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Installation failed : Couldn't work around bad skimage installation #2245

Closed
Nicolas-Pinon opened this issue Apr 30, 2019 · 4 comments · Fixed by #2238
Closed

Installation failed : Couldn't work around bad skimage installation #2245

Nicolas-Pinon opened this issue Apr 30, 2019 · 4 comments · Fixed by #2238
Labels
bug category: fixes an error in the code installation category: install_sct or pip/setup.py

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@Nicolas-Pinon
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Nicolas-Pinon commented Apr 30, 2019 •
edited

When trying to install sct on my laptop (Debian 9), abbey (Ubuntu 16.04.5 LTS) and my station (OSX 10.13.6) on master, commit b0bc30bea4dd43cbea5f8b89d940daf6d8121632.

I get this error :

Couldn't work around bad skimage installation
Here's some info:

Traceback (most recent call last):
 File "<string>", line 1, in <module>
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/__init__.py", line 167, in <module>
   from .util.dtype import (img_as_float32,
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 6, in <module>
   from .apply_parallel import apply_parallel
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/util/apply_parallel.py", line 8, in <module>
   import dask.array as da
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/__init__.py", line 5, in <module>
   from .core import (Array, block, concatenate, stack, from_array, store,
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/core.py", line 29, in <module>
   from . import chunk
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/chunk.py", line 73, in <module>
   nancumprod = npcompat.nancumprod
AttributeError: 'module' object has no attribute 'nancumprod'

Traceback (most recent call last):
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/install/install_dependencies_with_workarounds.py", line 61, in <module>
   skimage_workarounds()
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/install/install_dependencies_with_workarounds.py", line 57, in skimage_workarounds
   raise RuntimeError("Couldn't apply an skimage workaround")
RuntimeError: Couldn't apply an skimage workaround
Working around distribution issues failed.
Feel free to open an issue after looking at https://github.com/neuropoly/spinalcordtoolbox/issues/1704
Installation failed

It might be the kind of error which will be fixed by #2238, but can someone tell me if they get the same problem when installing sct ?

Full installation logs :

Debian 9 
nicolas@nipin:~/PycharmProjects/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: no
--> Crash reports will not be sent.

SCT will be installed here: [/home/nicolas/PycharmProjects/spinalcordtoolbox]
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/nicolas/PycharmProjects/spinalcordtoolbox/bin

Installing conda...
>> rm -rf /home/nicolas/PycharmProjects/spinalcordtoolbox/python
>> mkdir -p /home/nicolas/PycharmProjects/spinalcordtoolbox/python
--2019-04-30 14:45:21--  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:c94f, ...
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.7IKMwcG5AW/miniconda.sh'

/tmp/tmp.7IKMwcG5AW 100%[===================>]  26.50M  3.04MB/s    in 8.6s    

2019-04-30 14:45:30 (3.08 MB/s) - '/tmp/tmp.7IKMwcG5AW/miniconda.sh' saved [27792209/27792209]

exit status is 0
>> bash /tmp/tmp.7IKMwcG5AW/miniconda.sh -p /home/nicolas/PycharmProjects/spinalcordtoolbox/python -b -f
PREFIX=/home/nicolas/PycharmProjects/spinalcordtoolbox/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/nicolas/PycharmProjects/spinalcordtoolbox/python/bin/activate /home/nicolas/PycharmProjects/spinalcordtoolbox/python
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /home/nicolas/PycharmProjects/spinalcordtoolbox/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   3.92 MB/s
libffi-3.2.1-3 100% |################################| Time: 0:00:00   4.68 MB/s
asn1crypto-0.2 100% |################################| Time: 0:00:00   2.84 MB/s
certifi-2019.3 100% |################################| Time: 0:00:00   2.39 MB/s
chardet-3.0.4- 100% |################################| Time: 0:00:00   3.19 MB/s
decorator-4.4. 100% |################################| Time: 0:00:00   7.02 MB/s
enum34-1.1.6-p 100% |################################| Time: 0:00:00   4.58 MB/s
functools32-3. 100% |################################| Time: 0:00:00   7.04 MB/s
futures-3.2.0- 100% |################################| Time: 0:00:00   4.37 MB/s
idna-2.8-py27_ 100% |################################| Time: 0:00:00   6.31 MB/s
ipaddress-1.0. 100% |################################| Time: 0:00:00  10.78 MB/s
ipython_genuti 100% |################################| Time: 0:00:00   5.93 MB/s
pycosat-0.6.3- 100% |################################| Time: 0:00:00   4.09 MB/s
pycparser-2.19 100% |################################| Time: 0:00:00   7.24 MB/s
pysocks-1.6.8- 100% |################################| Time: 0:00:00  10.07 MB/s
pytz-2019.1-py 100% |################################| Time: 0:00:00   4.71 MB/s
pyyaml-3.12-py 100% |################################| Time: 0:00:00   4.77 MB/s
six-1.12.0-py2 100% |################################| Time: 0:00:00  14.22 MB/s
cffi-1.11.5-py 100% |################################| Time: 0:00:00   3.38 MB/s
jsonschema-2.6 100% |################################| Time: 0:00:00   7.22 MB/s
python-dateuti 100% |################################| Time: 0:00:00   3.46 MB/s
setuptools-41. 100% |################################| Time: 0:00:00   4.01 MB/s
traitlets-4.3. 100% |################################| Time: 0:00:00   2.52 MB/s
clyent-1.2.2-p 100% |################################| Time: 0:00:00   9.62 MB/s
cryptography-2 100% |################################| Time: 0:00:00   3.86 MB/s
jupyter_core-4 100% |################################| Time: 0:00:00   7.97 MB/s
nbformat-4.4.0 100% |################################| Time: 0:00:00   7.99 MB/s
pyopenssl-19.0 100% |################################| Time: 0:00:00   7.14 MB/s
urllib3-1.24.2 100% |################################| Time: 0:00:00   7.29 MB/s
requests-2.21. 100% |################################| Time: 0:00:00   5.86 MB/s
anaconda-clien 100% |################################| Time: 0:00:00   5.69 MB/s
conda-4.6.14-p 100% |################################| Time: 0:00:01   1.12 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/nicolas/PycharmProjects/spinalcordtoolbox/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-1.2.1            |             py_0         534 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-5.6.2               |   py27h516909a_0         314 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-1.2.1-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-5.6.2-py27h516909a_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% 
tensorflow-1.3.0     | 36.2 MB   | ##################################### | 100% 
xlwt-1.3.0           | 83 KB     | ##################################### | 100% 
icu-56.1             | 21.9 MB   | ##################################### | 100% 
openblas-0.2.18      | 14.1 MB   | ##################################### | 100% 
dask-core-1.2.1      | 534 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% 
psutil-5.6.2         | 314 KB    | ##################################### | 100% 
xz-5.2.4             | 366 KB    | ##################################### | 100% 
bleach-1.5.0         | 23 KB     | ##################################### | 100% 
fontconfig-2.11.1    | 876 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% 
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% 
xlutils-2.0.0        | 76 KB     | ##################################### | 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/nicolas/PycharmProjects/spinalcordtoolbox
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) (5.6.2)
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)
 Downloading https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl (226kB)
    |████████████████████████████████| 235kB 4.3MB/s 
Collecting pytz (from matplotlib->spinalcordtoolbox===dev)
 Downloading https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl (510kB)
    |████████████████████████████████| 512kB 5.5MB/s 
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)
 Downloading 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: 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: 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: 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: 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
Trying workaround
Collecting package metadata: done
Solving environment: done

## Package Plan ##

 environment location: /home/nicolas/PycharmProjects/spinalcordtoolbox/python

 added / updated specs:
   - nomkl


The following packages will be downloaded:

   package                    |            build
   ---------------------------|-----------------
   ca-certificates-2019.1.23  |                0         126 KB
   cairo-1.12.18              |                6         594 KB
   certifi-2019.3.9           |           py27_0         155 KB
   conda-4.6.14               |           py27_0         2.1 MB
   cryptography-2.6.1         |   py27h1ba5d50_0         607 KB
   fontconfig-2.11.1          |                6         405 KB
   freetype-2.5.5             |                2         2.5 MB
   harfbuzz-0.9.39            |                1         1.1 MB
   libedit-3.1.20181209       |       hc058e9b_0         188 KB
   libpng-1.6.37              |       hbc83047_0         364 KB
   libprotobuf-3.6.1          |       hd408876_0         4.1 MB
   libtiff-4.0.10             |       h2733197_2         604 KB
   matplotlib-1.5.1           |      np111py27_0         8.4 MB
   ncurses-6.1                |       he6710b0_1         958 KB
   nomkl-3.0                  |                0          48 KB
   openssl-1.1.1b             |       h7b6447c_1         4.0 MB
   pango-1.39.0               |                0         777 KB
   pillow-4.2.1               |           py27_0         843 KB
   pixman-0.32.6              |                0         2.4 MB
   protobuf-3.6.1             |   py27he6710b0_0         620 KB
   pycairo-1.10.0             |           py27_0          81 KB
   python-2.7.16              |       h9bab390_0        12.8 MB
   qt-4.8.7                   |                2        34.1 MB
   readline-7.0               |       h7b6447c_5         392 KB
   scipy-0.18.1               |np111py27_blas_openblas_200        32.3 MB  conda-forge
   sqlite-3.28.0              |       h7b6447c_0         1.9 MB
   tk-8.6.8                   |       hbc83047_0         3.1 MB
   zlib-1.2.11                |       h7b6447c_3         120 KB
   zstd-1.3.7                 |       h0b5b093_0         887 KB
   ------------------------------------------------------------
                                          Total:       116.4 MB

The following NEW packages will be INSTALLED:

 libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
 libprotobuf        pkgs/main/linux-64::libprotobuf-3.6.1-hd408876_0
 ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
 nomkl              pkgs/free/linux-64::nomkl-3.0-0
 pycairo            pkgs/free/linux-64::pycairo-1.10.0-py27_0
 zstd               pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0

The following packages will be UPDATED:

 cryptography       conda-forge::cryptography-2.5-py27hb7~ --> pkgs/main::cryptography-2.6.1-py27h1ba5d50_0
 libpng                       conda-forge::libpng-1.6.28-1 --> pkgs/main::libpng-1.6.37-hbc83047_0
 libtiff                      conda-forge::libtiff-4.0.7-0 --> pkgs/main::libtiff-4.0.10-h2733197_2
 openssl            conda-forge::openssl-1.0.2r-h14c3975_0 --> pkgs/main::openssl-1.1.1b-h7b6447c_1
 pillow                   conda-forge::pillow-4.0.0-py27_1 --> pkgs/free::pillow-4.2.1-py27_0
 protobuf               conda-forge::protobuf-3.4.0-py27_0 --> pkgs/main::protobuf-3.6.1-py27he6710b0_0
 python                         pkgs/free::python-2.7.12-1 --> pkgs/main::python-2.7.16-h9bab390_0
 readline                        pkgs/free::readline-6.2-2 --> pkgs/main::readline-7.0-h7b6447c_5
 sqlite                         pkgs/free::sqlite-3.13.0-0 --> pkgs/main::sqlite-3.28.0-h7b6447c_0
 tk                                 pkgs/free::tk-8.5.18-0 --> pkgs/main::tk-8.6.8-hbc83047_0
 zlib                              pkgs/free::zlib-1.2.8-3 --> pkgs/main::zlib-1.2.11-h7b6447c_3

