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

[André G. <and...@um...>]

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.