Re: [scipion-users] scipion install issue-name 'xmipp' is not defined

[Miao G. <gmh...@16...>]

Dear Jose,


Thanks very much for your reply.
I am using the binary installation. 
The problem was solved. Something was wrong with the pyworkflow/em/convert.py file. I downloaded the new V1.1  and installed again and it works well now. 
Defining SCIPION_HOME and SCIPION_USER_DATA in my env file is OK. But I removed them as your suggestion.


Best,
Miao 






At 2018-01-31 16:33:31, "Jose Miguel de la Rosa Trevin" <del...@gm...> wrote:

Dear Miao, 


You don't need to define neither SCIPION_HOME or SCIPION_USER_DATA. The first one is inferred from 
the location of the scipion script and the second is defined in the configuration file.


Try to remove those and execute Scipion again. I'm not sure if the 'xmipp' issue is related to that or not.
Are you using the binary installation or from source code? That error seems to me like xmipp libraries
(now required by Scipion) are not properly installed.


Best,
Jose Miguel




On Mon, Jan 29, 2018 at 3:52 AM, Miao Gui <gmh...@16...> wrote:

Dear scipion developers,

I am a new user of scipion. I have configured and installed the scipion on my workstation, everything looks fine. And I added the following lines in my ~/.cshrc

setenv SCIPION_HOME "/usr/local/scipion-master"
setenv SCIPION_USER_DATA "/usr/local/scipion-master/data"
alias setxmipp source /usr/local/scipion/software/em/xmipp/xmipp.csh

But when I run scipion under the /usr/local/scipion-master/ folder, it comes to an error  and the message is listed below. How could I solve this problem?

Scipion v1.1 (2017-06-14) Balbino

>>>>> python  /usr/local/scipion-master/pyworkflow/apps/pw_manager.py
Traceback (most recent call last):
  File "/usr/local/scipion-master/pyworkflow/apps/pw_manager.py", line 32, in <module>
    from pyworkflow.gui.project import ProjectManagerWindow
  File "/usr/local/scipion-master/pyworkflow/gui/project/__init__.py", line 27, in <module>
    from project import ProjectManagerWindow, ProjectWindow
  File "/usr/local/scipion-master/pyworkflow/gui/project/project.py", line 45, in <module>
    from pyworkflow.manager import Manager
  File "/usr/local/scipion-master/pyworkflow/manager.py", line 33, in <module>
    from project import Project
  File "/usr/local/scipion-master/pyworkflow/project.py", line 40, in <module>
    import pyworkflow.em as em
  File "/usr/local/scipion-master/pyworkflow/em/__init__.py", line 35, in <module>
    from data import *
  File "/usr/local/scipion-master/pyworkflow/em/data.py", line 39, in <module>
    from convert import ImageHandler
  File "/usr/local/scipion-master/pyworkflow/em/convert.py", line 39, in <module>
    class ImageHandler(object):
  File "/usr/local/scipion-master/pyworkflow/em/convert.py", line 42, in ImageHandler
    DT_DEFAULT = xmipp.DT_DEFAULT
NameError: name 'xmipp' is not defined

Best wishes,
Miao Gui





 


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