The following packages will be SUPERSEDED by a higher-priority channel:

 ca-certificates    conda-forge::ca-certificates-2019.3.9~ --> pkgs/main::ca-certificates-2019.1.23-0
 cairo                         conda-forge::cairo-1.14.6-0 --> pkgs/free::cairo-1.12.18-6
 certifi                                       conda-forge --> pkgs/main
 conda                                         conda-forge --> pkgs/main
 fontconfig                                    conda-forge --> pkgs/free
 freetype                    conda-forge::freetype-2.6.3-1 --> pkgs/free::freetype-2.5.5-2
 harfbuzz                    conda-forge::harfbuzz-1.3.4-0 --> pkgs/free::harfbuzz-0.9.39-1
 matplotlib         conda-forge::matplotlib-1.5.3-np111py~ --> pkgs/free::matplotlib-1.5.1-np111py27_0
 pango                         conda-forge::pango-1.40.3-0 --> pkgs/free::pango-1.39.0-0
 pixman             conda-forge::pixman-0.38.0-h516909a_1~ --> pkgs/free::pixman-0.32.6-0
 qt                                conda-forge::qt-4.8.7-3 --> pkgs/free::qt-4.8.7-2

The following packages will be DOWNGRADED:

 scipy                                1.2.1-py27h09a28d5_1 --> 0.18.1-np111py27_blas_openblas_200



Downloading and Extracting Packages
matplotlib-1.5.1     | 8.4 MB    | ##################################### | 100% 
cryptography-2.6.1   | 607 KB    | ##################################### | 100% 
libtiff-4.0.10       | 604 KB    | ##################################### | 100% 
pango-1.39.0         | 777 KB    | ##################################### | 100% 
freetype-2.5.5       | 2.5 MB    | ##################################### | 100% 
libprotobuf-3.6.1    | 4.1 MB    | ##################################### | 100% 
openssl-1.1.1b       | 4.0 MB    | ##################################### | 100% 
libpng-1.6.37        | 364 KB    | ##################################### | 100% 
pixman-0.32.6        | 2.4 MB    | ##################################### | 100% 
nomkl-3.0            | 48 KB     | ##################################### | 100% 
zlib-1.2.11          | 120 KB    | ##################################### | 100% 
cairo-1.12.18        | 594 KB    | ##################################### | 100% 
ca-certificates-2019 | 126 KB    | ##################################### | 100% 
zstd-1.3.7           | 887 KB    | ##################################### | 100% 
fontconfig-2.11.1    | 405 KB    | ##################################### | 100% 
tk-8.6.8             | 3.1 MB    | ##################################### | 100% 
certifi-2019.3.9     | 155 KB    | ##################################### | 100% 
harfbuzz-0.9.39      | 1.1 MB    | ##################################### | 100% 
ncurses-6.1          | 958 KB    | ##################################### | 100% 
sqlite-3.28.0        | 1.9 MB    | ##################################### | 100% 
python-2.7.16        | 12.8 MB   | ##################################### | 100% 
scipy-0.18.1         | 32.3 MB   | ##################################### | 100% 
protobuf-3.6.1       | 620 KB    | ##################################### | 100% 
libedit-3.1.20181209 | 188 KB    | ##################################### | 100% 
pycairo-1.10.0       | 81 KB     | ##################################### | 100% 
pillow-4.2.1         | 843 KB    | ##################################### | 100% 
conda-4.6.14         | 2.1 MB    | ##################################### | 100% 
readline-7.0         | 392 KB    | ##################################### | 100% 
qt-4.8.7             | 34.1 MB   | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Couldn't work around bad skimage installation
Here's some info:

Traceback (most recent call last):
 File "<string>", line 1, in <module>
 File "/home/nicolas/PycharmProjects/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/__init__.py", line 158, in <module>
   from .util.dtype import *
 File "/home/nicolas/PycharmProjects/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 5, in <module>
   from .apply_parallel import apply_parallel
 File "/home/nicolas/PycharmProjects/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/util/apply_parallel.py", line 8, in <module>
   import dask.array as da
 File "/home/nicolas/PycharmProjects/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/__init__.py", line 5, in <module>
   from .core import (Array, block, concatenate, stack, from_array, store,
 File "/home/nicolas/PycharmProjects/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/core.py", line 29, in <module>
   from . import chunk
 File "/home/nicolas/PycharmProjects/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/chunk.py", line 73, in <module>
   nancumprod = npcompat.nancumprod
AttributeError: 'module' object has no attribute 'nancumprod'

Traceback (most recent call last):
 File "/home/nicolas/PycharmProjects/spinalcordtoolbox/install/install_dependencies_with_workarounds.py", line 61, in <module>
   skimage_workarounds()
 File "/home/nicolas/PycharmProjects/spinalcordtoolbox/install/install_dependencies_with_workarounds.py", line 57, in skimage_workarounds
   raise RuntimeError("Couldn't apply an skimage workaround")
RuntimeError: Couldn't apply an skimage workaround
Working around distribution issues failed.
Feel free to open an issue after looking at https://github.com/neuropoly/spinalcordtoolbox/issues/1704
Installation failed
Ubuntu 16.04.5 LTS 
u100542@abbey:~/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
--2019-04-30 13:37:50--  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:c84f, ...
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.rEyw1PtATj/miniconda.sh'

/tmp/tmp.rEyw1PtATj 100%[===================>]  26.50M   101MB/s    in 0.3s    

2019-04-30 13:37:50 (101 MB/s) - '/tmp/tmp.rEyw1PtATj/miniconda.sh' saved [27792209/27792209]

exit status is 0
>> bash /tmp/tmp.rEyw1PtATj/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   1.95 MB/s
libffi-3.2.1-3 100% |################################| Time: 0:00:00  22.53 MB/s
asn1crypto-0.2 100% |################################| Time: 0:00:00  30.82 MB/s
certifi-2019.3 100% |################################| Time: 0:00:00  28.12 MB/s
chardet-3.0.4- 100% |################################| Time: 0:00:00  31.48 MB/s
decorator-4.4. 100% |################################| Time: 0:00:00   9.83 MB/s
enum34-1.1.6-p 100% |################################| Time: 0:00:00  24.21 MB/s
functools32-3. 100% |################################| Time: 0:00:00  12.79 MB/s
futures-3.2.0- 100% |################################| Time: 0:00:00  15.96 MB/s
idna-2.8-py27_ 100% |################################| Time: 0:00:00  27.02 MB/s
ipaddress-1.0. 100% |################################| Time: 0:00:00  12.50 MB/s
ipython_genuti 100% |################################| Time: 0:00:00  14.41 MB/s
pycosat-0.6.3- 100% |################################| Time: 0:00:00  28.85 MB/s
pycparser-2.19 100% |################################| Time: 0:00:00  28.95 MB/s
pysocks-1.6.8- 100% |################################| Time: 0:00:00  16.01 MB/s
pytz-2019.1-py 100% |################################| Time: 0:00:00  31.46 MB/s
pyyaml-3.12-py 100% |################################| Time: 0:00:00  32.27 MB/s
six-1.12.0-py2 100% |################################| Time: 0:00:00  14.41 MB/s
cffi-1.11.5-py 100% |################################| Time: 0:00:00  33.90 MB/s
jsonschema-2.6 100% |################################| Time: 0:00:00  25.88 MB/s
python-dateuti 100% |################################| Time: 0:00:00  30.90 MB/s
setuptools-41. 100% |################################| Time: 0:00:00  34.72 MB/s
traitlets-4.3. 100% |################################| Time: 0:00:00  30.05 MB/s
clyent-1.2.2-p 100% |################################| Time: 0:00:00   8.65 MB/s
cryptography-2 100% |################################| Time: 0:00:00  37.04 MB/s
jupyter_core-4 100% |################################| Time: 0:00:00  20.01 MB/s
nbformat-4.4.0 100% |################################| Time: 0:00:00  26.69 MB/s
pyopenssl-19.0 100% |################################| Time: 0:00:00  26.36 MB/s
urllib3-1.24.2 100% |################################| Time: 0:00:00  29.54 MB/s
requests-2.21. 100% |################################| Time: 0:00:00  24.23 MB/s
anaconda-clien 100% |################################| Time: 0:00:00  22.41 MB/s
conda-4.6.14-p 100% |################################| Time: 0:00:00  43.20 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-1.2.1            |             py_0         534 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-5.6.2               |   py27h516909a_0         314 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-1.2.1-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-5.6.2-py27h516909a_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% 
tensorflow-1.3.0     | 36.2 MB   | ##################################### | 100% 
xlwt-1.3.0           | 83 KB     | ##################################### | 100% 
icu-56.1             | 21.9 MB   | ##################################### | 100% 
openblas-0.2.18      | 14.1 MB   | ##################################### | 100% 
dask-core-1.2.1      | 534 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% 
psutil-5.6.2         | 314 KB    | ##################################### | 100% 
xz-5.2.4             | 366 KB    | ##################################### | 100% 
bleach-1.5.0         | 23 KB     | ##################################### | 100% 
fontconfig-2.11.1    | 876 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% 
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% 
xlutils-2.0.0        | 76 KB     | ##################################### | 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) (5.6.2)
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
Trying workaround
Collecting package metadata: done
Solving environment: done

## Package Plan ##

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

 added / updated specs:
   - nomkl


The following packages will be downloaded:

   package                    |            build
   ---------------------------|-----------------
   ca-certificates-2019.1.23  |                0         126 KB
   cairo-1.12.18              |                6         594 KB
   certifi-2019.3.9           |           py27_0         155 KB
   conda-4.6.14               |           py27_0         2.1 MB
   cryptography-2.6.1         |   py27h1ba5d50_0         607 KB
   fontconfig-2.11.1          |                6         405 KB
   freetype-2.5.5             |                2         2.5 MB
   harfbuzz-0.9.39            |                1         1.1 MB
   libedit-3.1.20181209       |       hc058e9b_0         188 KB
   libpng-1.6.37              |       hbc83047_0         364 KB
   libprotobuf-3.6.1          |       hd408876_0         4.1 MB
   libtiff-4.0.10             |       h2733197_2         604 KB
   matplotlib-1.5.1           |      np111py27_0         8.4 MB
   ncurses-6.1                |       he6710b0_1         958 KB
   nomkl-3.0                  |                0          48 KB
   openssl-1.1.1b             |       h7b6447c_1         4.0 MB
   pango-1.39.0               |                0         777 KB
   pillow-4.2.1               |           py27_0         843 KB
   pixman-0.32.6              |                0         2.4 MB
   protobuf-3.6.1             |   py27he6710b0_0         620 KB
   pycairo-1.10.0             |           py27_0          81 KB
   python-2.7.16              |       h9bab390_0        12.8 MB
   qt-4.8.7                   |                2        34.1 MB
   readline-7.0               |       h7b6447c_5         392 KB
   scipy-0.18.1               |np111py27_blas_openblas_200        32.3 MB  conda-forge
   sqlite-3.28.0              |       h7b6447c_0         1.9 MB
   tk-8.6.8                   |       hbc83047_0         3.1 MB
   zlib-1.2.11                |       h7b6447c_3         120 KB
   zstd-1.3.7                 |       h0b5b093_0         887 KB
   ------------------------------------------------------------
                                          Total:       116.4 MB

The following NEW packages will be INSTALLED:

 libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
 libprotobuf        pkgs/main/linux-64::libprotobuf-3.6.1-hd408876_0
 ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
 nomkl              pkgs/main/linux-64::nomkl-3.0-0
 pycairo            pkgs/free/linux-64::pycairo-1.10.0-py27_0
 zstd               pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0

