error? & importantly how to resolve it?

Many thanks,
Jagdish

[Cyrille Rossant]

I havent been using any desktop environment but simply through xterm.

What do you mean exactly by that? Don't you have a X server and a desktop env like KDE or Gnome? KlustaViewa requires a graphical environment that can deal with GPU acceleration via OpenGL.

 

I tried to get tips from online by googling the error message but it seems no one has/had this specific case of incompatibility of Qt lib ver 40801 with Qt lib ver 40805 (I did find solutions when different Qt lib versions were incompatible, but since those were with different ver numbers I wasnt sure if I should try those solutions). Do you have any idea why I may be getting this error? & importantly how to resolve it?

I think you can try those solutions even if the lib versions are not the same.

 

[jag...@gmail.com]

On Thursday, July 21, 2016 at 6:18:43 PM UTC-4, jag...@gmail.com wrote:
> Hi,
Thanks Cyrille.

I confirmed that I have indeed been using KDE with X server. So of course I expect klustaviewa to work.

After realizing that those solutions given by people on web relating to different version problems may not work for me for 2 reasons:
1) those qt issues seems to be from yester era - almost 4-5 years back. I couldnt find any current posts with qt issues.
2) they seem dirty & partially un-safe. each solution is kinda unique and informs you of the issues that it may lead you into & are therefore unclean solutions. They seem to be linked with applications like Genymotion, Spyder, IEP, and Pyzo: none of which seems to be connected to my problem.

Given this uncertainty, I tried the 3rd suggestion: To Uninstall and reinstall anaconda3.
During reinstallation I noticed that the following step:
"conda env create -n klusta -f environment-linux.yml"

gave the following error:
Traceback (most recent call last):
File "/home/patelj65/anaconda3/bin/conda-env", line 6, in <module>
sys.exit(conda_env.cli.main.main())
File "/home/patelj65/anaconda3/lib/python3.5/site-packages/conda_env/cli/main.py", line 68, in main
return args_func(args, parser)
File "/home/patelj65/anaconda3/lib/python3.5/site-packages/conda/cli/main.py", line 180, in args_func
args.func(args, p)
File "/home/patelj65/anaconda3/lib/python3.5/site-packages/conda_env/cli/main_create.py", line 99, in execute
installer.install(prefix, pkg_specs, args, env)
File "/home/patelj65/anaconda3/lib/python3.5/site-packages/conda_env/installers/conda.py", line 16, in install
actions = plan.install_actions(prefix, index, specs, prune=prune)
TypeError: install_actions() got an unexpected keyword argument 'prune'"

I could find the solution on web (https://github.com/conda/conda-env/pull/246 ; https://github.com/conda/conda-env/blob/e01ba6f3894be107fc0b14f5eb7326b012a51cbd/conda_env/cli/main_update.py) but I didnt know how to implement it. Could you give some hints?

Many thanks,
Jagdish

[jag...@gmail.com]

Hi Cyrille,

So I updated conda using: conda update --all
This step resolved the 'prune' error during the next step:
conda env create -n klusta -f environment-linux.yml.

However, after successfully installing klusta, when I run klustaviewa, I'm still getting the following error:
"ShimWarning: The `IPython.qt` package has been deprecated. You should import from qtconsole instead.".

I looked up on google for this error and followed all their following suggestions to overcome the error:
conda update ipython
conda install spyder
conda update spyder
conda install ipython=3.2.1
conda update spyder
pip install --upgrade spyder

However, efter these attempts also I'm still getting the same error: "ShimWarning: The `IPython.qt` package has been deprecated. You should import from qtconsole instead.".

Any suggestions?

Thank you,
Jagdish

[Cyrille Rossant]

Hi,

This warning isn't a problem and it shouldn't stop the program from working. Do you get another error message?

Cyrille

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[jag...@gmail.com]

Hi,

I upgraded our Ubuntu server to 14.04 (from 12.04). And Installed Gnome as Desktop environment. After this taking your advise I ignored the error it was giving when running klustaviewa & successfully loaded the .dat & .prm files and ran "klusta hybrid_10sec.prm". This generated the .kwik and .kwx files as expected. However, after this when I tried to run:
klustaviewa hybrid_10sec.kwik .........it still gave the same error as before.

