Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ImportError: cannot import name _validate_lengths on joplin #2240

Closed
Nicolas-Pinon opened this issue Apr 24, 2019 · 14 comments
Closed

ImportError: cannot import name _validate_lengths on joplin #2240

Nicolas-Pinon opened this issue Apr 24, 2019 · 14 comments
Labels
bug category: fixes an error in the code

Comments

@Nicolas-Pinon
Copy link
Contributor

When trying to use sct_propseg or sct_deepseg_sc or sct_label_vertebrae (I think the list goes on and on) on joplin, I am facing this issue (copy of the terminal) :

u100542@joplin:~/sct$ sct_label_vertebrae 
Traceback (most recent call last):
  File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_label_vertebrae.py", line 25, in <module>
    from spinalcordtoolbox.vertebrae.detect_c2c3 import detect_c2c3
  File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/vertebrae/detect_c2c3.py", line 24, in <module>
    from sct_flatten_sagittal import flatten_sagittal
  File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_flatten_sagittal.py", line 19, in <module>
    from skimage import transform, img_as_float
  File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
    from .util.dtype import *
  File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
    from .arraycrop import crop
  File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
    from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name _validate_lengths

This has been tested on master, commit 1251241008f8563bd4ff6244ce3722511af7adaa
@Nicolas-Pinon Nicolas-Pinon added the bug category: fixes an error in the code label Apr 24, 2019
@jcohenadad
Copy link
Member

could you please run sct_check_dependencies and sct_testing and copy/paste the output?

@Nicolas-Pinon
Copy link
Contributor Author

Nicolas-Pinon commented Apr 25, 2019 •
edited

Results of sct_check_dependencies 
`u100542@joplin:~$ sct_check_dependencies 
SCT info:
- version: git-master-1251241008f8563bd4ff6244ce3722511af7adaa
- path: /home/GRAMES.POLYMTL.CA/u100542/sct
OS: linux (Linux-4.4.0-142-generic-x86_64-with-debian-stretch-sid)
CPU cores: Available: 128, Used by SCT: 128
RAM: MemTotal:       264009372 kB
total        used        free      shared  buff/cache   available
Mem:         257821        1016      191441          18       65363      255208
Swap:           975           0         975
Check Python executable.............................[OK]
  Using bundled python 2.7.12 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:42:40) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] at /home/GRAMES.POLYMTL.CA/u100542/sct/python/bin/python
Check if data are installed.........................[OK]
Check if Keras is installed.........................[OK] (2.2.4)
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 matplotlib is installed....................[OK] (1.5.3)
Check if nibabel is installed.......................[OK] (2.4.0)
Check if nipy is installed..........................[OK] (0.4.2)
Check if pandas is installed........................[OK] (0.23.4)
Check if psutil is installed........................[OK] (5.6.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.21.0)
Check if numpy is installed.........................[OK] (1.16.0)
Check if scipy is installed.........................[OK] (1.2.1)
**Check if scikit-image is installed..................[FAIL]**
Check if scikit-learn (0.17.1) is installed.........[OK]
Check if tensorflow (1.3.0) is installed............[OK]
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] (4.31.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.24.2)
Check if portalocker is installed...................[OK] (1.4.0)
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]`
Results of sct_testing 

u100542@joplin:~$ sct_testing 

Trying URL: https://osf.io/z8gaj/?action=download
Downloading 20180125_sct_testing_data.zip...
Status: 100%|##########| 6.78M/6.78M [00:00<00:00, 41.4MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542

Remove temporary file...
Done!

Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 128 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_segment_graymatter sct_smooth_spinalcord sct_label_vertebrae
Checking sct_deepseg_gm.............................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_deepseg_gm.py", line 18, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_deepseg_lesion.........................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_deepseg_lesion.py", line 24, in <module>
       from spinalcordtoolbox.deepseg_lesion.core import deep_segmentation_MSlesion
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/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 "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/deepseg_sc/core.py", line 10, in <module>
       from skimage.exposure import rescale_intensity
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_deepseg_sc.............................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_deepseg_sc.py", line 21, in <module>
       from spinalcordtoolbox.deepseg_sc.core import deep_segmentation_spinalcord
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/deepseg_sc/core.py", line 10, in <module>
       from skimage.exposure import rescale_intensity
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_analyze_lesion.........................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_analyze_lesion.py", line 17, in <module>
       from skimage.measure import label
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_analyze_texture........................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_analyze_texture.py", line 20, in <module>
       from skimage.feature import greycomatrix, greycoprops
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_apply_transfo..........................[OK]
Checking sct_warp_template..........................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_warp_template.py", line 19, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
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.............................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_detect_pmj.py", line 25, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
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]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_flatten_sagittal.py", line 19, in <module>
       from skimage import transform, img_as_float
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
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]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_process_segmentation.py", line 25, in <module>
       from spinalcordtoolbox import process_seg
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/process_seg.py", line 9, in <module>
       from skimage import measure, transform
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_propseg................................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_propseg.py", line 29, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_register_multimodal....................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_register_multimodal.py", line 44, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_register_multimodal.py", line 44, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_register_multimodal.py", line 44, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_register_multimodal.py", line 44, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_straighten_spinalcord..................[OK]
Checking sct_register_to_template...................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_register_to_template.py", line 27, in <module>
       from sct_register_multimodal import Paramreg, ParamregMultiStep, register
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_register_multimodal.py", line 44, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_register_to_template.py", line 27, in <module>
       from sct_register_multimodal import Paramreg, ParamregMultiStep, register
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_register_multimodal.py", line 44, in <module>
       from spinalcordtoolbox.reports.qc import generate_qc
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/reports/qc.py", line 19, in <module>
       import skimage
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_segment_graymatter.....................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_segment_graymatter.py", line 56, in <module>
       import sct_process_segmentation
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_process_segmentation.py", line 25, in <module>
       from spinalcordtoolbox import process_seg
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/process_seg.py", line 9, in <module>
       from skimage import measure, transform
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
Checking sct_smooth_spinalcord......................[OK]
Checking sct_label_vertebrae........................[FAIL]
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_label_vertebrae.py", line 25, in <module>
       from spinalcordtoolbox.vertebrae.detect_c2c3 import detect_c2c3
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/vertebrae/detect_c2c3.py", line 24, in <module>
       from sct_flatten_sagittal import flatten_sagittal
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_flatten_sagittal.py", line 19, in <module>
       from skimage import transform, img_as_float
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
   Got exception: cannot import name _validate_lengths
   Traceback (most recent call last):
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_testing.py", line 494, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/importlib/__init__.py", line 37, in import_module
       __import__(name)
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_label_vertebrae.py", line 25, in <module>
       from spinalcordtoolbox.vertebrae.detect_c2c3 import detect_c2c3
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/spinalcordtoolbox/vertebrae/detect_c2c3.py", line 24, in <module>
       from sct_flatten_sagittal import flatten_sagittal
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/scripts/sct_flatten_sagittal.py", line 19, in <module>
       from skimage import transform, img_as_float
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
       from .util.dtype import *
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 7, in <module>
       from .arraycrop import crop
     File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
       from numpy.lib.arraypad import _validate_lengths
   ImportError: cannot import name _validate_lengths
status: [1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 1]
Failures: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc sct_analyze_lesion sct_analyze_texture sct_warp_template sct_detect_pmj sct_flatten_sagittal sct_process_segmentation sct_propseg sct_register_multimodal sct_register_to_template sct_segment_graymatter sct_label_vertebrae
Finished! Elapsed time: 92s

There seem to have a problem with scikit-image

@Nicolas-Pinon
Copy link
Contributor Author

Nicolas-Pinon commented Apr 25, 2019 •
edited

Results of install_sct 

u100542@joplin:~/sct$ ./install_sct

Welcome to the SCT installer!

SCT version ......... dev
Installation type ... in-place
Operating system .... linux
sudo mode ........... 0

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.
Do you agree to help us improve SCT? [y]es/[n]o: no
--> Crash reports will not be sent.

SCT will be installed here: [/home/GRAMES.POLYMTL.CA/u100542/sct]
Do you agree? [y]es/[n]o: yes

Skipping copy of source files (source and destination folders are the same)

Removing sct and isct softlink from /home/GRAMES.POLYMTL.CA/u100542/sct/bin

Installing conda...
>> rm -rf /home/GRAMES.POLYMTL.CA/u100542/sct/python
>> mkdir -p /home/GRAMES.POLYMTL.CA/u100542/sct/python
--2019-04-24 20:51:03--  https://repo.continuum.io/miniconda/Miniconda2-4.1.11-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.200.79, 104.18.201.79, 2606:4700::6812:c84f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.200.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 27792209 (27M) [application/x-sh]
Saving to: ‘/tmp/tmp.JOflf8OUL2/miniconda.sh’

/tmp/tmp.JOflf8OUL2 100%[===================>]  26.50M   112MB/s    in 0.2s    

2019-04-24 20:51:08 (112 MB/s) - ‘/tmp/tmp.JOflf8OUL2/miniconda.sh’ saved [27792209/27792209]