The following packages will be UPDATED:

 cryptography       conda-forge::cryptography-2.5-py27hb7~ --> pkgs/main::cryptography-2.6.1-py27h1ba5d50_0
 libpng                       conda-forge::libpng-1.6.28-1 --> pkgs/main::libpng-1.6.37-hbc83047_0
 libtiff                      conda-forge::libtiff-4.0.7-0 --> pkgs/main::libtiff-4.0.10-h2733197_2
 openssl            conda-forge::openssl-1.0.2r-h14c3975_0 --> pkgs/main::openssl-1.1.1b-h7b6447c_1
 pillow                   conda-forge::pillow-4.0.0-py27_1 --> pkgs/free::pillow-4.2.1-py27_0
 protobuf               conda-forge::protobuf-3.4.0-py27_0 --> pkgs/main::protobuf-3.6.1-py27he6710b0_0
 python                         pkgs/free::python-2.7.12-1 --> pkgs/main::python-2.7.16-h9bab390_0
 readline                        pkgs/free::readline-6.2-2 --> pkgs/main::readline-7.0-h7b6447c_5
 sqlite                         pkgs/free::sqlite-3.13.0-0 --> pkgs/main::sqlite-3.28.0-h7b6447c_0
 tk                                 pkgs/free::tk-8.5.18-0 --> pkgs/main::tk-8.6.8-hbc83047_0
 zlib                              pkgs/free::zlib-1.2.8-3 --> pkgs/main::zlib-1.2.11-h7b6447c_3

The following packages will be SUPERSEDED by a higher-priority channel:

 ca-certificates    conda-forge::ca-certificates-2019.3.9~ --> pkgs/main::ca-certificates-2019.1.23-0
 cairo                         conda-forge::cairo-1.14.6-0 --> pkgs/free::cairo-1.12.18-6
 certifi                                       conda-forge --> pkgs/main
 conda                                         conda-forge --> pkgs/main
 fontconfig                                    conda-forge --> pkgs/free
 freetype                    conda-forge::freetype-2.6.3-1 --> pkgs/free::freetype-2.5.5-2
 harfbuzz                    conda-forge::harfbuzz-1.3.4-0 --> pkgs/free::harfbuzz-0.9.39-1
 matplotlib         conda-forge::matplotlib-1.5.3-np111py~ --> pkgs/free::matplotlib-1.5.1-np111py27_0
 pango                         conda-forge::pango-1.40.3-0 --> pkgs/free::pango-1.39.0-0
 pixman             conda-forge::pixman-0.38.0-h516909a_1~ --> pkgs/free::pixman-0.32.6-0
 qt                                conda-forge::qt-4.8.7-3 --> pkgs/free::qt-4.8.7-2

The following packages will be DOWNGRADED:

 scipy                                1.2.1-py27h09a28d5_1 --> 0.18.1-np111py27_blas_openblas_200



Downloading and Extracting Packages
matplotlib-1.5.1     | 8.4 MB    | ##################################### | 100% 
cryptography-2.6.1   | 607 KB    | ##################################### | 100% 
libtiff-4.0.10       | 604 KB    | ##################################### | 100% 
pango-1.39.0         | 777 KB    | ##################################### | 100% 
freetype-2.5.5       | 2.5 MB    | ##################################### | 100% 
libprotobuf-3.6.1    | 4.1 MB    | ##################################### | 100% 
openssl-1.1.1b       | 4.0 MB    | ##################################### | 100% 
libpng-1.6.37        | 364 KB    | ##################################### | 100% 
pixman-0.32.6        | 2.4 MB    | ##################################### | 100% 
nomkl-3.0            | 48 KB     | ##################################### | 100% 
zlib-1.2.11          | 120 KB    | ##################################### | 100% 
cairo-1.12.18        | 594 KB    | ##################################### | 100% 
ca-certificates-2019 | 126 KB    | ##################################### | 100% 
zstd-1.3.7           | 887 KB    | ##################################### | 100% 
fontconfig-2.11.1    | 405 KB    | ##################################### | 100% 
tk-8.6.8             | 3.1 MB    | ##################################### | 100% 
certifi-2019.3.9     | 155 KB    | ##################################### | 100% 
harfbuzz-0.9.39      | 1.1 MB    | ##################################### | 100% 
ncurses-6.1          | 958 KB    | ##################################### | 100% 
sqlite-3.28.0        | 1.9 MB    | ##################################### | 100% 
python-2.7.16        | 12.8 MB   | ##################################### | 100% 
scipy-0.18.1         | 32.3 MB   | ##################################### | 100% 
protobuf-3.6.1       | 620 KB    | ##################################### | 100% 
libedit-3.1.20181209 | 188 KB    | ##################################### | 100% 
pycairo-1.10.0       | 81 KB     | ##################################### | 100% 
pillow-4.2.1         | 843 KB    | ##################################### | 100% 
conda-4.6.14         | 2.1 MB    | ##################################### | 100% 
readline-7.0         | 392 KB    | ##################################### | 100% 
qt-4.8.7             | 34.1 MB   | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Couldn't work around bad skimage installation
Here's some info:

Traceback (most recent call last):
 File "<string>", line 1, in <module>
 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 5, in <module>
   from .apply_parallel import apply_parallel
 File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/skimage/util/apply_parallel.py", line 8, in <module>
   import dask.array as da
 File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/dask/array/__init__.py", line 5, in <module>
   from .core import (Array, block, concatenate, stack, from_array, store,
 File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/dask/array/core.py", line 29, in <module>
   from . import chunk
 File "/home/GRAMES.POLYMTL.CA/u100542/sct/python/lib/python2.7/site-packages/dask/array/chunk.py", line 73, in <module>
   nancumprod = npcompat.nancumprod
AttributeError: 'module' object has no attribute 'nancumprod'

Traceback (most recent call last):
 File "/home/GRAMES.POLYMTL.CA/u100542/sct/install/install_dependencies_with_workarounds.py", line 61, in <module>
   skimage_workarounds()
 File "/home/GRAMES.POLYMTL.CA/u100542/sct/install/install_dependencies_with_workarounds.py", line 57, in skimage_workarounds
   raise RuntimeError("Couldn't apply an skimage workaround")
RuntimeError: Couldn't apply an skimage workaround
Working around distribution issues failed.
Feel free to open an issue after looking at https://github.com/neuropoly/spinalcordtoolbox/issues/1704
Installation failed
OSX 10.13.6 
billie:~/GitHub/spinalcordtoolbox $ ./install_sct 

Welcome to the SCT installer!

SCT version ......... dev
Installation type ... in-place
Operating system .... osx
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: [/Users/nipin_local/GitHub/spinalcordtoolbox]
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 /Users/nipin_local/GitHub/spinalcordtoolbox/bin

Installing conda...
>> rm -rf /Users/nipin_local/GitHub/spinalcordtoolbox/python
>> mkdir -p /Users/nipin_local/GitHub/spinalcordtoolbox/python
 % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                Dload  Upload   Total   Spent    Left  Speed
100 20.3M  100 20.3M    0     0  86.7M      0 --:--:-- --:--:-- --:--:-- 87.1M
exit status is 0
>> bash /var/folders/4b/j2kgzyls5g33kf_44k9mcb0r0000gr/T/tmp.iAzcNzg4/miniconda.sh -p /Users/nipin_local/GitHub/spinalcordtoolbox/python -b -f
PREFIX=/Users/nipin_local/GitHub/spinalcordtoolbox/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
>> . /Users/nipin_local/GitHub/spinalcordtoolbox/python/bin/activate /Users/nipin_local/GitHub/spinalcordtoolbox/python
Fetching package metadata ...........
Solving package specifications: ..........

Package plan for installation in environment /Users/nipin_local/GitHub/spinalcordtoolbox/python:

The following packages will be downloaded:

