[scipion-users] warnings about missing plugins and CONDA

[Daniel L. <dan...@ic...>]

So I just installed Scipion 2.0 on a CentOS cluster and installed some plugins using the Plugin Manger and get some warnings. First, I installed Xmipp, but I stil get a warning about missing Xmipp binaries when I start Scipion. I ran the scipion installp --help --checkUpdates command (see below for the output). There are also warnings about locscale and eman2/PyQt4. And what is the CONDA warning about? Any suggestions?

Regards,
Daniel





> scipion installp --help --checkUpdates

Scipion v2.0 (2019-04-23) Diocletian

>>>>> python  /home/larsson/software/scipion_v2.0/pyworkflow/install/install-plugin.py /home/larsson/software/scipion_v2.0/scipion installp --help --checkUpdates

 >>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO!
  > Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp in Scipion manager window)

 > error when importing from eman2: No module named PyQt4
   Called by /home/larsson/software/scipion_v2.0/software/lib/python2.7/site-packages/locscale/constants.py, line 34
   Check the plugin manager (Configuration->Plugins in Scipion manager window)
   or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
   it could be a versions compatibility issue.

Warning: couldn't find Plugin for scipion-em-locscale
Dirname: locscale
WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
usage: /home/larsson/software/scipion_v2.0/scipion installp  [-h] [--noBin] [-p pluginName [pipVersion ...]]

optional arguments:
  -h, --help            show help
  --noBin               Optional flag to install plugins only as a python module,
                        without installing the plugin binaries. This will affect
                        all plugins specified in the command.
  --checkUpdates        Optional flag to check which plugins have new releases.
  -p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...]
                        - pluginName:     the name of the plugin to install from the list
                                         of available plugins shown below.
                        - pluginVersion: (optional) pip version to install. If not specified,
                                         will install the latest compatible with current Scipion.
  --devel               Optional flag to indicate that we will pass install sources instead
                        of pip names. Sources might be local paths or git urls. With local
                        paths, will do pip install -e (editable mode). It is expected to find
                        the plugin name in the basename of the path or in the repo name.
                        (i.e. it needs to match the one specified in setup.py). E.g:
                        scipion installp -p path/to/pluginName --devel
                        scipion installp -p https://github.com/someOrg/pluginName.git --devel
  -j j                  Number of CPUs to use for compilation

Example: /home/larsson/software/scipion_v2.0/scipion installp -p scipion-em-grigoriefflab 1.0.1 -p scipion-em-relion -p scipion-em-eman2

Available plugins: ([ ] not installed, [X] seems already installed)

scipion-em-appion      1.0.2 [X]
scipion-em-atomstructutils      1.0.7 [X]
scipion-em-atsas      1.0.6 [X]
scipion-em-bamfordlab            [ ]
scipion-em-bsoft      1.0.3 [X]
 scipion-em-ccp4     1.0.12 [X]
scipion-em-chimera      1.0.2 [X]
scipion-em-cryoef      1.0.5 [X]
scipion-em-cryomethods            [ ]
scipion-em-cryosparc2      1.0.7 [X]
scipion-em-eman2            [ ]
scipion-em-empiar      1.0.3 [X]
scipion-em-emxlib            [ ]
 scipion-em-esrf            [ ]
scipion-em-gautomatch      1.0.7 [X]
 scipion-em-gctf      1.0.7 [X]
scipion-em-grigoriefflab      1.0.6 [X]
scipion-em-imagic            [ ]
scipion-em-ispyb            [ ]
scipion-em-localrec        2.0 [X]
scipion-em-locscale      1.0.5 [X]
scipion-em-motioncorr      1.0.4 [X]
scipion-em-nysbc            [ ]
scipion-em-phenix            [ ]
scipion-em-powerfit            [ ]
scipion-em-relion      1.0.7 [X]
scipion-em-resmap      1.0.5 [X]
scipion-em-simple            [ ]
scipion-em-sphire      1.2.9 [X]
scipion-em-spider            [ ]
scipion-em-topaz            [ ]
scipion-em-xmipp     19.4.3 [X]










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