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

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Hi David,

 I tried moving the libraries as suggested in the Sep 5th 2019 thread.
I moved librariies around as suggested.  Now I get below.
Ubuntu version is

> lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.1 LTS
Release: 18.04
Codename: bionic

-----------------------------------------------------------

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:
/home/software/SCIPION/scipion/software/em/xmipp/lib/libXmipp.so: undefined
symbol: _ZNK2H56H5File14throwExceptionERKSsS2_

  > 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

On Mon, Mar 9, 2020 at 6:46 AM David Maluenda <dma...@cn...> wrote:

> Hi again Philip,
>
> I've just realized that a similar error was reported in this github-issue
> <https://github.com/I2PC/scipion-em-xmipp/issues/148>. Take it into
> account.
>
> Thanks to report and don't hesitate to contact us if still not working.
>
> <http://ucm.es/>
>
> *_____Dr. David Maluenda Niubó*
> dma...@cn... - (+34) 619 029 310
> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
> BioComputing Unit <http://biocomputingunit.es/>
>
> This email message and any documents attached to it may contain
> confidential or legally protected material and are intended solely for the
> use of the individual or organization to whom they are addressed. We remind
> you that if you are not the intended recipient of this email message or the
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>
>
>
> On Mon, Mar 9, 2020 at 11:39 AM David Maluenda <dma...@cn...>
> wrote:
>
>> 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/>
>>
>> This email message and any documents attached to it may contain
>> confidential or legally protected material and are intended solely for the
>> use of the individual or organization to whom they are addressed. We remind
>> you that if you are not the intended recipient of this email message or the
>> person responsible for processing it, then you are not authorized to read,
>> save, modify, send, copy or disclose any of its contents. If you have
>> received this email message by mistake, we kindly ask you to inform the
>> sender of this and to eliminate both the message and any attachments it
>> carries from your account. Thank you for your collaboration.
>>
>>
>>
>> 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
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>> _______________________________________________
> scipion-users mailing list
> sci...@li...
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>

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

Image processing framework to integrate EM software packages.

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