[vtkusers] No module named vtk when installing mayavi

[Ben Boeckel]

On Mon, Aug 24, 2015 at 09:03:32 +0200, KIM TRAN DONG wrote:
> 'sys.path' gives me this:
...
> '/usr/local/VTKBuild/Wrapping/Python/vtk',
> '/usr/local/VTKBuild/Wrapping/Python', '/usr/local/VTKBuild/bin',
> '/usr/local/vtkpython/bin/vtk', '/usr/local/VTKBuild/lib',
...

These look to be the paths you need.

> and for the 'set -x':
> + source /Users/kimtran/.bash_profile

This file seems to have the wrong commands (based on the '+' context
used).

> ++ set -x
> ++ FSLDIR=/usr/fsl
> ++ . /usr/fsl/etc/fslconf/fsl.sh
> +++ FSLOUTPUTTYPE=NIFTI_GZ
> +++ export FSLOUTPUTTYPE
> +++ FSLMULTIFILEQUIT=TRUE
> +++ export FSLMULTIFILEQUIT
> +++ FSLTCLSH=/usr/fsl/bin/fsltclsh
> +++ FSLWISH=/usr/fsl/bin/fslwish
> +++ export FSLTCLSH FSLWISH
> +++ FSLLOCKDIR=
> +++ FSLMACHINELIST=
> +++ FSLREMOTECALL=
> +++ export FSLLOCKDIR FSLMACHINELIST FSLREMOTECALL
> +++ FSLGECUDAQ=cuda.q
> +++ export FSLGECUDAQ
> +++ '[' -f /usr/local/etc/fslconf/fsl.sh ']'
> +++ '[' -f /etc/fslconf/fsl.sh ']'
> +++ '[' -f /Users/kimtran/.fslconf/fsl.sh ']'
> ++ PATH=/usr/fsl/bin:/usr/local/VTKBuild/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> ++ export FSLDIR PATH
> ++ export FREESURFER_HOME=/Applications/freesurfer
> ++ FREESURFER_HOME=/Applications/freesurfer
> ++ source /Applications/freesurfer/SetUpFreeSurfer.sh
...output from SetUpFreeSurfer.sh...
> ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5 stat.sh voxel_volume.txt
> -bash: Desktop: command not found

Here's one problem.

> ++ PERL_MB_OPT='--install_base "/Users/kimtran/perl5"'
> ++ export PERL_MB_OPT
> ++ PERL_MM_OPT=INSTALL_BASE=/Users/kimtran/perl5
> ++ export PERL_MM_OPT
> ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5 stat.sh voxel_volume.txt
> -bash: Desktop: command not found

A second.

> ++ export
> PATH=/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> ++
> PATH=/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5 stat.sh voxel_volume.txt
> -bash: Desktop: command not found

Third.

> ++ export PATH=/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> ++ PATH=/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5 stat.sh voxel_volume.txt
> -bash: Desktop: command not found

Fourth.

> ++ export LD_LIBRARY_PATH=/usr/local/VTKBuild/lib:/usr/lib/python2.7:/usr/local/VTKBuild/lib:/usr/lib/python2.7:/usr/local/VTKBuild/lib:/usr/lib/python2.7:
> ++ LD_LIBRARY_PATH=/usr/local/VTKBuild/lib:/usr/lib/python2.7:/usr/local/VTKBuild/lib:/usr/lib/python2.7:/usr/local/VTKBuild/lib:/usr/lib/python2.7:
> ++ export DYLD_LIBRARY_PATH=/usr/local/VTKBuild/lib:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/lib:
> ++ DYLD_LIBRARY_PATH=/usr/local/VTKBuild/lib:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/lib:
> ++ export PYTHONPATH=/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:
> ++ PYTHONPATH=/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:
> ++ export PATH=/usr/local/VTKBuild/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> ++ PATH=/usr/local/VTKBuild/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5 stat.sh voxel_volume.txt
> -bash: Desktop: command not found

Fifth.

> ++ update_terminal_cwd
> ++ local 'SEARCH= '
> ++ local REPLACE=%20
> ++ local PWD_URL=file://Kims-Mac-2.local/Users/kimtran
> ++ printf '\e]7;%s\a' file://Kims-Mac-2.local/Users/kimtran

It appears that some variable may contain a listing of your home
directory and is being used as a command? I'd check what's around the
SetUpFreeSurfer.sh line to see what variables are being used and see if
the logs mention it being set or overridden inside that
SetUpFreeSurfer.sh output section.

--Ben