Error loading GPA module (Slicermorph)

Support
1

Hi I did a fresh install of Slicer (4.11.20210226) in a Linux machine (Debian stable branch). I installed Slicermorph trough Extension Manager without a problem. But after restart can’t run GPA module. Running Slicer in terminal I get this error:

./Slicer
Traceback (most recent call last):
File “”, line 1, in
File “/home/marmo/Descargas/Slicer-4.11.20210226-linux-amd64/lib/Python/lib/python3.6/imp.py”, line 170, in load_source
module = _exec(spec, sys.modules[name])
File “”, line 618, in _exec
File “”, line 678, in exec_module
File “”, line 219, in _call_with_frames_removed
File “/home/marmo/Descargas/Slicer-4.11.20210226-linux-amd64/NA-MIC/Extensions-29738/SlicerMorph/lib/Slicer-4.11/qt-scripted-modules/GPA.py”, line 14, in
import Support.gpa_lib as gpa_lib
File “/home/marmo/Descargas/Slicer-4.11.20210226-linux-amd64/NA-MIC/Extensions-29738/SlicerMorph/lib/Slicer-4.11/qt-scripted-modules/Support/gpa_lib.py”, line 4, in
import scipy.linalg as sp
File “/home/marmo/Descargas/Slicer-4.11.20210226-linux-amd64/lib/Python/lib/python3.6/site-packages/scipy/linalg/init.py”, line 194, in
from .misc import *
File “/home/marmo/Descargas/Slicer-4.11.20210226-linux-amd64/lib/Python/lib/python3.6/site-packages/scipy/linalg/misc.py”, line 3, in
from .blas import get_blas_funcs
File “/home/marmo/Descargas/Slicer-4.11.20210226-linux-amd64/lib/Python/lib/python3.6/site-packages/scipy/linalg/blas.py”, line 213, in
from scipy.linalg import _fblas
ImportError: /home/marmo/Descargas/Slicer-4.11.20210226-linux-amd64/lib/Python/lib/python3.6/site-packages/scipy/linalg/_fblas.cpython-36m-x86_64-linux-gnu.so: ELF load command address/offset not properly aligned
loadSourceAsModule - Failed to load file “/home/marmo/Descargas/Slicer-4.11.20210226-linux-amd64/NA-MIC/Extensions-29738/SlicerMorph/lib/Slicer-4.11/qt-scripted-modules/GPA.py” as module “GPA” !
Fail to instantiate module “GPA”
libpng warning: iCCP: profile ‘ICC Profile’: ‘CMYK’: invalid ICC profile color space
libpng warning: iCCP: known incorrect sRGB profile
The following modules failed to be instantiated:
GPA
Switch to module: “Welcome”

Sytem:
Distributor ID: Debian
Description: Debian GNU/Linux 11 (bullseye)
Release: 11
Codename: bullseye

Thanks in advance

Ale

2

I have seen this error, not sure why it happens,as we do not install scipy. But this should fix:

  1. Open a fresh slicer,
  2. go to python window and type
  3. pip_uninstall("scipy")
  4. pip_install("scipy")
  5. restart your slicer and try gpa again.
3

This was resolved in BUG: Fix import of python modules on Linux selectively stripping libr… · Slicer/Slicer@fef09b5 · GitHub. It shouldn’t be a problem if you use latest Slicer Preview as that commit came a few days after the latest Stable release back in February.