exit status is 0
>> bash /tmp/tmp.JOflf8OUL2/miniconda.sh -p /home/GRAMES.POLYMTL.CA/u100542/sct/python -b -f
PREFIX=/home/GRAMES.POLYMTL.CA/u100542/sct/python
installing: python-2.7.12-1 ...
installing: conda-env-2.5.2-py27_0 ...
installing: openssl-1.0.2h-1 ...
installing: pycosat-0.6.1-py27_1 ...
installing: pyyaml-3.11-py27_4 ...
installing: readline-6.2-2 ...
installing: requests-2.10.0-py27_0 ...
installing: ruamel_yaml-0.11.14-py27_0 ...
installing: sqlite-3.13.0-0 ...
installing: tk-8.5.18-0 ...
installing: yaml-0.1.6-0 ...
installing: zlib-1.2.8-3 ...
installing: conda-4.1.11-py27_0 ...
installing: pycrypto-2.6.1-py27_4 ...
installing: pip-8.1.2-py27_0 ...
installing: wheel-0.29.0-py27_0 ...
installing: setuptools-23.0.0-py27_0 ...
Python 2.7.12 :: Continuum Analytics, Inc.
creating default environment...
using -f (force) option
installation finished.
Conda installation successful
>> . /home/GRAMES.POLYMTL.CA/u100542/sct/python/bin/activate /home/GRAMES.POLYMTL.CA/u100542/sct/python
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /home/GRAMES.POLYMTL.CA/u100542/sct/python:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    conda-env-2.6.0            |                1           2 KB  conda-forge
    libffi-3.2.1               |                3          47 KB  conda-forge
    asn1crypto-0.24.0          |        py27_1003         154 KB  conda-forge
    certifi-2019.3.9           |           py27_0         149 KB  conda-forge
    chardet-3.0.4              |        py27_1003         180 KB  conda-forge
    decorator-4.4.0            |             py_0          11 KB  conda-forge
    enum34-1.1.6               |        py27_1001          56 KB  conda-forge
    functools32-3.2.3.2        |             py_3          15 KB  conda-forge
    futures-3.2.0              |        py27_1000          24 KB  conda-forge
    idna-2.8                   |        py27_1000         133 KB  conda-forge
    ipaddress-1.0.22           |             py_1          18 KB  conda-forge
    ipython_genutils-0.2.0     |             py_1          21 KB  conda-forge
    pycosat-0.6.3              |           py27_0         200 KB  conda-forge
    pycparser-2.19             |           py27_1         172 KB  conda-forge
    pysocks-1.6.8              |        py27_1002          22 KB  conda-forge
    pytz-2019.1                |             py_0         227 KB  conda-forge
    pyyaml-3.12                |           py27_1         368 KB  conda-forge
    six-1.12.0                 |        py27_1000          21 KB  conda-forge
    cffi-1.11.5                |           py27_0         390 KB  conda-forge
    jsonschema-2.6.0           |        py27_1002          61 KB  conda-forge
    python-dateutil-2.8.0      |             py_0         219 KB  conda-forge
    setuptools-41.0.1          |           py27_0         650 KB  conda-forge
    traitlets-4.3.2            |        py27_1000         125 KB  conda-forge
    clyent-1.2.2               |             py_1           9 KB  conda-forge
    cryptography-2.2.1         |           py27_0         856 KB  conda-forge
    jupyter_core-4.4.0         |             py_0          44 KB  conda-forge
    nbformat-4.4.0             |             py_1          91 KB  conda-forge
    pyopenssl-19.0.0           |           py27_0          79 KB  conda-forge
    urllib3-1.24.2             |           py27_0         147 KB  conda-forge
    requests-2.21.0            |        py27_1000          83 KB  conda-forge
    anaconda-client-1.7.2      |             py_0          69 KB  conda-forge
    conda-4.6.14               |           py27_0         2.1 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         6.6 MB

The following NEW packages will be INSTALLED:

    anaconda-client:  1.7.2-py_0       conda-forge
    asn1crypto:       0.24.0-py27_1003 conda-forge
    certifi:          2019.3.9-py27_0  conda-forge
    cffi:             1.11.5-py27_0    conda-forge
    chardet:          3.0.4-py27_1003  conda-forge
    clyent:           1.2.2-py_1       conda-forge
    cryptography:     2.2.1-py27_0     conda-forge
    decorator:        4.4.0-py_0       conda-forge
    enum34:           1.1.6-py27_1001  conda-forge
    functools32:      3.2.3.2-py_3     conda-forge
    futures:          3.2.0-py27_1000  conda-forge
    idna:             2.8-py27_1000    conda-forge
    ipaddress:        1.0.22-py_1      conda-forge
    ipython_genutils: 0.2.0-py_1       conda-forge
    jsonschema:       2.6.0-py27_1002  conda-forge
    jupyter_core:     4.4.0-py_0       conda-forge
    libffi:           3.2.1-3          conda-forge
    nbformat:         4.4.0-py_1       conda-forge
    pycparser:        2.19-py27_1      conda-forge
    pyopenssl:        19.0.0-py27_0    conda-forge
    pysocks:          1.6.8-py27_1002  conda-forge
    python-dateutil:  2.8.0-py_0       conda-forge
    pytz:             2019.1-py_0      conda-forge
    six:              1.12.0-py27_1000 conda-forge
    traitlets:        4.3.2-py27_1000  conda-forge
    urllib3:          1.24.2-py27_0    conda-forge

The following packages will be UPDATED:

    conda:            4.1.11-py27_0                --> 4.6.14-py27_0    conda-forge
    conda-env:        2.5.2-py27_0                 --> 2.6.0-1          conda-forge
    pycosat:          0.6.1-py27_1                 --> 0.6.3-py27_0     conda-forge
    pyyaml:           3.11-py27_4                  --> 3.12-py27_1      conda-forge
    requests:         2.10.0-py27_0                --> 2.21.0-py27_1000 conda-forge
    setuptools:       23.0.0-py27_0                --> 41.0.1-py27_0    conda-forge

Fetching packages ...
conda-env-2.6. 100% |################################| Time: 0:00:00   3.33 MB/s
libffi-3.2.1-3 100% |################################| Time: 0:00:00  43.23 MB/s
asn1crypto-0.2 100% |################################| Time: 0:00:00  25.21 MB/s
certifi-2019.3 100% |################################| Time: 0:00:00  29.63 MB/s
chardet-3.0.4- 100% |################################| Time: 0:00:00  25.23 MB/s
decorator-4.4. 100% |################################| Time: 0:00:00   9.04 MB/s
enum34-1.1.6-p 100% |################################| Time: 0:00:00  18.58 MB/s
functools32-3. 100% |################################| Time: 0:00:00  11.89 MB/s
futures-3.2.0- 100% |################################| Time: 0:00:00  14.06 MB/s
idna-2.8-py27_ 100% |################################| Time: 0:00:00  25.31 MB/s
ipaddress-1.0. 100% |################################| Time: 0:00:00  10.68 MB/s
ipython_genuti 100% |################################| Time: 0:00:00  12.31 MB/s
pycosat-0.6.3- 100% |################################| Time: 0:00:00  25.25 MB/s
pycparser-2.19 100% |################################| Time: 0:00:00  30.06 MB/s
pysocks-1.6.8- 100% |################################| Time: 0:00:00  12.66 MB/s
pytz-2019.1-py 100% |################################| Time: 0:00:00  28.02 MB/s
pyyaml-3.12-py 100% |################################| Time: 0:00:00  28.69 MB/s
six-1.12.0-py2 100% |################################| Time: 0:00:00  14.43 MB/s
cffi-1.11.5-py 100% |################################| Time: 0:00:00  28.50 MB/s
jsonschema-2.6 100% |################################| Time: 0:00:00  25.31 MB/s
python-dateuti 100% |################################| Time: 0:00:00  29.56 MB/s
setuptools-41. 100% |################################| Time: 0:00:00  33.21 MB/s
traitlets-4.3. 100% |################################| Time: 0:00:00  26.77 MB/s
clyent-1.2.2-p 100% |################################| Time: 0:00:00   9.34 MB/s
cryptography-2 100% |################################| Time: 0:00:00  34.18 MB/s
jupyter_core-4 100% |################################| Time: 0:00:00  21.08 MB/s
nbformat-4.4.0 100% |################################| Time: 0:00:00  22.44 MB/s
pyopenssl-19.0 100% |################################| Time: 0:00:00  22.29 MB/s
urllib3-1.24.2 100% |################################| Time: 0:00:00  26.25 MB/s
requests-2.21. 100% |################################| Time: 0:00:00  24.36 MB/s
anaconda-clien 100% |################################| Time: 0:00:00  19.90 MB/s
conda-4.6.14-p 100% |################################| Time: 0:00:00  35.86 MB/s
Extracting packages ...
[      COMPLETE      ]|###################################################| 100%
Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%
Warning: 'conda-forge' already in 'channels' list, moving to the top

Installing Python dependencies...
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /home/GRAMES.POLYMTL.CA/u100542/sct/python

  added / updated specs:
    - cryptography
    - matplotlib
    - mkl-service
    - numpy
    - pandas
    - pip
    - psutil
    - pyqt=4
    - requests
    - scikit-image
    - scikit-learn=0.17
    - scipy
    - tensorflow==1.3.0
    - xlrd
    - xlutils
    - xlwt


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    backports-1.0              |             py_2           4 KB  conda-forge
    backports.weakref-1.0rc1   |           py27_1           7 KB  conda-forge
    blas-1.1                   |         openblas           1 KB  conda-forge
    bleach-1.5.0               |           py27_0          23 KB  conda-forge
    ca-certificates-2019.3.9   |       hecc5488_0         146 KB  conda-forge
    cairo-1.14.6               |                0         1.2 MB  conda-forge
    cryptography-2.5           |   py27hb7f436b_1         634 KB  conda-forge
    cycler-0.10.0              |             py_1           8 KB  conda-forge
    dask-core-1.2.0            |             py_0         530 KB  conda-forge
    fontconfig-2.11.1          |                6         876 KB  conda-forge
    freetype-2.6.3             |                1         2.8 MB  conda-forge
    funcsigs-1.0.2             |             py_3          14 KB  conda-forge
    gettext-0.19.8.1           |    hc5be6a0_1002         3.6 MB  conda-forge
    glib-2.51.4                |                0         6.0 MB  conda-forge
    harfbuzz-1.3.4             |                0         3.4 MB  conda-forge
    html5lib-0.9999999         |           py27_0         187 KB  conda-forge
    icu-56.1                   |                4        21.9 MB  conda-forge
    imageio-2.5.0              |           py27_0         3.4 MB  conda-forge
    intel-openmp-2019.3        |              199         886 KB
    jpeg-9c                    |    h14c3975_1001         251 KB  conda-forge
    libblas-3.8.0              |5_h6e990d7_netlib         181 KB  conda-forge
    libcblas-3.8.0             |5_h6e990d7_netlib          47 KB  conda-forge
    libgcc-ng-8.2.0            |       hdf63c60_1         7.6 MB
    libgfortran-3.0.0          |                1         281 KB  conda-forge
    libgfortran-ng-7.3.0       |       hdf63c60_0         1.3 MB
    libiconv-1.15              |    h516909a_1005         2.0 MB  conda-forge
    liblapack-3.8.0            |5_h6e990d7_netlib         2.9 MB  conda-forge
    libpng-1.6.28              |                1         301 KB  conda-forge
    libstdcxx-ng-8.2.0         |       hdf63c60_1         2.9 MB
    libtiff-4.0.7              |                0         488 KB  conda-forge
    libxml2-2.9.4              |                3         4.9 MB  conda-forge
    markdown-2.6.11            |             py_0          56 KB  conda-forge
    matplotlib-1.5.3           |      np111py27_2         6.6 MB  conda-forge
    mkl-2018.0.3               |                1       198.7 MB
    mkl-service-1.1.2          |   py27h651fb7a_4          11 KB
    mock-2.0.0                 |        py27_1001         102 KB  conda-forge
    networkx-2.2               |             py_1         1.1 MB  conda-forge
    numpy-1.11.3               |py27_blas_openblas_201         7.2 MB  conda-forge
    olefile-0.46               |             py_0          31 KB  conda-forge
    openblas-0.2.18            |                6        14.1 MB  conda-forge
    openssl-1.0.2r             |       h14c3975_0         3.1 MB  conda-forge
    pandas-0.23.4              |py27h637b7d7_1000         9.8 MB  conda-forge
    pango-1.40.3               |                0         923 KB  conda-forge
    pbr-5.1.3                  |             py_0          70 KB  conda-forge
    pcre-8.41                  |    hf484d3e_1003         249 KB  conda-forge
    pillow-4.0.0               |           py27_1         908 KB  conda-forge
    pip-19.1                   |           py27_0         1.8 MB  conda-forge
    pixman-0.38.0              |    h516909a_1003         594 KB  conda-forge
    protobuf-3.4.0             |           py27_0         5.6 MB  conda-forge
    psutil-5.6.1               |   py27h14c3975_0         308 KB  conda-forge
    pyparsing-2.4.0            |             py_0          55 KB  conda-forge
    pyqt-4.11.4                |           py27_3         3.5 MB  conda-forge
    pywavelets-1.0.3           |   py27hd352d35_1         4.4 MB  conda-forge
    qt-4.8.7                   |                3        31.3 MB  conda-forge
    scikit-image-0.13.1        |           py27_0        32.8 MB  conda-forge
    scikit-learn-0.17.1        |np111py27_blas_openblas_202         9.1 MB  conda-forge
    scipy-1.2.1                |   py27h09a28d5_1        18.1 MB  conda-forge
    sip-4.18                   |           py27_1         265 KB  conda-forge
    tensorflow-1.3.0           |           py27_0        36.2 MB  conda-forge
    toolz-0.9.0                |             py_1          42 KB  conda-forge
    webencodings-0.5.1         |             py_1          12 KB  conda-forge
    werkzeug-0.15.2            |             py_0         257 KB  conda-forge
    xlrd-1.2.0                 |             py_0         108 KB  conda-forge
    xlutils-2.0.0              |           py27_1          76 KB
    xlwt-1.3.0                 |             py_1          83 KB  conda-forge
    xz-5.2.4                   |    h14c3975_1001         366 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       456.4 MB