ShimWarning: The `IPython.qt` package has been deprecated. You should import from qtconsole instead.
"You should import from qtconsole instead.", ShimWarning)

Cannot mix incompatible Qt library (version 0x40806) with this library (version 0x40805)

thank you,
Jagdish

[jag...@gmail.com]

So I tried following suggestions from various links to overcome the Qt issues, but still didnt succeed in resolving it.

1) modifed (added the last line in) qt.conf file in ~/anaconda3/bin/qt.conf to be
[Paths]
Prefix = /home/patelj65/anaconda3
Binaries = /home/patelj65/anaconda3/bin
Libraries = /home/patelj65/anaconda3/lib
# Headers = /home/patelj65/anaconda3/include/qt
Plugins = '.'

2) modified the set environment path with following:
export QT_PLUGIN_PATH=''
& with : export QT_PLUGIN_PATH=" "

3) moved all libQt* files to a temp different location using following:
cd anaconda/lib
mkdir oldqt
mv libQt* oldqt
cd

4) installed pyqt by:
conda install pyqt

All these suggestions came from: https://github.com/ContinuumIO/anaconda-issues/issues/32. After each change I adopted, I retried to run klustaviewa hybrid_10sec.kwik.

But it still gives the same error:
~/anaconda3/envs/klusta/lib/python2.7/site-packages/IPython/qt.py:13: ShimWarning: The `IPython.qt` package has been deprecated. You should import from qtconsole instead.

"You should import from qtconsole instead.", ShimWarning)

Cannot mix incompatible Qt library (version 0x40806) with this library (version 0x40805)

Aborted (core dumped)


Any suggestions?

Thanks a lot,
Jagdish

[Cyrille Rossant]

I'm not sure... I think several people on this mailing list had this problem and managed to solve it but I don't remember how... Anyone could comment on this? Max maybe?

For more options, visit https://groups.google.com/d/optout.

[Max Hunter]

I've had it a couple of times, and it's always been on Linux distros which don't use GNOME (in fact, almost always KDE), and I've never been able to fix it without reinstalling the OS/DE. It seems reasonably clear that this is a lower-level issue than KlustaViewa though - perhaps the Anaconda support channels might have something to say?

[jag...@gmail.com]

This is unbelievable.
But basically, I deleted/removed *kde* initially with the following commands
--sudo apt-get install aptitude
aptitude search '?and(?and(?and(?reverse-depends(kubuntu),?not(?reverse-depends(ubuntu-desktop))),?automatic), ?not(?or(?priority(required), ?priority(important))))' ubuntu-desktop+
--sudo apt-get remove kde-full
--sudo apt-get --purge autoremove
--sudo apt-get install ppa-purge
--sudo ppa-purge ppa:kubuntu-ppa/backports

& then from each individual folders with
sudo rm *kde* -R

When I then tried klustaviewa through a terminal on my Mac laptop, it still gave the same error. However, I then connected a screen directly to my server and logged in through gnome, and even though it still gave the same error of [`IPython.qt` package has been deprecated ...], it still opened klustaviewa!!!

Great. Thanks for all your help.
One final question: Could I load my old data that I had partially clustered with old klusters software, onto this klustaviewa/klusta to complete the clustering? or will it damage the files/may not work for some other reason?

Thanks, again.
Jagdish

[Ronny Eichler]

Just to chime in, as I ran into the same issues mentioned by Jagdish (Hi Jagdish!)

The conda error on creation of the environment

TypeError: install_actions() got an unexpected keyword argument 'prune' 

is caused by the forcing of conda=3 in the installation instructions and does not happen with conda 4. Leaving the

conda install conda=3 --yes

step out, or self-upgrading conda, fixed that for me.

Fixing the Qt library core dump works by following the suggestions from https://github.com/ContinuumIO/anaconda-issues/issues/32, as Jagdish wrote. However, the klusta venv created during the installation has its own libQt files that need to be removed, the instructions are for the base anaconda installation. So instead of doing these steps in the anaconda3/lib folder, it should be done in anaconda3/envs/klusta/lib. I (re)moved the libQt* files from there, and klustaviewa works now on Kubuntu 16.04.

Greetings,

Ronny

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