Re: [scipion-users] My Scipion installation fails the pwem.tests.data.test_data test.

[Grigory S. <sha...@gm...>]

Hello Jon,

1) to update scipion core packages you can run "scipion update" - this
should get you to 3.1.0
2) xmipp binaries are not installed or not linked/detected by scipion. Did
you follow step 6 in the guide? If yes, could you attach the full
install.log?

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Wed, Jun 28, 2023 at 3:52 PM Low, John J. <jl...@mc...> wrote:

> Grigory,
>
>
>
> As far as I can tell, I have installed xmipp and I still get the same
> error.
>
>
>
> I have attached my most recent install log (Install.log.2), the output
> from the command “scipion tests pwem.tests.data.test_data &>
> pwem.tests.data.test_data.log” and the output from the “command scipion
> installp --help --checkUpdates &>checkupdates.log.”
>
>
>
> I have some packages which need to be updated based on the following from
> the console output from the scipion command.
>
>
>
> The package scipion-pyworkflow is out of date. Your version is 3.0.32, the
> latest is 3.1.0.
>
> The package scipion-em is out of date. Your version is 3.0.27, the latest
> is 3.1.0.
>
> The package scipion-app is out of date. Your version is 3.0.12, the latest
> is 3.1.0.
>
>
>
> How do I update these packages?
>
>
>
> John Low
>
>
>
> *From: *Grigory Sharov <sha...@gm...>
> *Date: *Wednesday, June 28, 2023 at 5:04 AM
> *To: *Mailing list for Scipion users <sci...@li...>
> *Cc: *Low, John J. <jl...@mc...>
> *Subject: *Re: [scipion-users] My Scipion installation fails the
> pwem.tests.data.test_data test.
>
> Dear Jon,
>
>
>
> I would not expect it to pass all tests since you have not installed xmipp.
>
>
> Best regards,
> Grigory
>
>
>
>
> --------------------------------------------------------------------------------
>
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <+44%201223%20267228>
>
> e-mail: gs...@mr...
>
>
>
>
>
> On Wed, Jun 28, 2023 at 11:01 AM Low, John J. via scipion-users <
> sci...@li...> wrote:
>
> To Whom It May Concern:
>
>
>
> I followed the instructions at
> https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html
> to install scipion.
>
>
>
> My build passes the basic tests
> pyworkflowtests.tests.test_object.TestObject and
> pyworkflowtests.tests.test_mappers but fails the pwem.tests.data.test_data
> test.
>
>
>
> I have attached the output from the failed test.
>
>
>
> Could someone please help me debug this failed test?
>
>
>
> Thanks!
>
>
>
> John J. Low
> Argonne National Laboratory
>
>
>
>
>
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>