I’m using 4.11.20200930 r29402 / 002be18 in ArchLinux. I could not load DICOM data now, but it used to work with 4.10.2. Here is the output log:
loadSourceAsModule - Failed to load file "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/sceneImport2428.py" as module "sceneImport2428" !
Fail to instantiate module "sceneImport2428"
The following modules failed to be instantiated:
ThresholdThreadingTest
sceneImport2428
DICOMScalarVolumePlugin
MultiVolumeImporterPlugin
DICOMImageSequencePlugin
DICOMVolumeSequencePlugin
Editor
Traceback (most recent call last):
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 22, in <module>
from . import multiarray
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/multiarray.py", line 12, in <module>
from . import overrides
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Python/lib/python3.6/imp.py", line 170, in load_source
module = _exec(spec, sys.modules[name])
File "<frozen importlib._bootstrap>", line 618, in _exec
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/sceneImport2428.py", line 8, in <module>
import EditorLib
File "/opt/3dslicer/lib/Slicer-4.11/qt-scripted-modules/EditorLib/__init__.py", line 37, in <module>
exec("from .{0} import {0}Options, {0}Tool, {0}Logic, {0}".format(effectName))
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Slicer-4.11/qt-scripted-modules/EditorLib/PaintEffect.py", line 10, in <module>
import numpy
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/__init__.py", line 140, in <module>
from . import core
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 48, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.6 from ""
* The NumPy version is: "1.19.1"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
loadSourceAsModule - Failed to load file "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/ThresholdThreadingTest.py" as module "ThresholdThreadingTest" !
Fail to instantiate module "ThresholdThreadingTest"
Traceback (most recent call last):
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 22, in <module>
from . import multiarray
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/multiarray.py", line 12, in <module>
from . import overrides
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Python/lib/python3.6/imp.py", line 170, in load_source
module = _exec(spec, sys.modules[name])
File "<frozen importlib._bootstrap>", line 618, in _exec
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/ThresholdThreadingTest.py", line 6, in <module>
import EditorLib
File "/opt/3dslicer/lib/Slicer-4.11/qt-scripted-modules/EditorLib/__init__.py", line 37, in <module>
exec("from .{0} import {0}Options, {0}Tool, {0}Logic, {0}".format(effectName))
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Slicer-4.11/qt-scripted-modules/EditorLib/PaintEffect.py", line 10, in <module>
import numpy
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/__init__.py", line 140, in <module>
from . import core
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 48, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.6 from ""
* The NumPy version is: "1.19.1"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
loadSourceAsModule - Failed to load file "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/MultiVolumeImporterPlugin.py" as module "MultiVolumeImporterPlugin" !
Fail to instantiate module "MultiVolumeImporterPlugin"
Traceback (most recent call last):
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 22, in <module>
from . import multiarray
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/multiarray.py", line 12, in <module>
from . import overrides
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Python/lib/python3.6/imp.py", line 170, in load_source
module = _exec(spec, sys.modules[name])
File "<frozen importlib._bootstrap>", line 618, in _exec
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/MultiVolumeImporterPlugin.py", line 5, in <module>
import vtk.util.numpy_support
File "/opt/3dslicer/lib/Slicer-4.11/python3.6/site-packages/vtkmodules/util/numpy_support.py", line 31, in <module>
import numpy
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/__init__.py", line 140, in <module>
from . import core
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 48, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.6 from ""
* The NumPy version is: "1.19.1"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
loadSourceAsModule - Failed to load file "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/Editor.py" as module "Editor" !