   package                    |            build
   ---------------------------|-----------------
   conda-env-2.6.0            |                1           2 KB  conda-forge
   libcxxabi-8.0.0            |                2         134 KB  conda-forge
   libcxx-8.0.0               |                2         1.0 MB  conda-forge
   asn1crypto-0.24.0          |        py27_1003         154 KB  conda-forge
   attrs-19.1.0               |             py_0          32 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         132 KB  conda-forge
   ipaddress-1.0.22           |             py_1          18 KB  conda-forge
   ipython_genutils-0.2.0     |             py_1          21 KB  conda-forge
   libffi-3.2.1               |    h6de7cb9_1006          43 KB  conda-forge
   pycosat-0.6.3              |py27h1de35cc_1001         106 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         160 KB  conda-forge
   six-1.12.0                 |        py27_1000          21 KB  conda-forge
   cffi-1.12.3                |   py27hccf1714_0         207 KB  conda-forge
   pyrsistent-0.15.1          |   py27h01d97ff_0          84 KB  conda-forge
   python-dateutil-2.8.0      |             py_0         219 KB  conda-forge
   setuptools-41.0.1          |           py27_0         622 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         411 KB  conda-forge
   jsonschema-3.0.1           |           py27_0          83 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:         6.9 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
   attrs:            19.1.0-py_0           conda-forge
   certifi:          2019.3.9-py27_0       conda-forge
   cffi:             1.12.3-py27hccf1714_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:       3.0.1-py27_0          conda-forge
   jupyter_core:     4.4.0-py_0            conda-forge
   libcxx:           8.0.0-2               conda-forge
   libcxxabi:        8.0.0-2               conda-forge
   libffi:           3.2.1-h6de7cb9_1006   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
   pyrsistent:       0.15.1-py27h01d97ff_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-py27h1de35cc_1001 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   2.74 MB/s
libcxxabi-8.0. 100% |################################| Time: 0:00:00  32.59 MB/s
libcxx-8.0.0-2 100% |################################| Time: 0:00:00  53.60 MB/s
asn1crypto-0.2 100% |################################| Time: 0:00:00  48.89 MB/s
attrs-19.1.0-p 100% |################################| Time: 0:00:00  16.69 MB/s
certifi-2019.3 100% |################################| Time: 0:00:00  36.98 MB/s
chardet-3.0.4- 100% |################################| Time: 0:00:00  36.03 MB/s
decorator-4.4. 100% |################################| Time: 0:00:00  11.49 MB/s
enum34-1.1.6-p 100% |################################| Time: 0:00:00  34.04 MB/s
functools32-3. 100% |################################| Time: 0:00:00  11.48 MB/s
futures-3.2.0- 100% |################################| Time: 0:00:00  22.73 MB/s
idna-2.8-py27_ 100% |################################| Time: 0:00:00  38.20 MB/s
ipaddress-1.0. 100% |################################| Time: 0:00:00  17.46 MB/s
ipython_genuti 100% |################################| Time: 0:00:00  15.92 MB/s
libffi-3.2.1-h 100% |################################| Time: 0:00:00  23.42 MB/s
pycosat-0.6.3- 100% |################################| Time: 0:00:00  33.62 MB/s
pycparser-2.19 100% |################################| Time: 0:00:00  39.87 MB/s
pysocks-1.6.8- 100% |################################| Time: 0:00:00  18.78 MB/s
pytz-2019.1-py 100% |################################| Time: 0:00:00  49.30 MB/s
pyyaml-3.12-py 100% |################################| Time: 0:00:00  41.59 MB/s
six-1.12.0-py2 100% |################################| Time: 0:00:00  17.42 MB/s
cffi-1.12.3-py 100% |################################| Time: 0:00:00  40.64 MB/s
pyrsistent-0.1 100% |################################| Time: 0:00:00  27.80 MB/s
python-dateuti 100% |################################| Time: 0:00:00  42.20 MB/s
setuptools-41. 100% |################################| Time: 0:00:00   4.91 MB/s
traitlets-4.3. 100% |################################| Time: 0:00:00  35.66 MB/s
clyent-1.2.2-p 100% |################################| Time: 0:00:00   8.88 MB/s
cryptography-2 100% |################################| Time: 0:00:00  34.41 MB/s
jsonschema-3.0 100% |################################| Time: 0:00:00  30.69 MB/s
jupyter_core-4 100% |################################| Time: 0:00:00  21.30 MB/s
nbformat-4.4.0 100% |################################| Time: 0:00:00  32.85 MB/s
pyopenssl-19.0 100% |################################| Time: 0:00:00  27.00 MB/s
urllib3-1.24.2 100% |################################| Time: 0:00:00  30.33 MB/s
requests-2.21. 100% |################################| Time: 0:00:00  28.03 MB/s
anaconda-clien 100% |################################| Time: 0:00:00  24.05 MB/s
conda-4.6.14-p 100% |################################| Time: 0:00:00  64.71 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: /Users/nipin_local/GitHub/spinalcordtoolbox/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.functools_lru_cache-1.5|             py_1           6 KB  conda-forge
   backports.weakref-1.0rc1   |           py27_1           7 KB  conda-forge
   backports_abc-0.5          |             py_1           5 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
   cloudpickle-0.8.1          |             py_0          17 KB  conda-forge
   cryptography-2.6.1         |   py27h212c5bf_0         568 KB  conda-forge
   cycler-0.10.0              |             py_1           8 KB  conda-forge
   cytoolz-0.9.0.1            |py27h1de35cc_1001         354 KB  conda-forge
   dask-core-1.2.1            |             py_0         534 KB  conda-forge
   freetype-2.10.0            |       h24853df_0         881 KB  conda-forge
   funcsigs-1.0.2             |             py_3          14 KB  conda-forge
   html5lib-0.9999999         |           py27_0         187 KB  conda-forge
   imageio-2.5.0              |           py27_0         3.4 MB  conda-forge
   intel-openmp-2019.3        |              199         1.1 MB
   jpeg-9c                    |    h1de35cc_1001         237 KB  conda-forge
   kiwisolver-1.1.0           |   py27h770b8ee_0          58 KB  conda-forge
   libblas-3.8.0              |5_hd44dcd8_netlib         194 KB  conda-forge
   libcblas-3.8.0             |5_hd44dcd8_netlib          42 KB  conda-forge
   libgfortran-3.0.1          |                0         495 KB  conda-forge
   liblapack-3.8.0            |5_hd44dcd8_netlib         2.8 MB  conda-forge
   libpng-1.6.37              |       h2573ce8_0         298 KB  conda-forge
   libprotobuf-3.7.1          |       hfbae3c0_0         4.3 MB  conda-forge
   libtiff-4.0.10             |    h79f4b77_1001         486 KB  conda-forge
   markdown-2.6.11            |             py_0          56 KB  conda-forge
   matplotlib-2.2.3           |           py27_1           6 KB  conda-forge
   matplotlib-base-2.2.3      |   py27hd64abcd_1         6.4 MB  conda-forge
   mkl-2018.0.3               |                1       149.2 MB
   mkl-service-1.1.2          |   py27h6b9c3cc_4          10 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         3.5 MB  conda-forge
   olefile-0.46               |             py_0          31 KB  conda-forge
   openblas-0.2.18            |                6        16.5 MB  conda-forge
   openssl-1.1.1b             |       h01d97ff_2         3.5 MB  conda-forge
   pandas-0.23.4              |py27h1702cab_1000         9.1 MB  conda-forge
   pbr-5.1.3                  |             py_0          70 KB  conda-forge
   pillow-6.0.0               |   py27h7095ceb_0         583 KB  conda-forge
   pip-19.1                   |           py27_0         1.8 MB  conda-forge
   protobuf-3.7.1             |   py27h6de7cb9_0         626 KB  conda-forge
   psutil-5.6.2               |   py27h01d97ff_0         322 KB  conda-forge
   pyparsing-2.4.0            |             py_0          55 KB  conda-forge
   pyqt-4.11.4                |           py27_2         3.9 MB  conda-forge
   python-2.7.3               |                5        10.0 MB
   pywavelets-1.0.3           |   py27h1e5eb4f_1         4.3 MB  conda-forge
   qt-4.8.7                   |                1        39.0 MB
   scikit-image-0.14.2        |   py27h0a44026_1        23.3 MB  conda-forge
   scikit-learn-0.17.1        |np111py27_blas_openblas_202         3.8 MB  conda-forge
   scipy-1.2.1                |   py27hbd7caa9_1        15.7 MB  conda-forge
   singledispatch-3.4.0.3     |        py27_1000          15 KB  conda-forge
   sip-4.18                   |           py27_1         247 KB  conda-forge
   subprocess32-3.5.3         |   py27h470a237_0          43 KB  conda-forge
   tensorflow-1.3.0           |           py27_0        32.5 MB  conda-forge
   tk-8.6.9                   |    ha441bb4_1001         3.2 MB  conda-forge
   toolz-0.9.0                |             py_1          42 KB  conda-forge
   tornado-5.1.1              |py27h1de35cc_1000         642 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                   |    h1de35cc_1001         268 KB  conda-forge
   zlib-1.2.11                |    h1de35cc_1004         101 KB  conda-forge
   ------------------------------------------------------------
                                          Total:       346.6 MB

The following NEW packages will be INSTALLED:

 backports          conda-forge/noarch::backports-1.0-py_2
 backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.5-py_1
 backports.weakref  conda-forge/osx-64::backports.weakref-1.0rc1-py27_1
 backports_abc      conda-forge/noarch::backports_abc-0.5-py_1
 blas               conda-forge/osx-64::blas-1.1-openblas
 bleach             conda-forge/osx-64::bleach-1.5.0-py27_0
 ca-certificates    conda-forge/osx-64::ca-certificates-2019.3.9-hecc5488_0
 cloudpickle        conda-forge/noarch::cloudpickle-0.8.1-py_0
 cycler             conda-forge/noarch::cycler-0.10.0-py_1
 cytoolz            conda-forge/osx-64::cytoolz-0.9.0.1-py27h1de35cc_1001
 dask-core          conda-forge/noarch::dask-core-1.2.1-py_0
 freetype           conda-forge/osx-64::freetype-2.10.0-h24853df_0
 funcsigs           conda-forge/noarch::funcsigs-1.0.2-py_3
 html5lib           conda-forge/osx-64::html5lib-0.9999999-py27_0
 imageio            conda-forge/osx-64::imageio-2.5.0-py27_0
 intel-openmp       pkgs/main/osx-64::intel-openmp-2019.3-199
 jpeg               conda-forge/osx-64::jpeg-9c-h1de35cc_1001
 kiwisolver         conda-forge/osx-64::kiwisolver-1.1.0-py27h770b8ee_0
 libblas            conda-forge/osx-64::libblas-3.8.0-5_hd44dcd8_netlib
 libcblas           conda-forge/osx-64::libcblas-3.8.0-5_hd44dcd8_netlib
 libgfortran        conda-forge/osx-64::libgfortran-3.0.1-0
 liblapack          conda-forge/osx-64::liblapack-3.8.0-5_hd44dcd8_netlib
 libpng             conda-forge/osx-64::libpng-1.6.37-h2573ce8_0
 libprotobuf        conda-forge/osx-64::libprotobuf-3.7.1-hfbae3c0_0
 libtiff            conda-forge/osx-64::libtiff-4.0.10-h79f4b77_1001
 markdown           conda-forge/noarch::markdown-2.6.11-py_0
 matplotlib         conda-forge/osx-64::matplotlib-2.2.3-py27_1
 matplotlib-base    conda-forge/osx-64::matplotlib-base-2.2.3-py27hd64abcd_1
 mkl                pkgs/main/osx-64::mkl-2018.0.3-1
 mkl-service        pkgs/main/osx-64::mkl-service-1.1.2-py27h6b9c3cc_4
 mock               conda-forge/osx-64::mock-2.0.0-py27_1001
 networkx           conda-forge/noarch::networkx-2.2-py_1
 numpy              conda-forge/osx-64::numpy-1.11.3-py27_blas_openblas_201
 olefile            conda-forge/noarch::olefile-0.46-py_0
 openblas           conda-forge/osx-64::openblas-0.2.18-6
 pandas             conda-forge/osx-64::pandas-0.23.4-py27h1702cab_1000
 pbr                conda-forge/noarch::pbr-5.1.3-py_0
 pillow             conda-forge/osx-64::pillow-6.0.0-py27h7095ceb_0
 protobuf           conda-forge/osx-64::protobuf-3.7.1-py27h6de7cb9_0
 psutil             conda-forge/osx-64::psutil-5.6.2-py27h01d97ff_0
 pyparsing          conda-forge/noarch::pyparsing-2.4.0-py_0
 pyqt               conda-forge/osx-64::pyqt-4.11.4-py27_2
 pywavelets         conda-forge/osx-64::pywavelets-1.0.3-py27h1e5eb4f_1
 qt                 pkgs/free/osx-64::qt-4.8.7-1
 scikit-image       conda-forge/osx-64::scikit-image-0.14.2-py27h0a44026_1
 scikit-learn       conda-forge/osx-64::scikit-learn-0.17.1-np111py27_blas_openblas_202
 scipy              conda-forge/osx-64::scipy-1.2.1-py27hbd7caa9_1
 singledispatch     conda-forge/osx-64::singledispatch-3.4.0.3-py27_1000
 sip                conda-forge/osx-64::sip-4.18-py27_1
 subprocess32       conda-forge/osx-64::subprocess32-3.5.3-py27h470a237_0
 tensorflow         conda-forge/osx-64::tensorflow-1.3.0-py27_0
 toolz              conda-forge/noarch::toolz-0.9.0-py_1
 tornado            conda-forge/osx-64::tornado-5.1.1-py27h1de35cc_1000
 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/osx-64::xlutils-2.0.0-py27_1
 xlwt               conda-forge/noarch::xlwt-1.3.0-py_1
 xz                 conda-forge/osx-64::xz-5.2.4-h1de35cc_1001

The following packages will be UPDATED:

 cryptography                                 2.2.1-py27_0 --> 2.6.1-py27h212c5bf_0
 openssl                       pkgs/free::openssl-1.0.2h-1 --> conda-forge::openssl-1.1.1b-h01d97ff_2
 pip                           pkgs/free::pip-8.1.2-py27_0 --> conda-forge::pip-19.1-py27_0
 tk                                 pkgs/free::tk-8.5.18-0 --> conda-forge::tk-8.6.9-ha441bb4_1001
 zlib                              pkgs/free::zlib-1.2.8-3 --> conda-forge::zlib-1.2.11-h1de35cc_1004

