Re: [scipion-users] scipion install issues: xmipp won't install underneath

[David M. <dma...@cn...>]

Hi Philip, thanks for reporting

This error usually raise when installing xmippBin_Centos in a debian distro
or the opposite.

Which OS is the system?

If you get the same or similar error when installing the other
xmippBin_xxx, then I will recommend you to install Scipion and Xmipp from
sources.


Kind regards,

<http://ucm.es/>

*_____Dr. David Maluenda Niubó*Hi
dma...@cn... - (+34) 619 029 310
CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

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On Mon, Mar 9, 2020 at 5:26 AM Philip R. Baldwin <pr...@gm...> wrote:

> Hi Everyone,
>  I am sure it is an old topic, but I am having trouble installing xmipp
> underneath
> scipion which seemed to install quite nicely at the high level.
>
>  Here is the scipion error after xmipp installation through the scipion
> gui.
>
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------
>
> Scipion v2.0 (2019-04-23) Diocletian
>
> >>>>> python  /home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py
>
> Xmipp installation have failed or xmipp's C++ binnding have some problem:
> /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3: undefined symbol:
> fftw_set_planner_hooks
>
>   > Please, remove the Xmipp installation (usually 'rm software/em/xmipp')
> and re-install it
>
> Traceback (most recent call last):
>   File "/home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py",
> line 32, in <module>
>     from pyworkflow.gui.project import ProjectManagerWindow
>   File
> "/home/software/SCIPION/scipion/pyworkflow/gui/project/__init__.py", line
> 27, in <module>
>     from project import ProjectManagerWindow, ProjectWindow
>   File "/home/software/SCIPION/scipion/pyworkflow/gui/project/project.py",
> line 45, in <module>
>     from pyworkflow.project import MenuConfig, ProjectSettings
>   File "/home/software/SCIPION/scipion/pyworkflow/project/__init__.py",
> line 28, in <module>
>     from .project import Project, MissingProjectDbException
>   File "/home/software/SCIPION/scipion/pyworkflow/project/project.py",
> line 37, in <module>
>     import pyworkflow.em as em
>   File "/home/software/SCIPION/scipion/pyworkflow/em/__init__.py", line
> 31, in <module>
>     from data import *
>   File "/home/software/SCIPION/scipion/pyworkflow/em/data.py", line 36, in
> <module>
>     from convert import ImageHandler
>   File "/home/software/SCIPION/scipion/pyworkflow/em/convert/__init__.py",
> line 28, in <module>
>     from .image_handler import ImageHandler, DT_FLOAT
>   File
> "/home/software/SCIPION/scipion/pyworkflow/em/convert/image_handler.py",
> line 38, in <module>
>     sys.exit(-1)
> NameError: name 'sys' is not defined
>
>
> --------------------------------------------------------------------------------------------
>
>    Thank you in advance,
>
>                        Philip Baldwin
>                     The Salk Institute
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