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

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

Please do not drop the CC to the mailing list.

Xmipp installation has failed because you are missing dependencies.
Dependencies installation also failed because in the first log file you
have:

environment: line 5: __conda_exe: command not found
> environment: line 6: __conda_exe: command not found


Is your conda initialized in ~/.bashrc or ~/.bash_profile ? I think your
issue is described here: https://stackoverflow.com/a/69654559

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 Thu, Jun 29, 2023 at 1:06 PM Low, John J. <jl...@mc...> wrote:

> Grigory,
>
>
>
> I have attached the logs from my first two attempts to install Xmipp.
>
>
>
> Install.log.2 is the log from my third attempt.
>
>
>
> The second to last line in install.log.2 is:
>
>
>
> /home/jlow/.conda/envs/scipion3/bin/python -m pip install
> scipion-em-xmipp==23.3.0.3
>
>
>
> Which looks similar to the command in step 6.  I did not capture the exact
> command that I used to install Xmipp.
>
>
>
> Should I try to reinstall Scipion and then Xmipp with all the dependencies
> in my environment.  Did my three sequential installs corrupt my scipion3
> environment?
>
>
>
> John
>
> *From: *Grigory Sharov <sha...@gm...>
> *Date: *Thursday, June 29, 2023 at 3:29 AM
> *To: *Low, John J. <jl...@mc...>, Mailing list for Scipion users <
> sci...@li...>
> *Subject: *Re: [scipion-users] My Scipion installation fails the
> pwem.tests.data.test_data test.
>
> 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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