The following packages will be DOWNGRADED:

 python                                           2.7.12-1 --> 2.7.3-5



Downloading and Extracting Packages
cycler-0.10.0        | 8 KB      | ##################################### | 100% 
toolz-0.9.0          | 42 KB     | ##################################### | 100% 
networkx-2.2         | 1.1 MB    | ##################################### | 100% 
jpeg-9c              | 237 KB    | ##################################### | 100% 
werkzeug-0.15.2      | 257 KB    | ##################################### | 100% 
markdown-2.6.11      | 56 KB     | ##################################### | 100% 
backports_abc-0.5    | 5 KB      | ##################################### | 100% 
libgfortran-3.0.1    | 495 KB    | ##################################### | 100% 
mkl-service-1.1.2    | 10 KB     | ##################################### | 100% 
imageio-2.5.0        | 3.4 MB    | ##################################### | 100% 
numpy-1.11.3         | 3.5 MB    | ##################################### | 100% 
tk-8.6.9             | 3.2 MB    | ##################################### | 100% 
pyqt-4.11.4          | 3.9 MB    | ##################################### | 100% 
cytoolz-0.9.0.1      | 354 KB    | ##################################### | 100% 
webencodings-0.5.1   | 12 KB     | ##################################### | 100% 
matplotlib-base-2.2. | 6.4 MB    | ##################################### | 100% 
pyparsing-2.4.0      | 55 KB     | ##################################### | 100% 
ca-certificates-2019 | 146 KB    | ##################################### | 100% 
backports.functools_ | 6 KB      | ##################################### | 100% 
protobuf-3.7.1       | 626 KB    | ##################################### | 100% 
scikit-image-0.14.2  | 23.3 MB   | ##################################### | 100% 
dask-core-1.2.1      | 534 KB    | ##################################### | 100% 
pywavelets-1.0.3     | 4.3 MB    | ##################################### | 100% 
backports-1.0        | 4 KB      | ##################################### | 100% 
subprocess32-3.5.3   | 43 KB     | ##################################### | 100% 
xlrd-1.2.0           | 108 KB    | ##################################### | 100% 
zlib-1.2.11          | 101 KB    | ##################################### | 100% 
sip-4.18             | 247 KB    | ##################################### | 100% 
html5lib-0.9999999   | 187 KB    | ##################################### | 100% 
libblas-3.8.0        | 194 KB    | ##################################### | 100% 
scipy-1.2.1          | 15.7 MB   | ##################################### | 100% 
mock-2.0.0           | 102 KB    | ##################################### | 100% 
xlutils-2.0.0        | 76 KB     | ##################################### | 100% 
xlwt-1.3.0           | 83 KB     | ##################################### | 100% 
backports.weakref-1. | 7 KB      | ##################################### | 100% 
libcblas-3.8.0       | 42 KB     | ##################################### | 100% 
pandas-0.23.4        | 9.1 MB    | ##################################### | 100% 
python-2.7.3         | 10.0 MB   | ##################################### | 100% 
libpng-1.6.37        | 298 KB    | ##################################### | 100% 
singledispatch-3.4.0 | 15 KB     | ##################################### | 100% 
libtiff-4.0.10       | 486 KB    | ##################################### | 100% 
qt-4.8.7             | 39.0 MB   | ##################################### | 100% 
cryptography-2.6.1   | 568 KB    | ##################################### | 100% 
pbr-5.1.3            | 70 KB     | ##################################### | 100% 
openssl-1.1.1b       | 3.5 MB    | ##################################### | 100% 
matplotlib-2.2.3     | 6 KB      | ##################################### | 100% 
mkl-2018.0.3         | 149.2 MB  | ##################################### | 100% 
tensorflow-1.3.0     | 32.5 MB   | ##################################### | 100% 
pillow-6.0.0         | 583 KB    | ##################################### | 100% 
pip-19.1             | 1.8 MB    | ##################################### | 100% 
psutil-5.6.2         | 322 KB    | ##################################### | 100% 
openblas-0.2.18      | 16.5 MB   | ##################################### | 100% 
xz-5.2.4             | 268 KB    | ##################################### | 100% 
cloudpickle-0.8.1    | 17 KB     | ##################################### | 100% 
bleach-1.5.0         | 23 KB     | ##################################### | 100% 
scikit-learn-0.17.1  | 3.8 MB    | ##################################### | 100% 
intel-openmp-2019.3  | 1.1 MB    | ##################################### | 100% 
funcsigs-1.0.2       | 14 KB     | ##################################### | 100% 
olefile-0.46         | 31 KB     | ##################################### | 100% 
freetype-2.10.0      | 881 KB    | ##################################### | 100% 
tornado-5.1.1        | 642 KB    | ##################################### | 100% 
liblapack-3.8.0      | 2.8 MB    | ##################################### | 100% 
blas-1.1             | 1 KB      | ##################################### | 100% 
libprotobuf-3.7.1    | 4.3 MB    | ##################################### | 100% 
kiwisolver-1.1.0     | 58 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:///Users/nipin_local/GitHub/spinalcordtoolbox
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/98/06/0e711ae0c95d92ec238218448a15c23590cb117ded59e4bfa322b085b59e/h5py-2.9.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already satisfied: matplotlib in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.2.3)
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/ed/7f/c4e27b1701ce1fc86cfe7c75c981ccab9be30f38dd409dcc2b1a50c0b4e2/nipy-0.4.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_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) (5.6.2)
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) (0.14.2)
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
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
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)
Requirement already satisfied: cycler>=0.10 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2.4.0)
Collecting python-dateutil>=2.1 (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: kiwisolver>=1.0.1 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (1.1.0)
Requirement already satisfied: backports.functools_lru_cache in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (1.5)
Requirement already satisfied: subprocess32 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (3.5.3)
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: certifi>=2017.4.17 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (2019.3.9)
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: networkx>=1.8 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (2.2)
Requirement already satisfied: pillow>=4.3.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (6.0.0)
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: dask[array]>=1.0.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (1.2.1)
Requirement already satisfied: cloudpickle>=0.2.1 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (0.8.1)
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: wheel in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (0.29.0)
Requirement already satisfied: backports.weakref>=1.0rc1 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (1.0rc1)
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: protobuf>=3.3.0 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (3.7.1)
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) (2.6.1)
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
Requirement already satisfied: setuptools in ./python/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib->spinalcordtoolbox===dev) (41.0.1)
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: toolz>=0.7.3; extra == "array" in ./python/lib/python2.7/site-packages (from dask[array]>=1.0.0->scikit-image->spinalcordtoolbox===dev) (0.9.0)
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: 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: 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: 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: 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) (1.12.3)
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: h5py, keras-applications, keras-preprocessing, 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
Trying workaround
/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible.
 utils.PersistentlyDeprecated2018,
Collecting package metadata: done
Solving environment: done

## Package Plan ##

 environment location: /Users/nipin_local/GitHub/spinalcordtoolbox/python

 added / updated specs:
   - nomkl


The following packages will be downloaded:

   package                    |            build
   ---------------------------|-----------------
   blas-2.7                   |         openblas           6 KB  conda-forge
   ca-certificates-2019.1.23  |                0         126 KB
   certifi-2019.3.9           |           py27_0         155 KB
   conda-4.6.14               |           py27_0         2.1 MB
   libblas-3.8.0              |       7_openblas           6 KB  conda-forge
   libcblas-3.8.0             |       7_openblas           6 KB  conda-forge
   liblapack-3.8.0            |       7_openblas           6 KB  conda-forge
   liblapacke-3.8.0           |       7_openblas           6 KB  conda-forge
   libopenblas-0.3.3          |       hdc02c5d_3         8.4 MB
   nomkl-3.0                  |                0          48 KB
   numpy-1.11.3               |  py27h926163e_12          16 KB
   numpy-base-1.11.3          |  py27ha711998_12         3.4 MB
   openblas-0.3.5             |    h436c29b_1001        17.5 MB  conda-forge
   openssl-1.1.1b             |       h1de35cc_1         3.4 MB
   scikit-learn-0.17.1        |np111py27_nomkl_2         3.7 MB
   ------------------------------------------------------------
                                          Total:        39.0 MB

The following NEW packages will be INSTALLED:

 liblapacke         conda-forge/osx-64::liblapacke-3.8.0-7_openblas
 libopenblas        pkgs/main/osx-64::libopenblas-0.3.3-hdc02c5d_3
 nomkl              pkgs/free/osx-64::nomkl-3.0-0
 numpy-base         pkgs/main/osx-64::numpy-base-1.11.3-py27ha711998_12

The following packages will be UPDATED:

 blas                                         1.1-openblas --> 2.7-openblas
 libblas                           3.8.0-5_hd44dcd8_netlib --> 3.8.0-7_openblas
 libcblas                          3.8.0-5_hd44dcd8_netlib --> 3.8.0-7_openblas
 liblapack                         3.8.0-5_hd44dcd8_netlib --> 3.8.0-7_openblas
 openblas                                         0.2.18-6 --> 0.3.5-h436c29b_1001

The following packages will be SUPERSEDED by a higher-priority channel:

 ca-certificates    conda-forge::ca-certificates-2019.3.9~ --> pkgs/main::ca-certificates-2019.1.23-0
 certifi                                       conda-forge --> pkgs/main
 conda                                         conda-forge --> pkgs/main
 numpy              conda-forge::numpy-1.11.3-py27_blas_o~ --> pkgs/main::numpy-1.11.3-py27h926163e_12
 openssl            conda-forge::openssl-1.1.1b-h01d97ff_2 --> pkgs/main::openssl-1.1.1b-h1de35cc_1
 scikit-learn       conda-forge::scikit-learn-0.17.1-np11~ --> pkgs/free::scikit-learn-0.17.1-np111py27_nomkl_2



Downloading and Extracting Packages
scikit-learn-0.17.1  | 3.7 MB    | ##################################### | 100% 
openssl-1.1.1b       | 3.4 MB    | ##################################### | 100% 
libopenblas-0.3.3    | 8.4 MB    | ##################################### | 100% 
liblapack-3.8.0      | 6 KB      | ##################################### | 100% 
conda-4.6.14         | 2.1 MB    | ##################################### | 100% 
openblas-0.3.5       | 17.5 MB   | ##################################### | 100% 
ca-certificates-2019 | 126 KB    | ##################################### | 100% 
certifi-2019.3.9     | 155 KB    | ##################################### | 100% 
blas-2.7             | 6 KB      | ##################################### | 100% 
libblas-3.8.0        | 6 KB      | ##################################### | 100% 
numpy-base-1.11.3    | 3.4 MB    | ##################################### | 100% 
nomkl-3.0            | 48 KB     | ##################################### | 100% 
libcblas-3.8.0       | 6 KB      | ##################################### | 100% 
liblapacke-3.8.0     | 6 KB      | ##################################### | 100% 
numpy-1.11.3         | 16 KB     | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Couldn't work around bad skimage installation
Here's some info:

Traceback (most recent call last):
 File "<string>", line 1, in <module>
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/__init__.py", line 167, in <module>
   from .util.dtype import (img_as_float32,
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/util/__init__.py", line 6, in <module>
   from .apply_parallel import apply_parallel
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/skimage/util/apply_parallel.py", line 8, in <module>
   import dask.array as da
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/__init__.py", line 5, in <module>
   from .core import (Array, block, concatenate, stack, from_array, store,
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/core.py", line 29, in <module>
   from . import chunk
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/python/lib/python2.7/site-packages/dask/array/chunk.py", line 73, in <module>
   nancumprod = npcompat.nancumprod
AttributeError: 'module' object has no attribute 'nancumprod'

Traceback (most recent call last):
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/install/install_dependencies_with_workarounds.py", line 61, in <module>
   skimage_workarounds()
 File "/Users/nipin_local/GitHub/spinalcordtoolbox/install/install_dependencies_with_workarounds.py", line 57, in skimage_workarounds
   raise RuntimeError("Couldn't apply an skimage workaround")
RuntimeError: Couldn't apply an skimage workaround
Working around distribution issues failed.
Feel free to open an issue after looking at https://github.com/neuropoly/spinalcordtoolbox/issues/1704
Installation failed
@Nicolas-Pinon Nicolas-Pinon added bug category: fixes an error in the code installation category: install_sct or pip/setup.py labels Apr 30, 2019
@jcohenadad
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@alexfoias can you try please?

i suspect this is a py2k compatibility issue, which means we should merge #2238 asap. @Nicolas-Pinon do you get an error when installing the jca/py3k branch?