The following NEW packages will be INSTALLED:

  backports          conda-forge/noarch::backports-1.0-py_2
  backports.weakref  conda-forge/linux-64::backports.weakref-1.0rc1-py27_1
  blas               conda-forge/linux-64::blas-1.1-openblas
  bleach             conda-forge/linux-64::bleach-1.5.0-py27_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2019.3.9-hecc5488_0
  cairo              conda-forge/linux-64::cairo-1.14.6-0
  cycler             conda-forge/noarch::cycler-0.10.0-py_1
  dask-core          conda-forge/noarch::dask-core-1.2.0-py_0
  fontconfig         conda-forge/linux-64::fontconfig-2.11.1-6
  freetype           conda-forge/linux-64::freetype-2.6.3-1
  funcsigs           conda-forge/noarch::funcsigs-1.0.2-py_3
  gettext            conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
  glib               conda-forge/linux-64::glib-2.51.4-0
  harfbuzz           conda-forge/linux-64::harfbuzz-1.3.4-0
  html5lib           conda-forge/linux-64::html5lib-0.9999999-py27_0
  icu                conda-forge/linux-64::icu-56.1-4
  imageio            conda-forge/linux-64::imageio-2.5.0-py27_0
  intel-openmp       pkgs/main/linux-64::intel-openmp-2019.3-199
  jpeg               conda-forge/linux-64::jpeg-9c-h14c3975_1001
  libblas            conda-forge/linux-64::libblas-3.8.0-5_h6e990d7_netlib
  libcblas           conda-forge/linux-64::libcblas-3.8.0-5_h6e990d7_netlib
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-8.2.0-hdf63c60_1
  libgfortran        conda-forge/linux-64::libgfortran-3.0.0-1
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
  libiconv           conda-forge/linux-64::libiconv-1.15-h516909a_1005
  liblapack          conda-forge/linux-64::liblapack-3.8.0-5_h6e990d7_netlib
  libpng             conda-forge/linux-64::libpng-1.6.28-1
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-8.2.0-hdf63c60_1
  libtiff            conda-forge/linux-64::libtiff-4.0.7-0
  libxml2            conda-forge/linux-64::libxml2-2.9.4-3
  markdown           conda-forge/noarch::markdown-2.6.11-py_0
  matplotlib         conda-forge/linux-64::matplotlib-1.5.3-np111py27_2
  mkl                pkgs/main/linux-64::mkl-2018.0.3-1
  mkl-service        pkgs/main/linux-64::mkl-service-1.1.2-py27h651fb7a_4
  mock               conda-forge/linux-64::mock-2.0.0-py27_1001
  networkx           conda-forge/noarch::networkx-2.2-py_1
  numpy              conda-forge/linux-64::numpy-1.11.3-py27_blas_openblas_201
  olefile            conda-forge/noarch::olefile-0.46-py_0
  openblas           conda-forge/linux-64::openblas-0.2.18-6
  pandas             conda-forge/linux-64::pandas-0.23.4-py27h637b7d7_1000
  pango              conda-forge/linux-64::pango-1.40.3-0
  pbr                conda-forge/noarch::pbr-5.1.3-py_0
  pcre               conda-forge/linux-64::pcre-8.41-hf484d3e_1003
  pillow             conda-forge/linux-64::pillow-4.0.0-py27_1
  pixman             conda-forge/linux-64::pixman-0.38.0-h516909a_1003
  protobuf           conda-forge/linux-64::protobuf-3.4.0-py27_0
  psutil             conda-forge/linux-64::psutil-5.6.1-py27h14c3975_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.0-py_0
  pyqt               conda-forge/linux-64::pyqt-4.11.4-py27_3
  pywavelets         conda-forge/linux-64::pywavelets-1.0.3-py27hd352d35_1
  qt                 conda-forge/linux-64::qt-4.8.7-3
  scikit-image       conda-forge/linux-64::scikit-image-0.13.1-py27_0
  scikit-learn       conda-forge/linux-64::scikit-learn-0.17.1-np111py27_blas_openblas_202
  scipy              conda-forge/linux-64::scipy-1.2.1-py27h09a28d5_1
  sip                conda-forge/linux-64::sip-4.18-py27_1
  tensorflow         conda-forge/linux-64::tensorflow-1.3.0-py27_0
  toolz              conda-forge/noarch::toolz-0.9.0-py_1
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  werkzeug           conda-forge/noarch::werkzeug-0.15.2-py_0
  xlrd               conda-forge/noarch::xlrd-1.2.0-py_0
  xlutils            pkgs/main/linux-64::xlutils-2.0.0-py27_1
  xlwt               conda-forge/noarch::xlwt-1.3.0-py_1
  xz                 conda-forge/linux-64::xz-5.2.4-h14c3975_1001

The following packages will be UPDATED:

  cryptography                                 2.2.1-py27_0 --> 2.5-py27hb7f436b_1
  openssl                       pkgs/free::openssl-1.0.2h-1 --> conda-forge::openssl-1.0.2r-h14c3975_0
  pip                           pkgs/free::pip-8.1.2-py27_0 --> conda-forge::pip-19.1-py27_0



