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

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

Hi Hong,

Your solution worked. I incorrectly edited my config file, many thanks!

~C

On Tue, 16 Aug 2022 at 13:31, Christopher Borsa <chr...@gm...>
wrote:

> 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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