Fail to instantiate module "Editor"
Traceback (most recent call last):
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 22, in <module>
from . import multiarray
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/multiarray.py", line 12, in <module>
from . import overrides
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Python/lib/python3.6/imp.py", line 170, in load_source
module = _exec(spec, sys.modules[name])
File "<frozen importlib._bootstrap>", line 618, in _exec
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/Editor.py", line 4, in <module>
import EditorLib
File "/opt/3dslicer/lib/Slicer-4.11/qt-scripted-modules/EditorLib/__init__.py", line 37, in <module>
exec("from .{0} import {0}Options, {0}Tool, {0}Logic, {0}".format(effectName))
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Slicer-4.11/qt-scripted-modules/EditorLib/PaintEffect.py", line 10, in <module>
import numpy
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/__init__.py", line 140, in <module>
from . import core
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 48, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.6 from ""
* The NumPy version is: "1.19.1"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
loadSourceAsModule - Failed to load file "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/DICOMVolumeSequencePlugin.py" as module "DICOMVolumeSequencePlugin" !
Fail to instantiate module "DICOMVolumeSequencePlugin"
Traceback (most recent call last):
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 22, in <module>
from . import multiarray
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/multiarray.py", line 12, in <module>
from . import overrides
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Python/lib/python3.6/imp.py", line 170, in load_source
module = _exec(spec, sys.modules[name])
File "<frozen importlib._bootstrap>", line 618, in _exec
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/DICOMVolumeSequencePlugin.py", line 5, in <module>
import numpy
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/__init__.py", line 140, in <module>
from . import core
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 48, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.6 from ""
* The NumPy version is: "1.19.1"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
loadSourceAsModule - Failed to load file "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/DICOMScalarVolumePlugin.py" as module "DICOMScalarVolumePlugin" !
Fail to instantiate module "DICOMScalarVolumePlugin"
Traceback (most recent call last):
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 22, in <module>
from . import multiarray
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/multiarray.py", line 12, in <module>
from . import overrides
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Python/lib/python3.6/imp.py", line 170, in load_source
module = _exec(spec, sys.modules[name])
File "<frozen importlib._bootstrap>", line 618, in _exec
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 1, in <module>
import numpy
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/__init__.py", line 140, in <module>
from . import core
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 48, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.6 from ""
* The NumPy version is: "1.19.1"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
loadSourceAsModule - Failed to load file "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/DICOMImageSequencePlugin.py" as module "DICOMImageSequencePlugin" !
Fail to instantiate module "DICOMImageSequencePlugin"
Traceback (most recent call last):
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 22, in <module>
from . import multiarray
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/multiarray.py", line 12, in <module>
from . import overrides
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/3dslicer/lib/Python/lib/python3.6/imp.py", line 170, in load_source
module = _exec(spec, sys.modules[name])
File "<frozen importlib._bootstrap>", line 618, in _exec
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/opt/3dslicer/bin/../lib/Slicer-4.11/qt-scripted-modules/DICOMImageSequencePlugin.py", line 5, in <module>
import numpy
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/__init__.py", line 140, in <module>
from . import core
File "/opt/3dslicer/lib/Python/lib/python3.6/site-packages/numpy/core/__init__.py", line 48, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.6 from ""
* The NumPy version is: "1.19.1"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: libgfortran-2e0d59d6.so.5.0.0: ELF load command address/offset not properly aligned
Session start time .......: 2020-10-23 15:11:51
Slicer version ...........: 4.11.20200930 (revision 29402 / 002be18) linux-amd64 - installed release
Operating system .........: Linux / 5.4.72-1-lts / #1 SMP Sat, 17 Oct 2020 13:30:57 +0000 - 64-bit
Memory ...................: 15791 MB physical, 0 MB virtual
CPU ......................: GenuineIntel Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz, 8 cores, 8 logical processors
VTK configuration ........: OpenGL2 rendering, Sequential threading
Qt configuration .........: version 5.15.1, with SSL, requested OpenGL 3.2 (core profile)
Developer mode enabled ...: no
Prefer executable CLI ....: yes
Application path .........: /opt/3dslicer/bin
Additional module paths ..: (none)
It seems a lot of modules fail to init. BTW, where does slicer store its log file? I just copy these messages from the log message window.