Downloading and Extracting Packages
cycler-0.10.0        | 8 KB      | ##################################### | 100% 
backports.weakref-1. | 7 KB      | ##################################### | 100% 
toolz-0.9.0          | 42 KB     | ##################################### | 100% 
pyparsing-2.4.0      | 55 KB     | ##################################### | 100% 
werkzeug-0.15.2      | 257 KB    | ##################################### | 100% 
glib-2.51.4          | 6.0 MB    | ##################################### | 100% 
libxml2-2.9.4        | 4.9 MB    | ##################################### | 100% 
libblas-3.8.0        | 181 KB    | ##################################### | 100% 
liblapack-3.8.0      | 2.9 MB    | ##################################### | 100% 
libpng-1.6.28        | 301 KB    | ##################################### | 100% 
cairo-1.14.6         | 1.2 MB    | ##################################### | 100% 
pip-19.1             | 1.8 MB    | ##################################### | 100% 
pixman-0.38.0        | 594 KB    | ##################################### | 100% 
numpy-1.11.3         | 7.2 MB    | ##################################### | 100% 
imageio-2.5.0        | 3.4 MB    | ##################################### | 100% 
libtiff-4.0.7        | 488 KB    | ##################################### | 100% 
pywavelets-1.0.3     | 4.4 MB    | ##################################### | 100% 
openssl-1.0.2r       | 3.1 MB    | ##################################### | 100% 
libgfortran-3.0.0    | 281 KB    | ##################################### | 100% 
freetype-2.6.3       | 2.8 MB    | ##################################### | 100% 
matplotlib-1.5.3     | 6.6 MB    | ##################################### | 100% 
psutil-5.6.1         | 308 KB    | ##################################### | 100% 
xlwt-1.3.0           | 83 KB     | ##################################### | 100% 
icu-56.1             | 21.9 MB   | ##################################### | 100% 
openblas-0.2.18      | 14.1 MB   | ##################################### | 100% 
fontconfig-2.11.1    | 876 KB    | ##################################### | 100% 
scikit-learn-0.17.1  | 9.1 MB    | ##################################### | 100% 
pcre-8.41            | 249 KB    | ##################################### | 100% 
pandas-0.23.4        | 9.8 MB    | ##################################### | 100% 
backports-1.0        | 4 KB      | ##################################### | 100% 
jpeg-9c              | 251 KB    | ##################################### | 100% 
xlrd-1.2.0           | 108 KB    | ##################################### | 100% 
xz-5.2.4             | 366 KB    | ##################################### | 100% 
bleach-1.5.0         | 23 KB     | ##################################### | 100% 
xlutils-2.0.0        | 76 KB     | ##################################### | 100% 
ca-certificates-2019 | 146 KB    | ##################################### | 100% 
pango-1.40.3         | 923 KB    | ##################################### | 100% 
intel-openmp-2019.3  | 886 KB    | ##################################### | 100% 
markdown-2.6.11      | 56 KB     | ##################################### | 100% 
html5lib-0.9999999   | 187 KB    | ##################################### | 100% 
cryptography-2.5     | 634 KB    | ##################################### | 100% 
networkx-2.2         | 1.1 MB    | ##################################### | 100% 
dask-core-1.2.0      | 530 KB    | ##################################### | 100% 
tensorflow-1.3.0     | 36.2 MB   | ##################################### | 100% 
pbr-5.1.3            | 70 KB     | ##################################### | 100% 
scikit-image-0.13.1  | 32.8 MB   | ##################################### | 100% 
libgfortran-ng-7.3.0 | 1.3 MB    | ##################################### | 100% 
blas-1.1             | 1 KB      | ##################################### | 100% 
harfbuzz-1.3.4       | 3.4 MB    | ##################################### | 100% 
libgcc-ng-8.2.0      | 7.6 MB    | ##################################### | 100% 
gettext-0.19.8.1     | 3.6 MB    | ##################################### | 100% 
libiconv-1.15        | 2.0 MB    | ##################################### | 100% 
protobuf-3.4.0       | 5.6 MB    | ##################################### | 100% 
pillow-4.0.0         | 908 KB    | ##################################### | 100% 
mkl-2018.0.3         | 198.7 MB  | ##################################### | 100% 
qt-4.8.7             | 31.3 MB   | ##################################### | 100% 
libstdcxx-ng-8.2.0   | 2.9 MB    | ##################################### | 100% 
scipy-1.2.1          | 18.1 MB   | ##################################### | 100% 
mock-2.0.0           | 102 KB    | ##################################### | 100% 
webencodings-0.5.1   | 12 KB     | ##################################### | 100% 
funcsigs-1.0.2       | 14 KB     | ##################################### | 100% 
olefile-0.46         | 31 KB     | ##################################### | 100% 
sip-4.18             | 265 KB    | ##################################### | 100% 
pyqt-4.11.4          | 3.5 MB    | ##################################### | 100% 
mkl-service-1.1.2    | 11 KB     | ##################################### | 100% 
libcblas-3.8.0       | 47 KB     | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///home/GRAMES.POLYMTL.CA/u100542/sct
Collecting Keras (from spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/5e/10/aa32dad071ce52b5502266b5c659451cfd6ffcbf14e6c8c4f16c0ff5aaab/Keras-2.2.4-py2.py3-none-any.whl
Collecting dipy (from spinalcordtoolbox===dev)
Requirement already satisfied: futures in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (3.2.0)
Collecting h5py (from spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/53/08/27e4e9a369321862ffdce80ff1770553e9daec65d98befb2e14e7478b698/h5py-2.9.0-cp27-cp27mu-manylinux1_x86_64.whl
Requirement already satisfied: matplotlib in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.5.3)
Collecting nibabel (from spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/bc/d4/64957ef575ac6b47d02f7195347e3444538ab633460ff6e99d2acc304223/nibabel-2.4.0-py2-none-any.whl
Collecting nipy (from spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/6f/8b/6534f0bdb4f3683151fed3f8e3f575006645a48fd338618eb1a3c688bffa/nipy-0.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Requirement already satisfied: pandas in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.23.4)
Requirement already satisfied: psutil in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (5.6.1)
Collecting raven (from spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/bd/8e/62e26a88c0a1bbae677200baf0767c1022321a6555634f8129e6d55c5ddc/raven-6.10.0-py2.py3-none-any.whl
Requirement already satisfied: requests in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.21.0)
Requirement already satisfied: numpy in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.11.3)
Requirement already satisfied: scipy in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.2.1)
Requirement already satisfied: scikit-image in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.13.1)
Requirement already satisfied: scikit-learn==0.17.1 in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.17.1)
Requirement already satisfied: tensorflow==1.3.0 in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.3.0)
Requirement already satisfied: xlrd in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.2.0)
Requirement already satisfied: xlutils in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.0.0)
Requirement already satisfied: xlwt in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.3.0)
Collecting tqdm (from spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/6c/4b/c38b5144cf167c4f52288517436ccafefe9dc01b8d1c190e18a6b154cd4a/tqdm-4.31.1-py2.py3-none-any.whl
Collecting transforms3d (from spinalcordtoolbox===dev)
Requirement already satisfied: urllib3[secure] in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.24.2)
Collecting portalocker (from spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/eb/48/bf5e330d7d6d57d92157480db9ccad84da86efd045205f7133a53b29aace/portalocker-1.4.0-py2.py3-none-any.whl
Requirement already satisfied: pyyaml in ./python/lib/python2.7/site-packages (from Keras->spinalcordtoolbox===dev) (3.12)
Collecting keras-preprocessing>=1.0.5 (from Keras->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/c0/bf/0315ef6a9fd3fc2346e85b0ff1f5f83ca17073f2c31ac719ab2e4da0d4a3/Keras_Preprocessing-1.0.9-py2.py3-none-any.whl
Requirement already satisfied: six>=1.9.0 in ./python/lib/python2.7/site-packages (from Keras->spinalcordtoolbox===dev) (1.12.0)
Collecting keras-applications>=1.0.6 (from Keras->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/90/85/64c82949765cfb246bbdaf5aca2d55f400f792655927a017710a78445def/Keras_Applications-1.0.7-py2.py3-none-any.whl
Collecting python-dateutil (from matplotlib->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl
Collecting pytz (from matplotlib->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl
Requirement already satisfied: cycler in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,>=1.5.6 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2.4.0)
Collecting bz2file; python_version < "3.0" (from nibabel->spinalcordtoolbox===dev)
Collecting sympy>=0.7.0 (from nipy->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/21/21/f4105795ca7f35c541d82c5b06be684dd2f5cb4f508fb487cd7aea4de776/sympy-1.4-py2.py3-none-any.whl
Collecting contextlib2; python_version < "3.2" (from raven->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/a2/71/8273a7eeed0aff6a854237ab5453bc9aa67deb49df4832801c21f0ff3782/contextlib2-0.5.5-py2.py3-none-any.whl
Requirement already satisfied: idna<2.9,>=2.5 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (2.8)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (3.0.4)
Requirement already satisfied: certifi>=2017.4.17 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (2019.3.9)
Requirement already satisfied: networkx>=1.8 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (2.2)
Requirement already satisfied: pillow>=2.1.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (4.4.0)
Requirement already satisfied: PyWavelets>=0.4.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (1.0.3)
Requirement already satisfied: protobuf>=3.3.0 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (3.4.0)
Requirement already satisfied: backports.weakref>=1.0rc1 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (1.0rc1)
Requirement already satisfied: wheel in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (0.29.0)
Collecting tensorflow-tensorboard<0.2.0,>=0.1.0 (from tensorflow==1.3.0->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/fb/34/14c23665a725c73932891e09b8f017a53aad545c9d5019d2817102dc5d9b/tensorflow_tensorboard-0.1.8-py2-none-any.whl
Requirement already satisfied: mock>=2.0.0 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (2.0.0)
Requirement already satisfied: pyOpenSSL>=0.14 in ./python/lib/python2.7/site-packages (from urllib3[secure]->spinalcordtoolbox===dev) (19.0.0)
Requirement already satisfied: cryptography>=1.3.4 in ./python/lib/python2.7/site-packages (from urllib3[secure]->spinalcordtoolbox===dev) (2.5)
Collecting ipaddress (from urllib3[secure]->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting mpmath>=0.19 (from sympy>=0.7.0->nipy->spinalcordtoolbox===dev)
Collecting decorator>=4.3.0 (from networkx>=1.8->scikit-image->spinalcordtoolbox===dev)
  Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl
Requirement already satisfied: olefile in ./python/lib/python2.7/site-packages (from pillow>=2.1.0->scikit-image->spinalcordtoolbox===dev) (0.46)
Requirement already satisfied: setuptools in ./python/lib/python2.7/site-packages (from protobuf>=3.3.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (41.0.1)
Requirement already satisfied: markdown>=2.6.8 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (2.6.11)
Requirement already satisfied: werkzeug>=0.11.10 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (0.15.2)
Requirement already satisfied: bleach==1.5.0 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (1.5.0)
Requirement already satisfied: html5lib==0.9999999 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (0.9999999)
Requirement already satisfied: funcsigs>=1; python_version < "3.3" in ./python/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (1.0.2)
Requirement already satisfied: pbr>=0.11 in ./python/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (5.1.3)
Requirement already satisfied: enum34; python_version < "3" in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (1.1.6)
Requirement already satisfied: asn1crypto>=0.21.0 in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (0.24.0)
Requirement already satisfied: cffi!=1.11.3,>=1.8 in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (1.11.5)
Requirement already satisfied: pycparser in ./python/lib/python2.7/site-packages (from cffi!=1.11.3,>=1.8->cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (2.19)
ERROR: traitlets 4.3.2 requires ipython_genutils, which is not installed.
Installing collected packages: keras-preprocessing, h5py, keras-applications, Keras, bz2file, nibabel, dipy, mpmath, sympy, nipy, contextlib2, raven, tqdm, transforms3d, portalocker, spinalcordtoolbox, python-dateutil, pytz, tensorflow-tensorboard, ipaddress, decorator
  Running setup.py develop for spinalcordtoolbox
Successfully installed Keras-2.2.4 bz2file-0.98 contextlib2-0.5.5 decorator-4.4.0 dipy-0.16.0 h5py-2.9.0 ipaddress-1.0.22 keras-applications-1.0.7 keras-preprocessing-1.0.9 mpmath-1.1.0 nibabel-2.4.0 nipy-0.4.2 portalocker-1.4.0 python-dateutil-2.8.0 pytz-2019.1 raven-6.10.0 spinalcordtoolbox sympy-1.4 tensorflow-tensorboard-0.1.8 tqdm-4.31.1 transforms3d-0.3.1
Checking if TensorFlow is working, if not attempting to install another version
TensorFlow seems to be working.
Checking if skimage is working, if not attempting work around it
skimage seems to be working.

Creating launchers for Python scripts...

Installing binaries...
>> . /home/GRAMES.POLYMTL.CA/u100542/sct/python/bin/activate /home/GRAMES.POLYMTL.CA/u100542/sct/python
>> sct_download_data -d binaries_debian -o /home/GRAMES.POLYMTL.CA/u100542/sct/bin
Folder /home/GRAMES.POLYMTL.CA/u100542/sct/bin has been created.

Trying URL: https://osf.io/z72vn/?action=download
Downloading 20181204_sct_binaries_linux.tar.gz...
Status: 100%|##########| 92.2M/92.2M [00:01<00:00, 60.7MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/bin

Remove temporary file...
Done!

All requirements installed!
>> . /home/GRAMES.POLYMTL.CA/u100542/sct/python/bin/activate /home/GRAMES.POLYMTL.CA/u100542/sct/python

Installing data...
>> rm -rf /home/GRAMES.POLYMTL.CA/u100542/sct/data
>> mkdir -p /home/GRAMES.POLYMTL.CA/u100542/sct/data
>> cd /home/GRAMES.POLYMTL.CA/u100542/sct/data
>> sct_download_data -d PAM50

Trying URL: https://osf.io/kc3jx/?action=download
Downloading 20181214_PAM50.zip...
Status: 100%|##########| 70.8M/70.8M [00:01<00:00, 45.2MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/data

Remove temporary file...
Done!

>> sct_download_data -d gm_model

Trying URL: https://osf.io/ugscu/?action=download
Downloading 20160922_gm_model.zip...
Status: 100%|##########| 10.3M/10.3M [00:00<00:00, 38.9MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/data

Remove temporary file...
Done!

>> sct_download_data -d optic_models

Trying URL: https://osf.io/g4fwn/?action=download
Downloading 20170413_optic_models.zip...
Status: 100%|##########| 17.7k/17.7k [00:00<00:00, 5.72MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/data

Remove temporary file...
Done!

