Re: [scipion-users] eman-tomo : Missing Dependencies upon install

[HONG Z. <hz...@wi...>]

Hi Christopher, 

I think you that you might need to add this line in the first line  after [PLUGINS] in the scipion configuration (scipion.conf) file if not added yet, I have the same issue before:

CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda shell.bash hook)”.

Hope it is the same as my issue before…

Best,
Hong



> On Aug 16, 2022, at 11:39 AM, Christopher Borsa <chr...@gm...> wrote:
> 
> After downloading the installing the eman-tomo dev package, I receive the following error message pasted below. I'm not sure if this is in fact a conda issue or to do with OpenGL. Can someone shed some light on this?
> 
> ~Christopher
> 
> CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
> To initialize your shell, run
> 
>     $ conda init <SHELL_NAME>
> 
> Currently supported shells are:
>   - bash
>   - fish
>   - tcsh
>   - xonsh
>   - zsh
>   - powershell
> 
> See 'conda init --help' for more information and options.
> 
> IMPORTANT: You may need to close and restart your shell after running 'conda init'.
> 
> 
> 
> 
> --------------------------------------------
> 
> Sometimes installation fails due to missing dependencies:
> 
> 
> - OpenGL::OpenGL or similar does not exists --> sudo apt-get install libsm-dev libxrender-dev build-essential libgl1-mesa-dev mesa-utils mesa-common-dev libglu1-mesa libglu1-mesa-dev
> 
> 
> --------------------------------------------
> 
> Traceback (most recent call last):
>   File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 474, in <module>
>     main()
>   File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main
>     installPluginMethods()
>   File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 216, in installPluginMethods
>     plugin.installBin({'args': ['-j', numberProcessor]})
>   File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
>     environment.execute()
>   File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
>     self._executeTargets(targetList)
>   File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
>     tgt.execute()
>   File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
>     command.execute()
>   File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
>     assert glob(t), ("target '%s' not built (after "
> AssertionError: target '/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o' not built (after running 'conda create -y -n emantomo-2.91_211111 --file /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt && conda activate emantomo-2.91_211111 && cd eman-build && cmake ../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies; exit 1; } && make -j 1 && make install')
> Error at main: target '/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o' not built (after running 'conda create -y -n emantomo-2.91_211111 --file /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt && conda activate emantomo-2.91_211111 && cd eman-build && cmake ../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies; exit 1; } && make -j 1 && make install')
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