Could not import PyQt5 but the package is in conda list

[enazbngl]

Dear All,

I was trying to install the gmx_MMPBSA and encountered several problems which I was able to solve following this thread. After installation, I have encountered another problem when running gmx_MMPBSA_ana concerning PyQt5. When I check the package list with "conda list" i can see pyqt5 is already installed. The error is as follows:

[INFO ] Opening gmx_MMPBSA_ana... ERROR:root:MMPBSA_Error Could not import PyQt5. gmx_MMPBSA_ana will be disabled until you install it. Check the gmx_MMPBSA.log file to report the problem. Traceback (most recent call last): File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 115, in gmxmmpbsa_ana from GMXMMPBSA.analyzer.gui import GMX_MMPBSA_ANA File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/analyzer/gui.py", line 29, in from GMXMMPBSA.analyzer.plots import Charts File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/analyzer/plots.py", line 29, in import seaborn as sns File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/seaborn/init.py", line 2, in from .rcmod import # noqa: F401,F403 File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/seaborn/rcmod.py", line 7, in from . import palettes File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/seaborn/palettes.py", line 9, in from .utils import desaturate, get_color_cycle File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/seaborn/utils.py", line 10, in from scipy import stats File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/scipy/stats/init.py", line 441, in from .stats import File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/scipy/stats/stats.py", line 43, in from . import distributions File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/scipy/stats/distributions.py", line 8, in from ._distn_infrastructure import (rv_discrete, rv_continuous, rv_frozen) File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/scipy/stats/_distn_infrastructure.py", line 24, in from scipy import optimize File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/scipy/optimize/init.py", line 400, in from .optimize import * File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/scipy/optimize/optimize.py", line 36, in from ._numdiff import approx_derivative File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/scipy/optimize/_numdiff.py", line 8, in from ._group_columns import group_dense, group_sparse ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/scipy/optimize/_group_columns.cpython-39-x86_64-linux-gnu.so)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/enaz/anaconda3/envs/AmberTools21/bin/gmx_MMPBSA_ana", line 8, in sys.exit(gmxmmpbsa_ana()) File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 118, in gmxmmpbsa_ana GMXMMPBSA_ERROR('Could not import PyQt5. gmx_MMPBSA_ana will be disabled until you install it') File "/home/enaz/anaconda3/envs/AmberTools21/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in init raise exc(msg + '. Check the gmx_MMPBSA.log file to report the problem.') GMXMMPBSA.exceptions.MMPBSA_Error: Could not import PyQt5. gmx_MMPBSA_ana will be disabled until you install it. Check the gmx_MMPBSA.log file to report the problem.

The log file and the output of the "conda list" are attached.

gmx_MMPBSA.log condalist.txt

[Valdes-Tresanco-MS]

I think the error is due to this ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26 not found, only that it is reported associated with PyQt5 because we have a bad traceback design (which we will write down to improve it). Let's do some tests to be sure. Please run in a terminal sudo apt install libstdc ++ 6

In case it doesn't work, open a new terminal, activate the conda environment you are working in, and run python Once in the python console type import PyQt5 and show me the output.

Mario S.

[enazbngl]

Dear Mario,

Thank you for such a quick response. I've tried your suggestions. The first one did not work. The output for "sudo apt install libstdc ++ 6" was:

Reading package lists... Done

Building dependency tree Reading state information... Done libstdc++6 is already the newest version (8.4.0-1ubuntu1~18.04). 0 upgraded, 0 newly installed, 0 to remove and 80 not upgraded.

"Import PyQt5" from the python console was successful. So, there was no output.

I've tried installing it on another workstation and everything works just fine. But this one was not attended for a while. Maybe an upgrade will solve the problems.

Regards,

Elif Naz BINGOL

Computational Biology and Bioinformatics Research Group Marmara University, Department of Bioengineering Goztepe Campus 34722 Istanbul - Turkey

On Mon, Dec 6, 2021 at 7:15 PM Mario Sergio Valdés Tresanco < @.***> wrote:

I think the error is due to this ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.26 not found, only that it is reported associated with PyQt5 because we have a bad traceback design (which we will write down to improve it). Let's do some tests to be sure. Please run in a terminal sudo apt install libstdc ++ 6

In case it doesn't work, open a new terminal, activate the conda environment you are working in, and run python Once in the python console type import PyQt5 and show me the output.

Mario S.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/100#issuecomment-986926617, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC6V3JCIRWNSQLFH2SBLZWDUPTOTDANCNFSM5JOXR7GQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[Valdes-Tresanco-MS]

Ok, please show me the output of this command echo $PYTHONPATH

[enazbngl]

It's empty. The output of echo $PATH:

/home/enaz/anaconda3/envs/AmberTools21/bin:/home/enaz/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

Elif Naz BINGOL, PhD Student Computational Biology and Bioinformatics Research Group Marmara University, Department of Bioengineering Goztepe Campus 34722 Istanbul - Turkey

On Mon, Dec 6, 2021 at 10:40 PM Mario Sergio Valdés Tresanco < @.***> wrote:

Ok, please show me the output of this command echo $PYTHONPATH

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/100#issuecomment-987120644, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC6V3JBER2DIUH3EFXDNY5DUPUGR5ANCNFSM5JOXR7GQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[Valdes-Tresanco-MS]

Try installing libgcc from conda (conda install -c anaconda libgcc). I still believe that the problem is the one I described at the beginning

Mario S.

[enazbngl]

Sorry for the delay. The package was already installed.

Elif Naz

On Mon, Dec 6, 2021 at 10:55 PM Mario Sergio Valdés Tresanco < @.***> wrote:

Try installing libgcc from conda (conda install -c anaconda libgcc). I still believe that the problem is the one I described at the beginning

Mario S.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/100#issuecomment-987134105, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC6V3JEMIAFGQG2K5MBYI73UPUIKFANCNFSM5JOXR7GQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[Valdes-Tresanco-MS]

Have you tried creating another conda environment, switching to a new conda version (with another python version), or a fresh conda installation?. It is that at the moment in all the tests that I have done it works correctly. If possible, send me as much information about your work environment to try to recreate it and identify the error

[enazbngl]

Hi Mario,

Since I am away from the lab, my access to the workstation is limited. Therefore I wasn't able to find time to try your suggestions. I will get back to you on this as soon as I am back at the lab.

Elif Naz

On Wed, Dec 8, 2021 at 7:23 PM Mario Sergio Valdés Tresanco < @.***> wrote:

Have you tried creating another conda environment, switching to a new conda version (with another python version), or a fresh conda installation?. It is that at the moment in all the tests that I have done it works correctly. If possible, send me as much information about your work environment to try to recreate it and identify the error

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/100#issuecomment-988965441, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC6V3JGMBLNU5KGRNGFH5PDUP6BBNANCNFSM5JOXR7GQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[Valdes-Tresanco-MS]

Closing as there is no activity