>> sct_download_data -d pmj_models

Trying URL: https://osf.io/4gufr/?action=download
Downloading 20170922_pmj_models.zip...
Status: 100%|##########| 8.87k/8.87k [00:00<00:00, 6.93MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_sc_models

Trying URL: https://osf.io/avf97/?action=download
Downloading 20180610_deepseg_sc_models.zip...
Status: 100%|##########| 58.7M/58.7M [00:01<00:00, 50.3MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_gm_models

Trying URL: https://osf.io/b9y4x/?action=download
Downloading 20180205_deepseg_gm_models.zip...
Status: 100%|##########| 2.28M/2.28M [00:00<00:00, 13.9MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_lesion_models

Trying URL: https://osf.io/eg7v9/?action=download
Downloading 20180613_deepseg_lesion_models.zip...
Status: 100%|##########| 16.0M/16.0M [00:00<00:00, 50.9MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/data

Remove temporary file...
Done!

>> sct_download_data -d c2c3_disc_models

Trying URL: https://osf.io/t97ap/?action=download
Downloading 20190117_c2c3_disc_models.zip...
Status: 100%|##########| 8.94k/8.94k [00:00<00:00, 8.37MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/u100542/sct/data

Remove temporary file...
Done!


Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: no

Not adding /home/GRAMES.POLYMTL.CA/u100542/sct to $PATH
You can always add it later or call SCT functions with full path /home/GRAMES.POLYMTL.CA/u100542/sct/bin/sct_function

Validate installation...
SCT info:
- version: git-master-1251241008f8563bd4ff6244ce3722511af7adaa
- path: /home/GRAMES.POLYMTL.CA/u100542/sct
OS: linux (Linux-4.4.0-142-generic-x86_64-with-debian-stretch-sid)
CPU cores: Available: 128, Used by SCT: 128
RAM: MemTotal:       264009372 kB
total        used        free      shared  buff/cache   available
Mem:         257821        1011      191375          18       65435      255204
Swap:           975           0         975
Check Python executable.............................[OK]
  Using bundled python 2.7.12 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:42:40) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] at /home/GRAMES.POLYMTL.CA/u100542/sct/python/bin/python
Check if data are installed.........................[OK]
Check if Keras is installed.........................[OK] (2.2.4)
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 matplotlib is installed....................[OK] (1.5.3)
Check if nibabel is installed.......................[OK] (2.4.0)
Check if nipy is installed..........................[OK] (0.4.2)
Check if pandas is installed........................[OK] (0.23.4)
Check if psutil is installed........................[OK] (5.6.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.21.0)
Check if numpy is installed.........................[OK] (1.11.3)
Check if scipy is installed.........................[OK] (1.2.1)
Check if scikit-image is installed..................[OK] (0.13.1)
Check if scikit-learn (0.17.1) is installed.........[OK]
Check if tensorflow (1.3.0) is installed............[OK]
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] (4.31.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.24.2)
Check if portalocker is installed...................[OK] (1.4.0)
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]

To use SCT, please update your environment by running:

PATH+=":/home/GRAMES.POLYMTL.CA/u100542/sct/bin"
Installation finished successfully

Weird thing is when i do install no problem is detected

@jcohenadad
Copy link
Member

can't figure out how to make large chunks appear as "code"

here is an example

@jcohenadad
Copy link
Member

Hum, strange... maybe there was a glitch during the first installation, and when you installed the 2nd time scikit-image installed OK. What if you re-run sct_check_dependencies now?

@Nicolas-Pinon
Copy link
Contributor Author

Hum, strange... maybe there was a glitch during the first installation, and when you installed the 2nd time scikit-image installed OK. What if you re-run sct_check_dependencies now?

I had already re-installed sct before running everything (I always do when something's not right), so I guess it will be the same

@jcohenadad
Copy link
Member

ok, could you run sct_testing?

@Nicolas-Pinon
Copy link
Contributor Author

ok, could you run sct_testing?

It was already done in the comment but was TOTALLY not clear because of the presentation, now I edited everything it's a lot more clearer.

@alexfoias
Copy link
Contributor

alexfoias commented Apr 25, 2019 •
edited

@jcohenadad @Nicolas-Pinon
I tried the current master version 1251241008f8563bd4ff6244ce3722511af7adaa on joplin using my grames account without any problems.

./install_sct output:


alfoi@joplin:~/spinalcordtoolbox$ ./install_sct 

Welcome to the SCT installer!

SCT version ......... dev
Installation type ... in-place
Operating system .... linux
sudo mode ........... 0

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.
Do you agree to help us improve SCT? [y]es/[n]o: y
--> Crash reports will be sent to the SCT development team. Thank you!

SCT will be installed here: [/home/GRAMES.POLYMTL.CA/alfoi/spinalcordtoolbox]
Do you agree? [y]es/[n]o: n
Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0): /home/GRAMES.POLYMTL.CA/alfoi/sct  

Copying source files from /home/GRAMES.POLYMTL.CA/alfoi/spinalcordtoolbox to /home/GRAMES.POLYMTL.CA/alfoi/sct
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Installing conda...
>> rm -rf /home/GRAMES.POLYMTL.CA/alfoi/sct/python
>> mkdir -p /home/GRAMES.POLYMTL.CA/alfoi/sct/python
--2019-04-25 10:56:34--  https://repo.continuum.io/miniconda/Miniconda2-4.1.11-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.201.79, 104.18.200.79, 2606:4700::6812:c94f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.201.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 27792209 (27M) [application/x-sh]
Saving to: ‘/tmp/tmp.Tvdbl8Etp7/miniconda.sh’

/tmp/tmp.Tvdbl8Etp7/miniconda.sh          100%[====================================================================================>]  26.50M   112MB/s    in 0.2s    

2019-04-25 10:56:34 (112 MB/s) - ‘/tmp/tmp.Tvdbl8Etp7/miniconda.sh’ saved [27792209/27792209]

exit status is 0
>> bash /tmp/tmp.Tvdbl8Etp7/miniconda.sh -p /home/GRAMES.POLYMTL.CA/alfoi/sct/python -b -f
PREFIX=/home/GRAMES.POLYMTL.CA/alfoi/sct/python
installing: python-2.7.12-1 ...
installing: conda-env-2.5.2-py27_0 ...
installing: openssl-1.0.2h-1 ...
installing: pycosat-0.6.1-py27_1 ...
installing: pyyaml-3.11-py27_4 ...
installing: readline-6.2-2 ...
installing: requests-2.10.0-py27_0 ...
installing: ruamel_yaml-0.11.14-py27_0 ...
installing: sqlite-3.13.0-0 ...
installing: tk-8.5.18-0 ...
installing: yaml-0.1.6-0 ...
installing: zlib-1.2.8-3 ...
installing: conda-4.1.11-py27_0 ...
installing: pycrypto-2.6.1-py27_4 ...
installing: pip-8.1.2-py27_0 ...
installing: wheel-0.29.0-py27_0 ...
installing: setuptools-23.0.0-py27_0 ...
Python 2.7.12 :: Continuum Analytics, Inc.
creating default environment...
using -f (force) option
installation finished.
Conda installation successful
>> . /home/GRAMES.POLYMTL.CA/alfoi/sct/python/bin/activate /home/GRAMES.POLYMTL.CA/alfoi/sct/python
Fetching package metadata .......
Solving package specifications: ..........

Package plan for installation in environment /home/GRAMES.POLYMTL.CA/alfoi/sct/python:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    conda-env-2.6.0            |                0          502 B
    libffi-3.2.1               |                1          38 KB
    asn1crypto-0.22.0          |           py27_0         145 KB
    enum34-1.1.6               |           py27_0          53 KB
    idna-2.6                   |           py27_0         122 KB
    ipaddress-1.0.18           |           py27_0          31 KB
    pycparser-2.18             |           py27_0         165 KB
    pyparsing-2.2.0            |           py27_0          94 KB
    pytz-2017.2                |           py27_0         204 KB
    requests-2.14.2            |           py27_0         700 KB
    six-1.10.0                 |           py27_0          16 KB
    cffi-1.10.0                |           py27_0         329 KB
    clyent-1.2.2               |           py27_0          15 KB
    packaging-16.8             |           py27_0          30 KB
    python-dateutil-2.6.1      |           py27_0         236 KB
    anaconda-client-1.6.3      |           py27_0         129 KB
    cryptography-1.8.1         |           py27_0         850 KB
    pyopenssl-17.0.0           |           py27_0          74 KB
    conda-4.3.30               |   py27h6ae6dc7_0         507 KB
    ------------------------------------------------------------
                                           Total:         3.7 MB

The following NEW packages will be INSTALLED:

    anaconda-client: 1.6.3-py27_0 
    asn1crypto:      0.22.0-py27_0
    cffi:            1.10.0-py27_0
    clyent:          1.2.2-py27_0 
    cryptography:    1.8.1-py27_0 
    enum34:          1.1.6-py27_0 
    idna:            2.6-py27_0   
    ipaddress:       1.0.18-py27_0
    libffi:          3.2.1-1      
    packaging:       16.8-py27_0  
    pycparser:       2.18-py27_0  
    pyopenssl:       17.0.0-py27_0
    pyparsing:       2.2.0-py27_0 
    python-dateutil: 2.6.1-py27_0 
    pytz:            2017.2-py27_0
    six:             1.10.0-py27_0

The following packages will be UPDATED:

    conda:           4.1.11-py27_0 --> 4.3.30-py27h6ae6dc7_0
    conda-env:       2.5.2-py27_0  --> 2.6.0-0              
    requests:        2.10.0-py27_0 --> 2.14.2-py27_0        

Fetching packages ...
conda-env-2.6. 100% |#######################################################################################################################| Time: 0:00:00 393.71 kB/s
libffi-3.2.1-1 100% |#######################################################################################################################| Time: 0:00:00  18.38 MB/s
asn1crypto-0.2 100% |#######################################################################################################################| Time: 0:00:00  28.01 MB/s
enum34-1.1.6-p 100% |#######################################################################################################################| Time: 0:00:00  19.01 MB/s
idna-2.6-py27_ 100% |#######################################################################################################################| Time: 0:00:00  28.80 MB/s
ipaddress-1.0. 100% |#######################################################################################################################| Time: 0:00:00  17.83 MB/s
pycparser-2.18 100% |#######################################################################################################################| Time: 0:00:00  29.91 MB/s
pyparsing-2.2. 100% |#######################################################################################################################| Time: 0:00:00  30.64 MB/s
pytz-2017.2-py 100% |#######################################################################################################################| Time: 0:00:00  30.38 MB/s
requests-2.14. 100% |#######################################################################################################################| Time: 0:00:00  34.21 MB/s
six-1.10.0-py2 100% |#######################################################################################################################| Time: 0:00:00  10.96 MB/s
cffi-1.10.0-py 100% |#######################################################################################################################| Time: 0:00:00  32.48 MB/s
clyent-1.2.2-p 100% |#######################################################################################################################| Time: 0:00:00  12.02 MB/s
packaging-16.8 100% |#######################################################################################################################| Time: 0:00:00  16.59 MB/s
python-dateuti 100% |#######################################################################################################################| Time: 0:00:00  30.01 MB/s
anaconda-clien 100% |#######################################################################################################################| Time: 0:00:00  30.42 MB/s
cryptography-1 100% |#######################################################################################################################| Time: 0:00:00  37.21 MB/s
pyopenssl-17.0 100% |#######################################################################################################################| Time: 0:00:00  23.30 MB/s
conda-4.3.30-p 100% |#######################################################################################################################| Time: 0:00:00  32.79 MB/s
Extracting packages ...
[      COMPLETE      ]|##########################################################################################################################################| 100%
Unlinking packages ...
[      COMPLETE      ]|##########################################################################################################################################| 100%
Linking packages ...
[      COMPLETE      ]|##########################################################################################################################################| 100%

Installing Python dependencies...
Fetching package metadata .............
Solving package specifications: .