@alexfoias
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@jcohenadad It failed for me on OSX 10.14.3 on commit b0bc30bea4dd43cbea5f8b89d940daf6d8121632.


alex-macbook:~/code/spinalcordtoolbox $ ./install_sct 

Welcome to the SCT installer!

SCT version ......... dev
Installation type ... in-place
Operating system .... osx
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: [/Users/alfoi/code/spinalcordtoolbox]
Do you agree? [y]es/[n]o: y

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

Installing conda...
>> rm -rf /Users/alfoi/code/spinalcordtoolbox/python
>> mkdir -p /Users/alfoi/code/spinalcordtoolbox/python
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 20.3M  100 20.3M    0     0  58.5M      0 --:--:-- --:--:-- --:--:-- 58.5M
exit status is 0
>> bash /var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/tmp.44Nb763D/miniconda.sh -p /Users/alfoi/code/spinalcordtoolbox/python -b -f
PREFIX=/Users/alfoi/code/spinalcordtoolbox/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
>> . /Users/alfoi/code/spinalcordtoolbox/python/bin/activate /Users/alfoi/code/spinalcordtoolbox/python
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /Users/alfoi/code/spinalcordtoolbox/python:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    conda-env-2.6.0            |                1           2 KB  conda-forge
    libcxxabi-8.0.0            |                2         134 KB  conda-forge
    libcxx-8.0.0               |                2         1.0 MB  conda-forge
    asn1crypto-0.24.0          |        py27_1003         154 KB  conda-forge
    attrs-19.1.0               |             py_0          32 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         132 KB  conda-forge
    ipaddress-1.0.22           |             py_1          18 KB  conda-forge
    ipython_genutils-0.2.0     |             py_1          21 KB  conda-forge
    libffi-3.2.1               |    h6de7cb9_1006          43 KB  conda-forge
    pycosat-0.6.3              |py27h1de35cc_1001         106 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         160 KB  conda-forge
    six-1.12.0                 |        py27_1000          21 KB  conda-forge
    cffi-1.12.3                |   py27hccf1714_0         207 KB  conda-forge
    pyrsistent-0.15.1          |   py27h01d97ff_0          84 KB  conda-forge
    python-dateutil-2.8.0      |             py_0         219 KB  conda-forge
    setuptools-41.0.1          |           py27_0         622 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         411 KB  conda-forge
    jsonschema-3.0.1           |           py27_0          83 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:         6.9 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
    attrs:            19.1.0-py_0           conda-forge
    certifi:          2019.3.9-py27_0       conda-forge
    cffi:             1.12.3-py27hccf1714_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:       3.0.1-py27_0          conda-forge
    jupyter_core:     4.4.0-py_0            conda-forge
    libcxx:           8.0.0-2               conda-forge
    libcxxabi:        8.0.0-2               conda-forge
    libffi:           3.2.1-h6de7cb9_1006   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
    pyrsistent:       0.15.1-py27h01d97ff_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-py27h1de35cc_1001 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   1.60 MB/s
libcxxabi-8.0. 100% |################################| Time: 0:00:00  19.31 MB/s
libcxx-8.0.0-2 100% |################################| Time: 0:00:00  34.89 MB/s
asn1crypto-0.2 100% |################################| Time: 0:00:00  25.96 MB/s
attrs-19.1.0-p 100% |################################| Time: 0:00:00  18.94 MB/s
certifi-2019.3 100% |################################| Time: 0:00:00  28.27 MB/s
chardet-3.0.4- 100% |################################| Time: 0:00:00  26.94 MB/s
decorator-4.4. 100% |################################| Time: 0:00:00   8.75 MB/s
enum34-1.1.6-p 100% |################################| Time: 0:00:00  19.27 MB/s
functools32-3. 100% |################################| Time: 0:00:00  12.93 MB/s
futures-3.2.0- 100% |################################| Time: 0:00:00  14.91 MB/s
idna-2.8-py27_ 100% |################################| Time: 0:00:00  26.94 MB/s
ipaddress-1.0. 100% |################################| Time: 0:00:00  12.43 MB/s
ipython_genuti 100% |################################| Time: 0:00:00  10.79 MB/s
libffi-3.2.1-h 100% |################################| Time: 0:00:00  19.26 MB/s
pycosat-0.6.3- 100% |################################| Time: 0:00:00  22.70 MB/s
pycparser-2.19 100% |################################| Time: 0:00:00  28.80 MB/s
pysocks-1.6.8- 100% |################################| Time: 0:00:00   6.25 MB/s
pytz-2019.1-py 100% |################################| Time: 0:00:00  23.03 MB/s
pyyaml-3.12-py 100% |################################| Time: 0:00:00  26.47 MB/s
six-1.12.0-py2 100% |################################| Time: 0:00:00  11.58 MB/s
cffi-1.12.3-py 100% |################################| Time: 0:00:00  23.34 MB/s
pyrsistent-0.1 100% |################################| Time: 0:00:00  24.33 MB/s
python-dateuti 100% |################################| Time: 0:00:00  30.78 MB/s
setuptools-41. 100% |################################| Time: 0:00:00  29.59 MB/s
traitlets-4.3. 100% |################################| Time: 0:00:00  21.29 MB/s
clyent-1.2.2-p 100% |################################| Time: 0:00:00   8.78 MB/s
cryptography-2 100% |################################| Time: 0:00:00  33.61 MB/s
jsonschema-3.0 100% |################################| Time: 0:00:00  23.37 MB/s
jupyter_core-4 100% |################################| Time: 0:00:00   8.22 MB/s
nbformat-4.4.0 100% |################################| Time: 0:00:00  24.51 MB/s
pyopenssl-19.0 100% |################################| Time: 0:00:00  22.80 MB/s
urllib3-1.24.2 100% |################################| Time: 0:00:00  21.36 MB/s
requests-2.21. 100% |################################| Time: 0:00:00  23.38 MB/s
anaconda-clien 100% |################################| Time: 0:00:00  19.96 MB/s
conda-4.6.14-p 100% |################################| Time: 0:00:00  24.99 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: /Users/alfoi/code/spinalcordtoolbox/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.functools_lru_cache-1.5|             py_1           6 KB  conda-forge
    backports.weakref-1.0rc1   |           py27_1           7 KB  conda-forge
    backports_abc-0.5          |             py_1           5 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
    cloudpickle-0.8.1          |             py_0          17 KB  conda-forge
    cryptography-2.6.1         |   py27h212c5bf_0         568 KB  conda-forge
    cycler-0.10.0              |             py_1           8 KB  conda-forge
    cytoolz-0.9.0.1            |py27h1de35cc_1001         354 KB  conda-forge
    dask-core-1.2.1            |             py_0         534 KB  conda-forge
    freetype-2.10.0            |       h24853df_0         881 KB  conda-forge
    funcsigs-1.0.2             |             py_3          14 KB  conda-forge
    html5lib-0.9999999         |           py27_0         187 KB  conda-forge
    imageio-2.5.0              |           py27_0         3.4 MB  conda-forge
    intel-openmp-2019.3        |              199         1.1 MB
    jpeg-9c                    |    h1de35cc_1001         237 KB  conda-forge
    kiwisolver-1.1.0           |   py27h770b8ee_0          58 KB  conda-forge
    libblas-3.8.0              |5_hd44dcd8_netlib         194 KB  conda-forge
    libcblas-3.8.0             |5_hd44dcd8_netlib          42 KB  conda-forge
    libgfortran-3.0.1          |                0         495 KB  conda-forge
    liblapack-3.8.0            |5_hd44dcd8_netlib         2.8 MB  conda-forge
    libpng-1.6.37              |       h2573ce8_0         298 KB  conda-forge
    libprotobuf-3.7.1          |       hfbae3c0_0         4.3 MB  conda-forge
    libtiff-4.0.10             |    h79f4b77_1001         486 KB  conda-forge
    markdown-2.6.11            |             py_0          56 KB  conda-forge
    matplotlib-2.2.3           |           py27_1           6 KB  conda-forge
    matplotlib-base-2.2.3      |   py27hd64abcd_1         6.4 MB  conda-forge
    mkl-2018.0.3               |                1       149.2 MB
    mkl-service-1.1.2          |   py27h6b9c3cc_4          10 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         3.5 MB  conda-forge
    olefile-0.46               |             py_0          31 KB  conda-forge
    openblas-0.2.18            |                6        16.5 MB  conda-forge
    openssl-1.1.1b             |       h01d97ff_2         3.5 MB  conda-forge
    pandas-0.23.4              |py27h1702cab_1000         9.1 MB  conda-forge
    pbr-5.1.3                  |             py_0          70 KB  conda-forge
    pillow-6.0.0               |   py27h7095ceb_0         583 KB  conda-forge
    pip-19.1                   |           py27_0         1.8 MB  conda-forge
    protobuf-3.7.1             |   py27h6de7cb9_0         626 KB  conda-forge
    psutil-5.6.2               |   py27h01d97ff_0         322 KB  conda-forge
    pyparsing-2.4.0            |             py_0          55 KB  conda-forge
    pyqt-4.11.4                |           py27_2         3.9 MB  conda-forge
    python-2.7.3               |                5        10.0 MB
    pywavelets-1.0.3           |   py27h1e5eb4f_1         4.3 MB  conda-forge
    qt-4.8.7                   |                1        39.0 MB
    scikit-image-0.14.2        |   py27h0a44026_1        23.3 MB  conda-forge
    scikit-learn-0.17.1        |np111py27_blas_openblas_202         3.8 MB  conda-forge
    scipy-1.2.1                |   py27hbd7caa9_1        15.7 MB  conda-forge
    singledispatch-3.4.0.3     |        py27_1000          15 KB  conda-forge
    sip-4.18                   |           py27_1         247 KB  conda-forge
    subprocess32-3.5.3         |   py27h470a237_0          43 KB  conda-forge
    tensorflow-1.3.0           |           py27_0        32.5 MB  conda-forge
    tk-8.6.9                   |    ha441bb4_1001         3.2 MB  conda-forge
    toolz-0.9.0                |             py_1          42 KB  conda-forge
    tornado-5.1.1              |py27h1de35cc_1000         642 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                   |    h1de35cc_1001         268 KB  conda-forge
    zlib-1.2.11                |    h1de35cc_1004         101 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       346.6 MB

