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

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

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/>

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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
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>