Package plan for installation in environment /home/GRAMES.POLYMTL.CA/alfoi/sct/python:

The following NEW packages will be INSTALLED:

    backports:         1.0-py_2                           conda-forge
    backports.weakref: 1.0rc1-py27_1                      conda-forge
    blas:              1.1-openblas                       conda-forge
    bleach:            1.5.0-py27_0                       conda-forge
    ca-certificates:   2019.3.9-hecc5488_0                conda-forge
    cairo:             1.14.6-0                           conda-forge
    certifi:           2019.3.9-py27_0                    conda-forge
    chardet:           3.0.4-py27_1003                    conda-forge
    cycler:            0.10.0-py_1                        conda-forge
    dask-core:         1.2.0-py_0                         conda-forge
    decorator:         4.4.0-py_0                         conda-forge
    fontconfig:        2.11.1-6                           conda-forge
    freetype:          2.6.3-1                            conda-forge
    funcsigs:          1.0.2-py_3                         conda-forge
    functools32:       3.2.3.2-py_3                       conda-forge
    futures:           3.2.0-py27_1000                    conda-forge
    gettext:           0.19.8.1-hc5be6a0_1002             conda-forge
    glib:              2.51.4-0                           conda-forge
    harfbuzz:          1.3.4-0                            conda-forge
    html5lib:          0.9999999-py27_0                   conda-forge
    icu:               56.1-4                             conda-forge
    imageio:           2.5.0-py27_0                       conda-forge
    intel-openmp:      2019.3-199                                    
    jpeg:              9c-h14c3975_1001                   conda-forge
    libblas:           3.8.0-5_h6e990d7_netlib            conda-forge
    libcblas:          3.8.0-5_h6e990d7_netlib            conda-forge
    libgcc-ng:         8.2.0-hdf63c60_1                              
    libgfortran:       3.0.0-1                            conda-forge
    libgfortran-ng:    7.3.0-hdf63c60_0                              
    libiconv:          1.15-h516909a_1005                 conda-forge
    liblapack:         3.8.0-5_h6e990d7_netlib            conda-forge
    libpng:            1.6.28-1                           conda-forge
    libstdcxx-ng:      8.2.0-hdf63c60_1                              
    libtiff:           4.0.7-0                            conda-forge
    libxml2:           2.9.4-3                            conda-forge
    markdown:          2.6.11-py_0                        conda-forge
    matplotlib:        1.5.3-np111py27_2                  conda-forge
    mkl:               2018.0.3-1                                    
    mkl-service:       1.1.2-py27h651fb7a_4                          
    mock:              2.0.0-py27_1001                    conda-forge
    networkx:          2.2-py_1                           conda-forge
    numpy:             1.11.3-py27_blas_openblas_201      conda-forge [blas_openblas]
    olefile:           0.46-py_0                          conda-forge
    openblas:          0.2.18-6                           conda-forge
    pandas:            0.23.4-py27h637b7d7_1000           conda-forge
    pango:             1.40.3-0                           conda-forge
    pbr:               5.1.3-py_0                         conda-forge
    pcre:              8.41-hf484d3e_1003                 conda-forge
    pillow:            4.0.0-py27_1                       conda-forge
    pixman:            0.38.0-h516909a_1003               conda-forge
    protobuf:          3.4.0-py27_0                       conda-forge
    psutil:            5.6.1-py27h14c3975_0               conda-forge
    pyqt:              4.11.4-py27_3                      conda-forge
    pysocks:           1.6.8-py27_1002                    conda-forge
    pywavelets:        1.0.3-py27hd352d35_1               conda-forge
    qt:                4.8.7-3                            conda-forge
    scikit-image:      0.13.1-py27_0                      conda-forge
    scikit-learn:      0.17.1-np111py27_blas_openblas_202 conda-forge [blas_openblas]
    scipy:             1.2.1-py27h09a28d5_1               conda-forge
    sip:               4.18-py27_1                        conda-forge
    tensorflow:        1.3.0-py27_0                       conda-forge
    toolz:             0.9.0-py_1                         conda-forge
    urllib3:           1.24.2-py27_0                      conda-forge
    webencodings:      0.5.1-py_1                         conda-forge
    werkzeug:          0.15.2-py_0                        conda-forge
    xlrd:              1.2.0-py_0                         conda-forge
    xlutils:           2.0.0-py27_1                                  
    xlwt:              1.3.0-py_1                         conda-forge
    xz:                5.2.4-h14c3975_1001                conda-forge

The following packages will be UPDATED:

    conda:             4.3.30-py27h6ae6dc7_0                          --> 4.6.14-py27_0           conda-forge
    conda-env:         2.6.0-0                                        --> 2.6.0-1                 conda-forge
    cryptography:      1.8.1-py27_0                                   --> 2.5-py27hb7f436b_1      conda-forge
    openssl:           1.0.2h-1                                       --> 1.0.2r-h14c3975_0       conda-forge
    pip:               8.1.2-py27_0                                   --> 19.1-py27_0             conda-forge
    pycosat:           0.6.1-py27_1                                   --> 0.6.3-py27h14c3975_1001 conda-forge
    requests:          2.14.2-py27_0                                  --> 2.21.0-py27_1000        conda-forge
    setuptools:        23.0.0-py27_0                                  --> 41.0.1-py27_0           conda-forge