The following NEW packages will be INSTALLED:

  backports          conda-forge/noarch::backports-1.0-py_2
  backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.5-py_1
  backports.weakref  conda-forge/osx-64::backports.weakref-1.0rc1-py27_1
  backports_abc      conda-forge/noarch::backports_abc-0.5-py_1
  blas               conda-forge/osx-64::blas-1.1-openblas
  bleach             conda-forge/osx-64::bleach-1.5.0-py27_0
  ca-certificates    conda-forge/osx-64::ca-certificates-2019.3.9-hecc5488_0
  cloudpickle        conda-forge/noarch::cloudpickle-0.8.1-py_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_1
  cytoolz            conda-forge/osx-64::cytoolz-0.9.0.1-py27h1de35cc_1001
  dask-core          conda-forge/noarch::dask-core-1.2.1-py_0
  freetype           conda-forge/osx-64::freetype-2.10.0-h24853df_0
  funcsigs           conda-forge/noarch::funcsigs-1.0.2-py_3
  html5lib           conda-forge/osx-64::html5lib-0.9999999-py27_0
  imageio            conda-forge/osx-64::imageio-2.5.0-py27_0
  intel-openmp       pkgs/main/osx-64::intel-openmp-2019.3-199
  jpeg               conda-forge/osx-64::jpeg-9c-h1de35cc_1001
  kiwisolver         conda-forge/osx-64::kiwisolver-1.1.0-py27h770b8ee_0
  libblas            conda-forge/osx-64::libblas-3.8.0-5_hd44dcd8_netlib
  libcblas           conda-forge/osx-64::libcblas-3.8.0-5_hd44dcd8_netlib
  libgfortran        conda-forge/osx-64::libgfortran-3.0.1-0
  liblapack          conda-forge/osx-64::liblapack-3.8.0-5_hd44dcd8_netlib
  libpng             conda-forge/osx-64::libpng-1.6.37-h2573ce8_0
  libprotobuf        conda-forge/osx-64::libprotobuf-3.7.1-hfbae3c0_0
  libtiff            conda-forge/osx-64::libtiff-4.0.10-h79f4b77_1001
  markdown           conda-forge/noarch::markdown-2.6.11-py_0
  matplotlib         conda-forge/osx-64::matplotlib-2.2.3-py27_1
  matplotlib-base    conda-forge/osx-64::matplotlib-base-2.2.3-py27hd64abcd_1
  mkl                pkgs/main/osx-64::mkl-2018.0.3-1
  mkl-service        pkgs/main/osx-64::mkl-service-1.1.2-py27h6b9c3cc_4
  mock               conda-forge/osx-64::mock-2.0.0-py27_1001
  networkx           conda-forge/noarch::networkx-2.2-py_1
  numpy              conda-forge/osx-64::numpy-1.11.3-py27_blas_openblas_201
  olefile            conda-forge/noarch::olefile-0.46-py_0
  openblas           conda-forge/osx-64::openblas-0.2.18-6
  pandas             conda-forge/osx-64::pandas-0.23.4-py27h1702cab_1000
  pbr                conda-forge/noarch::pbr-5.1.3-py_0
  pillow             conda-forge/osx-64::pillow-6.0.0-py27h7095ceb_0
  protobuf           conda-forge/osx-64::protobuf-3.7.1-py27h6de7cb9_0
  psutil             conda-forge/osx-64::psutil-5.6.2-py27h01d97ff_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.0-py_0
  pyqt               conda-forge/osx-64::pyqt-4.11.4-py27_2
  pywavelets         conda-forge/osx-64::pywavelets-1.0.3-py27h1e5eb4f_1
  qt                 pkgs/free/osx-64::qt-4.8.7-1
  scikit-image       conda-forge/osx-64::scikit-image-0.14.2-py27h0a44026_1
  scikit-learn       conda-forge/osx-64::scikit-learn-0.17.1-np111py27_blas_openblas_202
  scipy              conda-forge/osx-64::scipy-1.2.1-py27hbd7caa9_1
  singledispatch     conda-forge/osx-64::singledispatch-3.4.0.3-py27_1000
  sip                conda-forge/osx-64::sip-4.18-py27_1
  subprocess32       conda-forge/osx-64::subprocess32-3.5.3-py27h470a237_0
  tensorflow         conda-forge/osx-64::tensorflow-1.3.0-py27_0
  toolz              conda-forge/noarch::toolz-0.9.0-py_1
  tornado            conda-forge/osx-64::tornado-5.1.1-py27h1de35cc_1000
  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/osx-64::xlutils-2.0.0-py27_1
  xlwt               conda-forge/noarch::xlwt-1.3.0-py_1
  xz                 conda-forge/osx-64::xz-5.2.4-h1de35cc_1001

The following packages will be UPDATED:

  cryptography                                 2.2.1-py27_0 --> 2.6.1-py27h212c5bf_0
  openssl                       pkgs/free::openssl-1.0.2h-1 --> conda-forge::openssl-1.1.1b-h01d97ff_2
  pip                           pkgs/free::pip-8.1.2-py27_0 --> conda-forge::pip-19.1-py27_0
  tk                                 pkgs/free::tk-8.5.18-0 --> conda-forge::tk-8.6.9-ha441bb4_1001
  zlib                              pkgs/free::zlib-1.2.8-3 --> conda-forge::zlib-1.2.11-h1de35cc_1004

The following packages will be DOWNGRADED:

