Re: [scipion-users] Scipion/xmipp v3.0.0 compilation error

[Pablo C. <pc...@cn...>]

Hi, André, we might need some more log lines, some more before the ones 
you've sent?.


Probably if you run the installation again you'll get the same.


On 10/9/20 13:50, André Graça wrote:
>
> Hi,
>
>
> I have gone through other treads that seem to be similar to the 
> problem I am finding during installation of Scipion v3.0.0, but so far 
> nothing made it work.
>
>
> I hope someone here can give me a hint of what going wrong. We are 
> talking about installation with conda on Ubuntu 16.04.
>
> Check the last lines of the log bellow.
>
>
> Thank you,
>
> André
>
>
>
> collect2: error: ld returned 1 exit status
> scons: *** [bin/xmipp_resolution_fsc] Error 1
> scons: building terminated because of errors.
>
> Some error occurred during the compilation of 'xmipp' 
> ('bin/xmipp_resolution_fsc').
>
> Traceback (most recent call last):
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", 
> line 443, in <module>
>     main()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", 
> line 287, in main
>     installPluginMethods()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", 
> line 231, in installPluginMethods
>     plugin.installBin({'args': ['-j', numberProcessor]})
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", 
> line 166, in installBin
>     environment.execute()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 748, in execute
>     self._executeTargets(targetList)
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 690, in _executeTargets
>     tgt.execute()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 220, in execute
>     command.execute()
>   File 
> "/home/angr5008/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", 
> line 160, in execute
>     assert glob(t), ("target '%s' not built (after "
> AssertionError: target 
> '/home/angr5008/software/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' 
> not built (after running 'cd . && ./xmipp config noAsk &&./xmipp 
> check_config && ./xmipp compileAndInstall N=20 && ln -srf build 
> /home/angr5008/software/scipion/3.0.0/software/em/xmipp && cd - && 
> touch installation_finished && rm bindings_linked 2> /dev/null')
> Error at main: target 
> '/home/angr5008/software/scipion/3.0.0/software/em/xmipp/bin/xmipp_reconstruct_significant' 
> not built (after running 'cd . && ./xmipp config noAsk &&./xmipp 
> check_config && ./xmipp compileAndInstall N=20 && ln -srf build 
> /home/angr5008/software/scipion/3.0.0/software/em/xmipp && cd - && 
> touch installation_finished && rm bindings_linked 2> /dev/null')
>
> Something went wrong running:
>  eval "$(/home/angr5008/anaconda3/condabin/conda shell.bash hook)" &&
> conda create  -n .scipion3env python=3 &&
> conda activate .scipion3env &&
> cd /home/angr5008/software/scipion/3.0.0 &&
> mkdir -p software/lib &&
> mkdir -p software/bindings &&
> mkdir -p software/em &&
> export SCIPION_HOME=/home/angr5008/software/scipion/3.0.0 &&
> pip install scipion-pyworkflow &&
> pip install scipion-app &&
> python -m scipion installp -p scipion-em-xmipp -j 20
> Installation cancelled.
>
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*