ca-certificate 100% |#######################################################################################################################| Time: 0:00:00  23.77 MB/s
conda-env-2.6. 100% |#######################################################################################################################| Time: 0:00:00   3.40 MB/s
icu-56.1-4.tar 100% |#######################################################################################################################| Time: 0:00:00  47.80 MB/s
intel-openmp-2 100% |#######################################################################################################################| Time: 0:00:00  31.41 MB/s
libgcc-ng-8.2. 100% |#######################################################################################################################| Time: 0:00:00  45.52 MB/s
libgfortran-3. 100% |#######################################################################################################################| Time: 0:00:00  32.28 MB/s
libgfortran-ng 100% |#######################################################################################################################| Time: 0:00:00  32.06 MB/s
libstdcxx-ng-8 100% |#######################################################################################################################| Time: 0:00:00  41.54 MB/s
gettext-0.19.8 100% |#######################################################################################################################| Time: 0:00:00  36.47 MB/s
jpeg-9c-h14c39 100% |#######################################################################################################################| Time: 0:00:00  37.33 MB/s
libblas-3.8.0- 100% |#######################################################################################################################| Time: 0:00:00  37.85 MB/s
libiconv-1.15- 100% |#######################################################################################################################| Time: 0:00:00  42.47 MB/s
libpng-1.6.28- 100% |#######################################################################################################################| Time: 0:00:00  47.27 MB/s
mkl-2018.0.3-1 100% |#######################################################################################################################| Time: 0:00:03  60.71 MB/s
openblas-0.2.1 100% |#######################################################################################################################| Time: 0:00:00  45.82 MB/s
openssl-1.0.2r 100% |#######################################################################################################################| Time: 0:00:00  49.08 MB/s
pcre-8.41-hf48 100% |#######################################################################################################################| Time: 0:00:00  46.20 MB/s
pixman-0.38.0- 100% |#######################################################################################################################| Time: 0:00:00  49.48 MB/s
xz-5.2.4-h14c3 100% |#######################################################################################################################| Time: 0:00:00  50.91 MB/s
blas-1.1-openb 100% |#######################################################################################################################| Time: 0:00:00   2.81 MB/s
freetype-2.6.3 100% |#######################################################################################################################| Time: 0:00:00  49.04 MB/s
glib-2.51.4-0. 100% |#######################################################################################################################| Time: 0:00:00  49.39 MB/s
libcblas-3.8.0 100% |#######################################################################################################################| Time: 0:00:00  41.03 MB/s
liblapack-3.8. 100% |#######################################################################################################################| Time: 0:00:00  49.46 MB/s
libtiff-4.0.7- 100% |#######################################################################################################################| Time: 0:00:00  49.10 MB/s
libxml2-2.9.4- 100% |#######################################################################################################################| Time: 0:00:00  50.35 MB/s
backports-1.0- 100% |#######################################################################################################################| Time: 0:00:00   9.66 MB/s
certifi-2019.3 100% |#######################################################################################################################| Time: 0:00:00  41.69 MB/s
chardet-3.0.4- 100% |#######################################################################################################################| Time: 0:00:00  56.13 MB/s
dask-core-1.2. 100% |#######################################################################################################################| Time: 0:00:00  61.17 MB/s
decorator-4.4. 100% |#######################################################################################################################| Time: 0:00:00  26.11 MB/s
fontconfig-2.1 100% |#######################################################################################################################| Time: 0:00:00  62.42 MB/s
funcsigs-1.0.2 100% |#######################################################################################################################| Time: 0:00:00  32.80 MB/s
functools32-3. 100% |#######################################################################################################################| Time: 0:00:00  25.04 MB/s
futures-3.2.0- 100% |#######################################################################################################################| Time: 0:00:00  29.61 MB/s
markdown-2.6.1 100% |#######################################################################################################################| Time: 0:00:00  40.47 MB/s
mkl-service-1. 100% |#######################################################################################################################| Time: 0:00:00   9.38 MB/s
numpy-1.11.3-p 100% |#######################################################################################################################| Time: 0:00:00  48.27 MB/s
olefile-0.46-p 100% |#######################################################################################################################| Time: 0:00:00  47.89 MB/s
psutil-5.6.1-p 100% |#######################################################################################################################| Time: 0:00:00  63.34 MB/s
pycosat-0.6.3- 100% |#######################################################################################################################| Time: 0:00:00  31.03 MB/s
pysocks-1.6.8- 100% |#######################################################################################################################| Time: 0:00:00  13.66 MB/s
sip-4.18-py27_ 100% |#######################################################################################################################| Time: 0:00:00  36.02 MB/s
toolz-0.9.0-py 100% |#######################################################################################################################| Time: 0:00:00  28.40 MB/s
webencodings-0 100% |#######################################################################################################################| Time: 0:00:00  17.10 MB/s
werkzeug-0.15. 100% |#######################################################################################################################| Time: 0:00:00  35.82 MB/s
xlrd-1.2.0-py_ 100% |#######################################################################################################################| Time: 0:00:00  34.14 MB/s
xlwt-1.3.0-py_ 100% |#######################################################################################################################| Time: 0:00:00  31.17 MB/s
backports.weak 100% |#######################################################################################################################| Time: 0:00:00   9.70 MB/s
cairo-1.14.6-0 100% |#######################################################################################################################| Time: 0:00:00  36.34 MB/s
cycler-0.10.0- 100% |#######################################################################################################################| Time: 0:00:00  13.02 MB/s
html5lib-0.999 100% |#######################################################################################################################| Time: 0:00:00  34.77 MB/s
pillow-4.0.0-p 100% |#######################################################################################################################| Time: 0:00:00  32.81 MB/s
pywavelets-1.0 100% |#######################################################################################################################| Time: 0:00:00  43.58 MB/s
scipy-1.2.1-py 100% |#######################################################################################################################| Time: 0:00:00  50.15 MB/s
setuptools-41. 100% |#######################################################################################################################| Time: 0:00:00  50.22 MB/s
xlutils-2.0.0- 100% |#######################################################################################################################| Time: 0:00:00  20.95 MB/s
bleach-1.5.0-p 100% |#######################################################################################################################| Time: 0:00:00  18.50 MB/s
cryptography-2 100% |#######################################################################################################################| Time: 0:00:00  39.56 MB/s
harfbuzz-1.3.4 100% |#######################################################################################################################| Time: 0:00:00  46.62 MB/s
imageio-2.5.0- 100% |#######################################################################################################################| Time: 0:00:00  49.65 MB/s
networkx-2.2-p 100% |#######################################################################################################################| Time: 0:00:00  51.28 MB/s
pandas-0.23.4- 100% |#######################################################################################################################| Time: 0:00:00  49.37 MB/s
pip-19.1-py27_ 100% |#######################################################################################################################| Time: 0:00:00  50.34 MB/s
protobuf-3.4.0 100% |#######################################################################################################################| Time: 0:00:00  48.99 MB/s
scikit-learn-0 100% |#######################################################################################################################| Time: 0:00:00  58.06 MB/s
pango-1.40.3-0 100% |#######################################################################################################################| Time: 0:00:00  66.56 MB/s
pbr-5.1.3-py_0 100% |#######################################################################################################################| Time: 0:00:00  57.93 MB/s
mock-2.0.0-py2 100% |#######################################################################################################################| Time: 0:00:00  59.42 MB/s
qt-4.8.7-3.tar 100% |#######################################################################################################################| Time: 0:00:00  67.17 MB/s
urllib3-1.24.2 100% |#######################################################################################################################| Time: 0:00:00  48.74 MB/s
pyqt-4.11.4-py 100% |#######################################################################################################################| Time: 0:00:00  66.66 MB/s
requests-2.21. 100% |#######################################################################################################################| Time: 0:00:00  56.12 MB/s
tensorflow-1.3 100% |#######################################################################################################################| Time: 0:00:00  67.43 MB/s
conda-4.6.14-p 100% |#######################################################################################################################| Time: 0:00:00  56.92 MB/s
matplotlib-1.5 100% |#######################################################################################################################| Time: 0:00:00  66.73 MB/s
scikit-image-0 100% |#######################################################################################################################| Time: 0:00:00  61.75 MB/s
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///home/GRAMES.POLYMTL.CA/alfoi/sct
Collecting Keras (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/5e/10/aa32dad071ce52b5502266b5c659451cfd6ffcbf14e6c8c4f16c0ff5aaab/Keras-2.2.4-py2.py3-none-any.whl (312kB)
     |████████████████████████████████| 317kB 6.4MB/s 
Collecting dipy (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/e1/30/f1b41ecf027429bc8d714c776f40690ce1d3f28e891f061fe5617ce8b8bf/dipy-0.16.0.tar.gz (11.4MB)
     |████████████████████████████████| 11.4MB 22.5MB/s 
Requirement already satisfied: futures in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (3.2.0)
Collecting h5py (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/53/08/27e4e9a369321862ffdce80ff1770553e9daec65d98befb2e14e7478b698/h5py-2.9.0-cp27-cp27mu-manylinux1_x86_64.whl (2.8MB)
     |████████████████████████████████| 2.8MB 21.5MB/s 
Requirement already satisfied: matplotlib in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.5.3)
Collecting nibabel (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/bc/d4/64957ef575ac6b47d02f7195347e3444538ab633460ff6e99d2acc304223/nibabel-2.4.0-py2-none-any.whl (3.3MB)
     |████████████████████████████████| 3.3MB 22.5MB/s 
Collecting nipy (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/6f/8b/6534f0bdb4f3683151fed3f8e3f575006645a48fd338618eb1a3c688bffa/nipy-0.4.2-cp27-cp27mu-manylinux1_x86_64.whl (4.5MB)
     |████████████████████████████████| 4.5MB 21.7MB/s 
Requirement already satisfied: pandas in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.23.4)
Requirement already satisfied: psutil in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (5.6.1)
Collecting raven (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/bd/8e/62e26a88c0a1bbae677200baf0767c1022321a6555634f8129e6d55c5ddc/raven-6.10.0-py2.py3-none-any.whl (284kB)
     |████████████████████████████████| 286kB 25.7MB/s 
Requirement already satisfied: requests in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.21.0)
Requirement already satisfied: numpy in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.11.3)
Requirement already satisfied: scipy in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.2.1)
Requirement already satisfied: scikit-image in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.13.1)
Requirement already satisfied: scikit-learn==0.17.1 in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.17.1)
Requirement already satisfied: tensorflow==1.3.0 in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.3.0)
Requirement already satisfied: xlrd in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.2.0)
Requirement already satisfied: xlutils in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.0.0)
Requirement already satisfied: xlwt in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.3.0)
Collecting tqdm (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/6c/4b/c38b5144cf167c4f52288517436ccafefe9dc01b8d1c190e18a6b154cd4a/tqdm-4.31.1-py2.py3-none-any.whl (48kB)
     |████████████████████████████████| 51kB 12.9MB/s 
Collecting transforms3d (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/b5/f7/e85809168a548a854d7c1331560c27b4f5381698d29c12e57759192b2bc1/transforms3d-0.3.1.tar.gz (62kB)
     |████████████████████████████████| 71kB 13.1MB/s 
Requirement already satisfied: urllib3[secure] in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.24.2)
Collecting portalocker (from spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/eb/48/bf5e330d7d6d57d92157480db9ccad84da86efd045205f7133a53b29aace/portalocker-1.4.0-py2.py3-none-any.whl
Requirement already satisfied: pyyaml in ./python/lib/python2.7/site-packages (from Keras->spinalcordtoolbox===dev) (3.11)
Collecting keras-preprocessing>=1.0.5 (from Keras->spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/c0/bf/0315ef6a9fd3fc2346e85b0ff1f5f83ca17073f2c31ac719ab2e4da0d4a3/Keras_Preprocessing-1.0.9-py2.py3-none-any.whl (59kB)
     |████████████████████████████████| 61kB 15.1MB/s 
Requirement already satisfied: six>=1.9.0 in ./python/lib/python2.7/site-packages (from Keras->spinalcordtoolbox===dev) (1.10.0)
Collecting keras-applications>=1.0.6 (from Keras->spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/90/85/64c82949765cfb246bbdaf5aca2d55f400f792655927a017710a78445def/Keras_Applications-1.0.7-py2.py3-none-any.whl (51kB)
     |████████████████████████████████| 61kB 15.7MB/s 
Requirement already satisfied: python-dateutil in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2.6.1)
Requirement already satisfied: pytz in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2017.2)
Requirement already satisfied: cycler in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,>=1.5.6 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2.2.0)
Collecting bz2file; python_version < "3.0" (from nibabel->spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/61/39/122222b5e85cd41c391b68a99ee296584b2a2d1d233e7ee32b4532384f2d/bz2file-0.98.tar.gz
Collecting sympy>=0.7.0 (from nipy->spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/21/21/f4105795ca7f35c541d82c5b06be684dd2f5cb4f508fb487cd7aea4de776/sympy-1.4-py2.py3-none-any.whl (5.3MB)
     |████████████████████████████████| 5.3MB 21.1MB/s 
Collecting contextlib2; python_version < "3.2" (from raven->spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/a2/71/8273a7eeed0aff6a854237ab5453bc9aa67deb49df4832801c21f0ff3782/contextlib2-0.5.5-py2.py3-none-any.whl
Requirement already satisfied: idna<2.9,>=2.5 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (2.6)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (3.0.4)
Requirement already satisfied: certifi>=2017.4.17 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (2019.3.9)
Requirement already satisfied: networkx>=1.8 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (2.2)
Requirement already satisfied: pillow>=2.1.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (4.4.0)
Requirement already satisfied: PyWavelets>=0.4.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (1.0.3)
Requirement already satisfied: protobuf>=3.3.0 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (3.4.0)
Requirement already satisfied: backports.weakref>=1.0rc1 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (1.0rc1)
Requirement already satisfied: wheel in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (0.29.0)
Collecting tensorflow-tensorboard<0.2.0,>=0.1.0 (from tensorflow==1.3.0->spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/fb/34/14c23665a725c73932891e09b8f017a53aad545c9d5019d2817102dc5d9b/tensorflow_tensorboard-0.1.8-py2-none-any.whl (1.6MB)
     |████████████████████████████████| 1.6MB 22.5MB/s 
Requirement already satisfied: mock>=2.0.0 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (2.0.0)
Requirement already satisfied: pyOpenSSL>=0.14 in ./python/lib/python2.7/site-packages (from urllib3[secure]->spinalcordtoolbox===dev) (17.0.0)
Requirement already satisfied: cryptography>=1.3.4 in ./python/lib/python2.7/site-packages (from urllib3[secure]->spinalcordtoolbox===dev) (2.5)
Requirement already satisfied: ipaddress in ./python/lib/python2.7/site-packages (from urllib3[secure]->spinalcordtoolbox===dev) (1.0.18)
Collecting mpmath>=0.19 (from sympy>=0.7.0->nipy->spinalcordtoolbox===dev)
  Downloading https://files.pythonhosted.org/packages/ca/63/3384ebb3b51af9610086b23ea976e6d27d6d97bf140a76a365bd77a3eb32/mpmath-1.1.0.tar.gz (512kB)
     |████████████████████████████████| 522kB 28.5MB/s 
Requirement already satisfied: decorator>=4.3.0 in ./python/lib/python2.7/site-packages (from networkx>=1.8->scikit-image->spinalcordtoolbox===dev) (4.4.0)
Requirement already satisfied: olefile in ./python/lib/python2.7/site-packages (from pillow>=2.1.0->scikit-image->spinalcordtoolbox===dev) (0.46)
Requirement already satisfied: setuptools in ./python/lib/python2.7/site-packages (from protobuf>=3.3.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (41.0.1)
Requirement already satisfied: markdown>=2.6.8 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (2.6.11)
Requirement already satisfied: werkzeug>=0.11.10 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (0.15.2)
Requirement already satisfied: bleach==1.5.0 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (1.5.0)
Requirement already satisfied: html5lib==0.9999999 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (0.9999999)
Requirement already satisfied: funcsigs>=1; python_version < "3.3" in ./python/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (1.0.2)
Requirement already satisfied: pbr>=0.11 in ./python/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (5.1.3)
Requirement already satisfied: enum34; python_version < "3" in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (1.1.6)
Requirement already satisfied: asn1crypto>=0.21.0 in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (0.22.0)
Requirement already satisfied: cffi!=1.11.3,>=1.8 in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (1.10.0)
Requirement already satisfied: pycparser in ./python/lib/python2.7/site-packages (from cffi!=1.11.3,>=1.8->cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (2.18)
Building wheels for collected packages: dipy, transforms3d, bz2file, mpmath
  Building wheel for dipy (setup.py) ... done
  Stored in directory: /home/GRAMES.POLYMTL.CA/alfoi/.cache/pip/wheels/35/2a/c7/10ee52be596c8fca26eaa5524b16da8aef72fabdf0c5606c10
  Building wheel for transforms3d (setup.py) ... done
  Stored in directory: /home/GRAMES.POLYMTL.CA/alfoi/.cache/pip/wheels/3d/3c/84/28d36677f3c760c048bd02b5a547ea0c4027770cc9cdb9af1e
  Building wheel for bz2file (setup.py) ... done
  Stored in directory: /home/GRAMES.POLYMTL.CA/alfoi/.cache/pip/wheels/81/75/d6/e1317bf09bf1af5a30befc2a007869fa6e1f516b8f7c591cb9
  Building wheel for mpmath (setup.py) ... done
  Stored in directory: /home/GRAMES.POLYMTL.CA/alfoi/.cache/pip/wheels/63/9d/8e/37c3f6506ed3f152733a699e92d8e0c9f5e5f01dea262f80ad
Successfully built dipy transforms3d bz2file mpmath
Installing collected packages: keras-preprocessing, h5py, keras-applications, Keras, bz2file, nibabel, dipy, mpmath, sympy, nipy, contextlib2, raven, tqdm, transforms3d, portalocker, spinalcordtoolbox, tensorflow-tensorboard
  Running setup.py develop for spinalcordtoolbox
Successfully installed Keras-2.2.4 bz2file-0.98 contextlib2-0.5.5 dipy-0.16.0 h5py-2.9.0 keras-applications-1.0.7 keras-preprocessing-1.0.9 mpmath-1.1.0 nibabel-2.4.0 nipy-0.4.2 portalocker-1.4.0 raven-6.10.0 spinalcordtoolbox sympy-1.4 tensorflow-tensorboard-0.1.8 tqdm-4.31.1 transforms3d-0.3.1
Checking if TensorFlow is working, if not attempting to install another version
TensorFlow seems to be working.
Checking if skimage is working, if not attempting work around it
skimage seems to be working.

