SPM configuration fails

[kaurao]

I have installed pypreprocess in a Python 2.7 virtual environment on Debian 9.9 but without neurodebian travis as I do not have root access. I cannot get the SPM configured.

Here is my test code and associated output.

Code:
import os
from pypreprocess.configure_spm import _configure_spm

print 'SPM_DIR:', os.getenv('SPM_DIR')
print 'SPM_MCR:', os.getenv('SPM_MCR')
print 'SPM CONFIGURED:', _configure_spm(config_spm_dir=os.getenv('SPM_DIR'),
config_spm_mcr=os.getenv('SPM_MCR'))

Output:
191020-14:30:41,988 nipype.utils INFO:
Running nipype version 1.2.3 (latest: 1.2.3)
SPM_DIR: /home/homeGlobal/kpatil/opt/spm12/spm12/
SPM_MCR: /home/homeGlobal/kpatil/opt/spm12/spm12.sh
No handlers could be found for logger "pypreprocess"
SPM CONFIGURED: None

Is this due to travis not installed or something else?
Will be happy to provide any further information.

[KamalakerDadi]

Hi @kaustubhrpatil

Is this due to travis not installed or something else?

I think it might be related to #315

[kaurao]

@KamalakerDadi thanks for referencing #315 but I do not get any errors while installing spm mcr or any java related errors.

[KamalakerDadi]

Did you tried with install_spm12.sh in continuous_integration ?

[kaurao]

yes I used this script.

[KamalakerDadi]

Do you have MCRInstaller.bin in ~/opt/spm12 ?

Can you try this line in the same directory ?
./MCRInstaller.bin -P bean421.installLocation="mcr"

[kaurao]

It finished with this message:

The InstallShield Wizard has successfully installed MATLAB(R) Compiler Runtime 7.13.

Then I re-installed pyprocess producing following log but my test still fails (spm is still None):

Appending pypreprocess configuration to
Ignoring attempt to set 'name' (from '' to 'pypreprocess')
Appending pypreprocess/spm_loader configuration to
Ignoring attempt to set 'name' (from '' to 'pypreprocess/spm_loader')
Appending pypreprocess/external configuration to
Ignoring attempt to set 'name' (from '' to 'pypreprocess/external')
Appending pypreprocess/external/tempita configuration to
Ignoring attempt to set 'name' (from '' to 'pypreprocess/external/tempita')
Appending pypreprocess/external/nistats configuration to
Ignoring attempt to set 'name' (from '' to 'pypreprocess/external/nistats')
Appending pypreprocess/reporting configuration to
Ignoring attempt to set 'name' (from '' to 'pypreprocess/reporting')
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_py
running install_lib
running install_data
running install_egg_info
Removing /home/homeGlobal/kpatil/venv/pypreprocess/lib/python2.7/site-packages/pypreprocess-0.1_git-py2.7.egg-info
Writing /home/homeGlobal/kpatil/venv/pypreprocess/lib/python2.7/site-packages/pypreprocess-0.1_git-py2.7.egg-info
running install_clib
customize UnixCCompiler

[kaurao]

Aha while installing I also get multiple warnings, maybe that's a clue?

/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe'
warnings.warn(msg)
/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'include_package_data'
warnings.warn(msg)
Warning: Assuming default configuration (pypreprocess/{setup_pypreprocess,setup}.py was not found)Warning: Assuming default configuration (pypreprocess/spm_loader/setup_pypreprocess/{setup_pypreprocess/spm_loader,setup}.py was not found)Warning: Assuming default configuration (pypreprocess/external/setup_pypreprocess/{setup_pypreprocess/external,setup}.py was not found)Warning: Assuming default configuration (pypreprocess/external/tempita/setup_pypreprocess/external/{setup_pypreprocess/external/tempita,setup}.py was not found)Warning: Assuming default configuration (pypreprocess/external/nistats/setup_pypreprocess/external/{setup_pypreprocess/external/nistats,setup}.py was not found)Warning: Assuming default configuration (pypreprocess/reporting/setup_pypreprocess/{setup_pypreprocess/reporting,setup}.py was not found)

[KamalakerDadi]

The InstallShield Wizard has successfully installed MATLAB(R) Compiler Runtime 7.13.

Ok. so it not related to the issue #315 then. It is specific to Ubuntu 18.10. I am currently having the same problem.

Coming to your issue. I did a fresh installation without neurodebian travis and I am unable to reproduce the issue you are showing. On Ubuntu 16.04

 _configure_spm(config_spm_dir=os.getenv('SPM_DIR'), config_spm_mcr=os.getenv('SPM_MCR'))
'/home/parietal/kdadi/opt/spm12/spm12/spm12_mcr/spm12'

ATM I am unsure what's happening by looking at the warnings.

[kaurao]

I went through the error and after debugging for a while had to make two changes:

1. In pypreprocess/configure_spm.py added os.environ.get('SPM_DIR') in _SPM_DEFAULTS['spm_dir_template']: this was causing spm not to be detected as the code expects it to be in $HOME/opt or some other hard-coded locations. I also exported 'MATLAB_EXEC' variable pointing to the matlab binary.

2. Then it gave me another error 'This docstring was not generated by Nipype!' thrown from nipype.unils.spm_docs this was because matlab was not being correctly detected as in my installation command 'matlab' just displays available matlab versions. To fix this I needed to export environmental variable 'MATLABCMD' as 'MATLAB_EXEC' is not used by nipype.

So far the pipeline seems to progress.

Note that I switched to matlab executive with SPM12 directory mode instead of using MCR.