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

[Christopher B. <chr...@gm...>]

Hi Hong,

Thank you for your help, setting CONDA_ACTIVATION_CMD didn't do the trick.
As I'm running Centos7, this might perhaps be a compiler/OpenGL issue.

Many thanks,

Christopher

On Tue, 16 Aug 2022 at 12:46, HONG ZHAN via scipion-users <
sci...@li...> wrote:

> 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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