Creating launchers for Python scripts...

Installing binaries...
>> . /home/GRAMES.POLYMTL.CA/alfoi/sct/python/bin/activate /home/GRAMES.POLYMTL.CA/alfoi/sct/python
>> sct_download_data -d binaries_debian -o /home/GRAMES.POLYMTL.CA/alfoi/sct/bin
Folder /home/GRAMES.POLYMTL.CA/alfoi/sct/bin has been created.

Trying URL: https://osf.io/z72vn/?action=download
Downloading 20181204_sct_binaries_linux.tar.gz...
Status: 100%|##########| 92.2M/92.2M [00:02<00:00, 32.7MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/bin

Remove temporary file...
Done!

All requirements installed!
>> . /home/GRAMES.POLYMTL.CA/alfoi/sct/python/bin/activate /home/GRAMES.POLYMTL.CA/alfoi/sct/python

Installing data...
>> rm -rf /home/GRAMES.POLYMTL.CA/alfoi/sct/data
>> mkdir -p /home/GRAMES.POLYMTL.CA/alfoi/sct/data
>> cd /home/GRAMES.POLYMTL.CA/alfoi/sct/data
>> sct_download_data -d PAM50

Trying URL: https://osf.io/kc3jx/?action=download
Downloading 20181214_PAM50.zip...
Status: 100%|##########| 70.8M/70.8M [00:01<00:00, 41.2MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/data

Remove temporary file...
Done!

>> sct_download_data -d gm_model

Trying URL: https://osf.io/ugscu/?action=download
Downloading 20160922_gm_model.zip...
Status: 100%|##########| 10.3M/10.3M [00:00<00:00, 15.4MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/data

Remove temporary file...
Done!

>> sct_download_data -d optic_models

Trying URL: https://osf.io/g4fwn/?action=download
Downloading 20170413_optic_models.zip...
Status: 100%|##########| 17.7k/17.7k [00:00<00:00, 1.16MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/data

Remove temporary file...
Done!

>> sct_download_data -d pmj_models

Trying URL: https://osf.io/4gufr/?action=download
Downloading 20170922_pmj_models.zip...
Status: 100%|##########| 8.87k/8.87k [00:00<00:00, 6.80MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_sc_models

Trying URL: https://osf.io/avf97/?action=download
Downloading 20180610_deepseg_sc_models.zip...
Status: 100%|##########| 58.7M/58.7M [00:01<00:00, 38.7MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_gm_models

Trying URL: https://osf.io/b9y4x/?action=download
Downloading 20180205_deepseg_gm_models.zip...
Status: 100%|##########| 2.28M/2.28M [00:00<00:00, 13.9MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_lesion_models

Trying URL: https://osf.io/eg7v9/?action=download
Downloading 20180613_deepseg_lesion_models.zip...
Status: 100%|##########| 16.0M/16.0M [00:00<00:00, 26.0MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/data

Remove temporary file...
Done!

>> sct_download_data -d c2c3_disc_models

Trying URL: https://osf.io/t97ap/?action=download
Downloading 20190117_c2c3_disc_models.zip...
Status: 100%|##########| 8.94k/8.94k [00:00<00:00, 7.02MB/s]

Check if folder already exists...

Unzip data to: /home/GRAMES.POLYMTL.CA/alfoi/sct/data

Remove temporary file...
Done!


Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y



Validate installation...
SCT info:
- version: dev
- path: /home/GRAMES.POLYMTL.CA/alfoi/sct
OS: linux (Linux-4.4.0-142-generic-x86_64-with-debian-stretch-sid)
CPU cores: Available: 128, Used by SCT: 128
RAM: MemTotal:       264009372 kB
total        used        free      shared  buff/cache   available
Mem:         257821        1016      187631          18       69174      255203
Swap:           975           0         975
Check Python executable.............................[OK]
  Using bundled python 2.7.12 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:42:40) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] at /home/GRAMES.POLYMTL.CA/alfoi/sct/python/bin/python
Check if data are installed.........................[OK]
Check if Keras is installed.........................[OK] (2.2.4)
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 matplotlib is installed....................[OK] (1.5.3)
Check if nibabel is installed.......................[OK] (2.4.0)
Check if nipy is installed..........................[OK] (0.4.2)
Check if pandas is installed........................[OK] (0.23.4)
Check if psutil is installed........................[OK] (5.6.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.21.0)
Check if numpy is installed.........................[OK] (1.11.3)
Check if scipy is installed.........................[OK] (1.2.1)
Check if scikit-image is installed..................[OK] (0.13.1)
Check if scikit-learn (0.17.1) is installed.........[OK]
Check if tensorflow (1.3.0) is installed............[OK]
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] (4.31.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.24.2)
Check if portalocker is installed...................[OK] (1.4.0)
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]

Open a new Terminal window to load environment variables, or run:
 source /home/GRAMES.POLYMTL.CA/alfoi/.bashrc

@alexfoias
Copy link
Contributor

alexfoias commented Apr 25, 2019 •
edited

sct_check_dependencies output:


alfoi@joplin:~/spinalcordtoolbox$ sct_check_dependencies 
SCT info:
- version: dev
- path: /home/GRAMES.POLYMTL.CA/alfoi/sct
OS: linux (Linux-4.4.0-142-generic-x86_64-with-debian-stretch-sid)
CPU cores: Available: 128, Used by SCT: 128
RAM: MemTotal:       264009372 kB
total        used        free      shared  buff/cache   available
Mem:         257821        1015      187653          18       69152      255202
Swap:           975           0         975
Check Python executable.............................[OK]
  Using bundled python 2.7.12 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:42:40) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] at /home/GRAMES.POLYMTL.CA/alfoi/sct/python/bin/python
Check if data are installed.........................[OK]
Check if Keras is installed.........................[OK] (2.2.4)
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 matplotlib is installed....................[OK] (1.5.3)
Check if nibabel is installed.......................[OK] (2.4.0)
Check if nipy is installed..........................[OK] (0.4.2)
Check if pandas is installed........................[OK] (0.23.4)
Check if psutil is installed........................[OK] (5.6.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.21.0)
Check if numpy is installed.........................[OK] (1.11.3)
Check if scipy is installed.........................[OK] (1.2.1)
Check if scikit-image is installed..................[OK] (0.13.1)
Check if scikit-learn (0.17.1) is installed.........[OK]
Check if tensorflow (1.3.0) is installed............[OK]
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] (4.31.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.24.2)
Check if portalocker is installed...................[OK] (1.4.0)
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]

@Nicolas-Pinon
Copy link
Contributor Author

sct_check_dependencies output:

I really can't figure out why it doesn't work on my GRAMES account, everything is the same right ?

@Nicolas-Pinon
Copy link
Contributor Author

@jcohenadad check_dependencies on scikit image still failing

Thing that I really don't understand is, at the end of install_sct, check_dependencies is run, why does it give two different results when used at the end of installation and when used independently ?

@jcohenadad
Copy link
Member

jcohenadad commented Apr 25, 2019 •
edited

@Nicolas-Pinon since this is an isolated case and the installer will soon be replaced by py3k, i suggest we move on. So, ask @alexfoias to run the batch_processing.sh on master with his session, run it on your branch, and compare results.

UPDATE: let me run batch_processing on master-- there are other things i'd like to investigate.
UPDATE: Actually, @alexfoias if you could run batch_processing.sh on master on an OSX, that would be great, i'd like to verify something

@jcohenadad
Copy link
Member

Isolated case, closing

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug category: fixes an error in the code
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@jcohenadad @alexfoias @Nicolas-Pinon