Sure thing. I am assuming latest master version is v3.2.7. That’s what I see in git. I installed that one and the same error appeared once it reached the Keras install part. Then I ran the last two commands with checking dependencies and the testing. The output is below. For some reason it stil says that the SCT version is the beta one. Do I have to uninstall first before installing v3.2.7? Thanks.
ipac-imac:sct shazeebm$ sct_check_dependencies
SCT info:
- version: 4.0.0-beta.5
- path: /Users/shazeebm/sct_4.0.0-beta.5
OS: osx (Darwin-15.6.0-x86_64-i386-64bit)
CPU cores: Available: 2, Used by SCT: 2
RAM: Primary memory available: 4.00 gigabytes
Check Python executable.............................[OK]
Using bundled python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.16.4)
Check if cryptography is installed..................[OK] (2.7)
Check if dipy is installed..........................[OK] (0.16.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.9.0)
Check if Keras is installed.........................[FAIL]
Check if matplotlib is installed....................[OK] (3.1.0)
Check if nibabel is installed.......................[OK] (2.4.1)
Check if pandas is installed........................[OK] (0.24.2)
Check if psutil is installed........................[OK] (5.6.2)
Check if pyqt5 is installed.........................[OK]
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.22.0)
Check if scipy is installed.........................[OK] (1.3.0)
Check if scikit-image is installed..................[OK] (0.15.0)
Check if scikit-learn is installed..................[OK] (0.21.2)
Check if tensorflow is installed....................[FAIL]
Check if xlrd is installed..........................[OK] (1.2.0)
Check if xlutils is installed.......................[OK]
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.32.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.3)
Check if git+https://github.com/jcohenadad/nipy.git is installed[OK] (0.5.0.dev)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if figure can be opened.......................[OK]
ipac-imac:sct shazeebm$ sct_testing
Trying URL: https://osf.io/z8gaj/?action=download
Downloading 20180125_sct_testing_data.zip...
Status: 100%|##############################################################################################| 6.78M/6.78M [00:02<00:00, 2.91MB/s]
Check if folder already exists...
Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct
Remove temporary file...
Done!
Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 2 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_warp_template sct_resample sct_convert sct_image sct_maths sct_merge_images sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_create_noisemask sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_label_utils sct_process_segmentation sct_propseg sct_register_multimodal sct_straighten_spinalcord sct_register_to_template sct_smooth_spinalcord sct_label_vertebrae
Checking sct_deepseg_gm.............................[FAIL]
Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613152934.264374-_89ayj9o/sct_deepseg_gm:
====================================================================================================
sct_deepseg_gm -i /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2s/t2s_uncropped.nii.gz -igt /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2s/t2s_uncropped_gmseg_manual.nii.gz -o sct_deepseg_gm/output.nii.gz -qc testing-qc -m large -thr 0.999 -v 1
====================================================================================================
Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_gm.py", line 142, in <module>
run_main()
File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_gm.py", line 120, in run_main
from spinalcordtoolbox.deepseg_gm import deepseg_gm
File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_gm/deepseg_gm.py", line 30, in <module>
from keras import backend as K
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
from . import utils
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
from . import conv_utils
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
from .. import backend as K
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
from .tensorflow_backend import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
import tensorflow as tf
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
from tensorflow.python import pywrap_tensorflow
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
raise ImportError(msg)
ImportError: Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
Failed to load the native TensorFlow runtime.
See https://www.tensorflow.org/install/errors
for some common reasons and solutions. Include the entire stack trace
above this error message when asking for help.
Checking sct_deepseg_lesion.........................[FAIL]
Got exception: Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
Failed to load the native TensorFlow runtime.
See https://www.tensorflow.org/install/errors
for some common reasons and solutions. Include the entire stack trace
above this error message when asking for help.
Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 180, in process_function
param_test = test_function(param_test)
File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 495, in test_function
module_function_to_test = importlib.import_module(param_test.function_to_test)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 994, in _gcd_import
File "<frozen importlib._bootstrap>", line 971, in _find_and_load
File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_lesion.py", line 24, in <module>
from spinalcordtoolbox.deepseg_lesion.core import deep_segmentation_MSlesion
File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_lesion/core.py", line 19, in <module>
from spinalcordtoolbox.deepseg_sc.core import find_centerline, crop_image_around_centerline, uncrop_image, _normalize_data
File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/core.py", line 14, in <module>
from spinalcordtoolbox.deepseg_sc.cnn_models import nn_architecture_seg, nn_architecture_ctr
File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/cnn_models.py", line 18, in <module>
from keras.layers import Input, Conv2D, Conv2DTranspose
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
from . import utils
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
from . import conv_utils
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
from .. import backend as K
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
from .tensorflow_backend import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
import tensorflow as tf
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
from tensorflow.python import pywrap_tensorflow
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
raise ImportError(msg)
ImportError: Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
Failed to load the native TensorFlow runtime.
See https://www.tensorflow.org/install/errors
for some common reasons and solutions. Include the entire stack trace
above this error message when asking for help.
Checking sct_deepseg_sc.............................[FAIL]
Got exception: Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
Failed to load the native TensorFlow runtime.
See https://www.tensorflow.org/install/errors
for some common reasons and solutions. Include the entire stack trace
above this error message when asking for help.
Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 180, in process_function
param_test = test_function(param_test)
File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 495, in test_function
module_function_to_test = importlib.import_module(param_test.function_to_test)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 994, in _gcd_import
File "<frozen importlib._bootstrap>", line 971, in _find_and_load
File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_sc.py", line 21, in <module>
from spinalcordtoolbox.deepseg_sc.core import deep_segmentation_spinalcord
File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/core.py", line 14, in <module>
from spinalcordtoolbox.deepseg_sc.cnn_models import nn_architecture_seg, nn_architecture_ctr
File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/cnn_models.py", line 18, in <module>
from keras.layers import Input, Conv2D, Conv2DTranspose
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
from . import utils
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
from . import conv_utils
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
from .. import backend as K
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
from .tensorflow_backend import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
import tensorflow as tf
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
from tensorflow.python import pywrap_tensorflow
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
raise ImportError(msg)
ImportError: Traceback (most recent call last):
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
Failed to load the native TensorFlow runtime.
See https://www.tensorflow.org/install/errors
for some common reasons and solutions. Include the entire stack trace
above this error message when asking for help.
Checking sct_analyze_lesion.........................[OK]
Checking sct_analyze_texture........................[OK]
Checking sct_apply_transfo..........................[OK]
Checking sct_warp_template..........................[OK]
Checking sct_resample...............................[OK]
Checking sct_convert................................[OK]
Checking sct_image..................................[OK]
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[OK]
Checking sct_compute_ernst_angle....................[OK]
Checking sct_compute_hausdorff_distance.............[OK]
Checking sct_compute_mtr............................[OK]
Checking sct_compute_mscc...........................[OK]
Checking sct_compute_snr............................[OK]
Checking sct_concat_transfo.........................[OK]
Checking sct_create_mask............................[OK]
Checking sct_crop_image.............................[OK]
Checking sct_dice_coefficient.......................[OK]
Checking sct_detect_pmj.............................[OK]
Checking sct_dmri_compute_dti.......................[OK]
Checking sct_dmri_concat_bvals......................[OK]
Checking sct_dmri_concat_bvecs......................[OK]
Checking sct_dmri_create_noisemask..................[OK]
Checking sct_dmri_compute_bvalue....................[OK]
Checking sct_dmri_moco..............................[OK]
Checking sct_dmri_separate_b0_and_dwi...............[OK]
Checking sct_dmri_transpose_bvecs...................[OK]
Checking sct_extract_metric.........................[OK]
Checking sct_flatten_sagittal.......................[FAIL]
Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613152934.264374-_89ayj9o/sct_flatten_sagittal:
====================================================================================================
sct_flatten_sagittal -i /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2/t2.nii.gz -s /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2/t2_seg.nii.gz -v 1
====================================================================================================
Checking sct_fmri_compute_tsnr......................[OK]
Checking sct_fmri_moco..............................[OK]
Checking sct_get_centerline.........................[OK]
Checking sct_label_utils............................[OK]
Checking sct_process_segmentation...................[FAIL]
Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613152934.264374-_89ayj9o/sct_process_segmentation:
====================================================================================================
sct_process_segmentation -i /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2/t2_seg.nii.gz -vertfile ./label/template/PAM50_levels.nii.gz -r 1 -angle-corr 1 -v 1
====================================================================================================
Compute shape analysis: 0%| | 0/55 [00:00<?, ?iter/s]
Checking sct_propseg................................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_straighten_spinalcord..................[OK]
Checking sct_register_to_template...................[OK]
Checking sct_smooth_spinalcord......................[OK]
Checking sct_label_vertebrae........................[OK]
status: [1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0]
Failures: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc sct_flatten_sagittal sct_process_segmentation
Finished! Elapsed time: 344s