  python                                           2.7.12-1 --> 2.7.3-5



Downloading and Extracting Packages
cycler-0.10.0        | 8 KB      | ###################################################################################################################### | 100% 
toolz-0.9.0          | 42 KB     | ###################################################################################################################### | 100% 
networkx-2.2         | 1.1 MB    | ###################################################################################################################### | 100% 
jpeg-9c              | 237 KB    | ###################################################################################################################### | 100% 
werkzeug-0.15.2      | 257 KB    | ###################################################################################################################### | 100% 
markdown-2.6.11      | 56 KB     | ###################################################################################################################### | 100% 
backports_abc-0.5    | 5 KB      | ###################################################################################################################### | 100% 
libgfortran-3.0.1    | 495 KB    | ###################################################################################################################### | 100% 
mkl-service-1.1.2    | 10 KB     | ###################################################################################################################### | 100% 
imageio-2.5.0        | 3.4 MB    | ###################################################################################################################### | 100% 
numpy-1.11.3         | 3.5 MB    | ###################################################################################################################### | 100% 
tk-8.6.9             | 3.2 MB    | ###################################################################################################################### | 100% 
pyqt-4.11.4          | 3.9 MB    | ###################################################################################################################### | 100% 
cytoolz-0.9.0.1      | 354 KB    | ###################################################################################################################### | 100% 
webencodings-0.5.1   | 12 KB     | ###################################################################################################################### | 100% 
matplotlib-base-2.2. | 6.4 MB    | ###################################################################################################################### | 100% 
pyparsing-2.4.0      | 55 KB     | ###################################################################################################################### | 100% 
ca-certificates-2019 | 146 KB    | ###################################################################################################################### | 100% 
backports.functools_ | 6 KB      | ###################################################################################################################### | 100% 
protobuf-3.7.1       | 626 KB    | ###################################################################################################################### | 100% 
scikit-image-0.14.2  | 23.3 MB   | ###################################################################################################################### | 100% 
dask-core-1.2.1      | 534 KB    | ###################################################################################################################### | 100% 
pywavelets-1.0.3     | 4.3 MB    | ###################################################################################################################### | 100% 
backports-1.0        | 4 KB      | ###################################################################################################################### | 100% 
subprocess32-3.5.3   | 43 KB     | ###################################################################################################################### | 100% 
xlrd-1.2.0           | 108 KB    | ###################################################################################################################### | 100% 
zlib-1.2.11          | 101 KB    | ###################################################################################################################### | 100% 
sip-4.18             | 247 KB    | ###################################################################################################################### | 100% 
html5lib-0.9999999   | 187 KB    | ###################################################################################################################### | 100% 
libblas-3.8.0        | 194 KB    | ###################################################################################################################### | 100% 
scipy-1.2.1          | 15.7 MB   | ###################################################################################################################### | 100% 
mock-2.0.0           | 102 KB    | ###################################################################################################################### | 100% 
xlutils-2.0.0        | 76 KB     | ###################################################################################################################### | 100% 
xlwt-1.3.0           | 83 KB     | ###################################################################################################################### | 100% 
backports.weakref-1. | 7 KB      | ###################################################################################################################### | 100% 
libcblas-3.8.0       | 42 KB     | ###################################################################################################################### | 100% 
pandas-0.23.4        | 9.1 MB    | ###################################################################################################################### | 100% 
python-2.7.3         | 10.0 MB   | ###################################################################################################################### | 100% 
libpng-1.6.37        | 298 KB    | ###################################################################################################################### | 100% 
singledispatch-3.4.0 | 15 KB     | ###################################################################################################################### | 100% 
libtiff-4.0.10       | 486 KB    | ###################################################################################################################### | 100% 
qt-4.8.7             | 39.0 MB   | ###################################################################################################################### | 100% 
cryptography-2.6.1   | 568 KB    | ###################################################################################################################### | 100% 
pbr-5.1.3            | 70 KB     | ###################################################################################################################### | 100% 
openssl-1.1.1b       | 3.5 MB    | ###################################################################################################################### | 100% 
matplotlib-2.2.3     | 6 KB      | ###################################################################################################################### | 100% 
mkl-2018.0.3         | 149.2 MB  | ###################################################################################################################### | 100% 
tensorflow-1.3.0     | 32.5 MB   | ###################################################################################################################### | 100% 
pillow-6.0.0         | 583 KB    | ###################################################################################################################### | 100% 
pip-19.1             | 1.8 MB    | ###################################################################################################################### | 100% 
psutil-5.6.2         | 322 KB    | ###################################################################################################################### | 100% 
openblas-0.2.18      | 16.5 MB   | ###################################################################################################################### | 100% 
xz-5.2.4             | 268 KB    | ###################################################################################################################### | 100% 
cloudpickle-0.8.1    | 17 KB     | ###################################################################################################################### | 100% 
bleach-1.5.0         | 23 KB     | ###################################################################################################################### | 100% 
scikit-learn-0.17.1  | 3.8 MB    | ###################################################################################################################### | 100% 
intel-openmp-2019.3  | 1.1 MB    | ###################################################################################################################### | 100% 
funcsigs-1.0.2       | 14 KB     | ###################################################################################################################### | 100% 
olefile-0.46         | 31 KB     | ###################################################################################################################### | 100% 
freetype-2.10.0      | 881 KB    | ###################################################################################################################### | 100% 
tornado-5.1.1        | 642 KB    | ###################################################################################################################### | 100% 
liblapack-3.8.0      | 2.8 MB    | ###################################################################################################################### | 100% 
blas-1.1             | 1 KB      | ###################################################################################################################### | 100% 
libprotobuf-3.7.1    | 4.3 MB    | ###################################################################################################################### | 100% 
kiwisolver-1.1.0     | 58 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:///Users/alfoi/code/spinalcordtoolbox
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)
  Using cached https://files.pythonhosted.org/packages/e1/30/f1b41ecf027429bc8d714c776f40690ce1d3f28e891f061fe5617ce8b8bf/dipy-0.16.0.tar.gz
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/98/06/0e711ae0c95d92ec238218448a15c23590cb117ded59e4bfa322b085b59e/h5py-2.9.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already satisfied: matplotlib in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.2.3)
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/ed/7f/c4e27b1701ce1fc86cfe7c75c981ccab9be30f38dd409dcc2b1a50c0b4e2/nipy-0.4.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_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) (5.6.2)
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) (0.14.2)
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
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
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)
Requirement already satisfied: cycler>=0.10 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2.4.0)
Collecting python-dateutil>=2.1 (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: kiwisolver>=1.0.1 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (1.1.0)
Requirement already satisfied: backports.functools_lru_cache in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (1.5)
Requirement already satisfied: subprocess32 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (3.5.3)
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: certifi>=2017.4.17 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (2019.3.9)
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: networkx>=1.8 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (2.2)
Requirement already satisfied: pillow>=4.3.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (6.0.0)
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: dask[array]>=1.0.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (1.2.1)
Requirement already satisfied: cloudpickle>=0.2.1 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (0.8.1)
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: wheel in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (0.29.0)
Requirement already satisfied: backports.weakref>=1.0rc1 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (1.0rc1)
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: protobuf>=3.3.0 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (3.7.1)
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) (2.6.1)
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
Requirement already satisfied: setuptools in ./python/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib->spinalcordtoolbox===dev) (41.0.1)
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: toolz>=0.7.3; extra == "array" in ./python/lib/python2.7/site-packages (from dask[array]>=1.0.0->scikit-image->spinalcordtoolbox===dev) (0.9.0)
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: 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: 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: 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: 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) (1.12.3)
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)
Building wheels for collected packages: dipy
  Building wheel for dipy (setup.py) ... error
  ERROR: Complete output from command /Users/alfoi/code/spinalcordtoolbox/python/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/pip-install-7BVjgf/dipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/pip-wheel-DxWrb8 --python-tag cp27:
  ERROR: running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.5-x86_64-2.7
  creating build/lib.macosx-10.5-x86_64-2.7/dipy
  copying dipy/conftest.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
  copying dipy/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
  copying dipy/__config__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
  copying dipy/pkg_info.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
  copying dipy/info.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/tests
  copying dipy/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tests
  copying dipy/tests/scriptrunner.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tests
  copying dipy/tests/test_scripts.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/align
  copying dipy/align/streamlinear.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
  copying dipy/align/metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
  copying dipy/align/scalespace.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
  copying dipy/align/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
  copying dipy/align/imaffine.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
  copying dipy/align/imwarp.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
  copying dipy/align/reslice.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_expectmax.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_imwarp.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_vector_fields.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_sumsqdiff.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_whole_brain_slr.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_transforms.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_scalespace.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_streamlinear.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_imaffine.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_crosscorr.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_parzenhist.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  copying dipy/align/tests/test_reslice.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/optimize.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/rng.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/gradients.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/profile.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/graph.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/subdivide_octahedron.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/ndindex.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/wavelet.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/geometry.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/onetime.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/sphere.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/histeq.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  copying dipy/core/sphere_stats.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  copying dipy/core/tests/test_ndindex.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  copying dipy/core/tests/test_optimize.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  copying dipy/core/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  copying dipy/core/tests/test_sphere.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  copying dipy/core/tests/test_graph.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  copying dipy/core/tests/test_geometry.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  copying dipy/core/tests/test_gradients.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  copying dipy/core/tests/test_subdivide_octahedron.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/direction
  copying dipy/direction/peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction
  copying dipy/direction/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
  copying dipy/direction/tests/test_prob_direction_getter.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
  copying dipy/direction/tests/test_bootstrap_direction_getter.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
  copying dipy/direction/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
  copying dipy/direction/tests/test_peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
  copying dipy/direction/tests/test_pmf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  copying dipy/tracking/metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  copying dipy/tracking/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  copying dipy/tracking/streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  copying dipy/tracking/eudx.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  copying dipy/tracking/life.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  copying dipy/tracking/utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  copying dipy/tracking/learning.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  copying dipy/tracking/_utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local
  copying dipy/tracking/local/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local
  copying dipy/tracking/local/localtracking.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
  copying dipy/tracking/local/tests/test_interpolation.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
  copying dipy/tracking/local/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
  copying dipy/tracking/local/tests/test_tissue_classifier.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
  copying dipy/tracking/local/tests/test_tracking.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_track_volumes.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_learning.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_distances.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_life.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_fbc.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  copying dipy/tracking/tests/test_propagation.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/benchmarks
  copying dipy/tracking/benchmarks/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/benchmarks
  copying dipy/tracking/benchmarks/bench_streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/benchmarks
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/fwdti.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/qtdmri.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/dti.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/shm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/odf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/forecast.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/mapmri.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/dsi.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/multi_voxel.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/cache.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/shore.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/dki_micro.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/interpolate.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/csdeconv.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/ivim.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/gqi.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/dki.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/base.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/sfm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  copying dipy/reconst/cross_validation.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
  copying dipy/reconst/benchmarks/bench_csd.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
  copying dipy/reconst/benchmarks/bench_bounding_box.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
  copying dipy/reconst/benchmarks/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
  copying dipy/reconst/benchmarks/bench_squash.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
  copying dipy/reconst/benchmarks/bench_vec_val_sum.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
  copying dipy/reconst/benchmarks/bench_peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_dki_micro.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_peakdf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_multi_voxel.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_cross_validation.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_dti.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_shm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_shore_odf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_odf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_forecast.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_shore_metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_dsi.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_reco_utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_fwdti.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_csdeconv.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_gqi.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_qtdmri.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_dki.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_vec_val_vect.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_mapmri.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_sfm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_peak_finding.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_dsi_metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_cache.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_shore.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_ivim.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_interpolate.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  copying dipy/reconst/tests/test_dsi_deconv.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/trackvis.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/pickles.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/gradients.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/vtk.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/dpy.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/bvectxt.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  copying dipy/io/image.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  copying dipy/io/tests/test_utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  copying dipy/io/tests/test_io_gradients.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  copying dipy/io/tests/test_streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  copying dipy/io/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  copying dipy/io/tests/test_io.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  copying dipy/io/tests/test_io_peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  copying dipy/io/tests/test_dpy.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  copying dipy/io/tests/test_bvectxt.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/viz
  copying dipy/viz/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz
  copying dipy/viz/regtools.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz
  copying dipy/viz/app.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz
  copying dipy/viz/projections.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz
  copying dipy/viz/panel.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/viz/tests
  copying dipy/viz/tests/test_apps.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz/tests
  copying dipy/viz/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz/tests
  copying dipy/viz/tests/test_regtools.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/testing
  copying dipy/testing/spherepoints.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/testing
  copying dipy/testing/memory.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/testing
  copying dipy/testing/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/testing
  copying dipy/testing/decorators.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/testing
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/testing/tests
  copying dipy/testing/tests/test_decorators.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/testing/tests
  copying dipy/testing/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/testing/tests
  copying dipy/testing/tests/test_memory.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/testing/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/boots
  copying dipy/boots/resampling.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/boots
  copying dipy/boots/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/boots
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/data
  copying dipy/data/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/data
  copying dipy/data/fetcher.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/data
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/utils
  copying dipy/utils/tripwire.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils
  copying dipy/utils/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils
  copying dipy/utils/six.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils
  copying dipy/utils/optpkg.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils
  copying dipy/utils/_importlib.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils
  copying dipy/utils/arrfuncs.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils
  package init file 'dipy/data/tests/__init__.py' not found (or not a regular file)
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/data/tests
  copying dipy/data/tests/test_data.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/tests
  copying dipy/data/tests/test_fetcher.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/utils/tests
  copying dipy/utils/tests/test_tripwire.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils/tests
  copying dipy/utils/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils/tests
  copying dipy/utils/tests/test_arrfuncs.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils/tests
  copying dipy/utils/tests/test_omp.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/utils/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/fixes
  copying dipy/fixes/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/fixes
  copying dipy/fixes/scipy.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/fixes
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/external
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  copying dipy/external/fsl.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/external
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/external/tests
  copying dipy/external/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/external/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  copying dipy/segment/mask.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  copying dipy/segment/clustering.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  copying dipy/segment/tissue.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  copying dipy/segment/bundles.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  copying dipy/segment/quickbundles.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  copying dipy/segment/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  copying dipy/segment/threshold.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  copying dipy/segment/metric.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/segment/benchmarks
  copying dipy/segment/benchmarks/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/benchmarks
  copying dipy/segment/benchmarks/bench_quickbundles.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/benchmarks
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_metric.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_bundles.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_qb.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_refine_rb.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_adjustment.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_mask.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_feature.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_quickbundles.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_mrf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_qbx.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  copying dipy/segment/tests/test_clustering.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/segment/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/sims
  copying dipy/sims/phantom.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/sims
  copying dipy/sims/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/sims
  copying dipy/sims/voxel.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/sims
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/sims/tests
  copying dipy/sims/tests/test_voxel.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/sims/tests
  copying dipy/sims/tests/test_phantom.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/sims/tests
  copying dipy/sims/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/sims/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/stats
  copying dipy/stats/analysis.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/stats
  copying dipy/stats/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/stats
  package init file 'dipy/stats/tests/__init__.py' not found (or not a regular file)
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/stats/tests
  copying dipy/stats/tests/test_ba.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/stats/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
  copying dipy/denoise/non_local_means.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
  copying dipy/denoise/localpca.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
  copying dipy/denoise/noise_estimate.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
  copying dipy/denoise/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
  copying dipy/denoise/adaptive_soft_matching.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
  copying dipy/denoise/nlmeans.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  copying dipy/denoise/tests/test_ascm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  copying dipy/denoise/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  copying dipy/denoise/tests/test_noise_estimate.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  copying dipy/denoise/tests/test_non_local_means.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  copying dipy/denoise/tests/test_nlmeans.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  copying dipy/denoise/tests/test_lpca.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  copying dipy/denoise/tests/test_kernel.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  copying dipy/denoise/tests/test_denoise.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/mask.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/reconst.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/multi_io.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/combined_workflow.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/align.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/io.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/flow_runner.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/stats.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/workflow.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/segment.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/denoise.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/viz.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/tracking.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/base.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  copying dipy/workflows/docstring_parser.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_stats.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/workflow_tests_utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_docstring_parser.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_reconst_ivim.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_reconst_dki.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_masking.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_iap.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_io.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_reconst_dti.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_workflow.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_tracking.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_viz.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_align.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_reconst_mapmri.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_reconst_csa_csd.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  copying dipy/workflows/tests/test_segment.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/workflows/tests
  creating build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/test_ui_text_block.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/ScannerVectors_GQI101.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_64D.bvals.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/aniso_vox.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/55dir_grad.bvec -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/evenly_distributed_sphere_642.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/fib1.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/func_discrete.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/grad_514.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/dsi4169_b_table.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/life_matlab_weights.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/evenly_distributed_sphere_724.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/dipy_colormaps.json -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_101D.bvec -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/tracks300.trk -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/C.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/life_matlab_rmse.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_64D.gradients.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_101D.bval -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/gtab_3shell.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/repulsion724.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_25.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/55dir_grad.bval -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/test_piesno.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/cb_2.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/gtab_isbi2013_2shell.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/fib2.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/C3.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_64D.bval -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/func_coef.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/repulsion100.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_101D.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/eg_3voxels.pkl -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/C1.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/evenly_distributed_sphere_362.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_64D.nii -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_25.bvec -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/t1_coronal_slice.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/fib0.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/gtab_taiwan_dsi.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_64D.bvec -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/S0_10slices.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/small_25.bval -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/sphere_grad.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/dsi515_b_table.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/repulsion200.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/circle.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  copying dipy/data/files/ascm_out_test.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
  package init file 'dipy/data/tests/__init__.py' not found (or not a regular file)
  package init file 'dipy/stats/tests/__init__.py' not found (or not a regular file)
  running build_ext
  gcc -fno-strict-aliasing -I/Users/alfoi/code/spinalcordtoolbox/python/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/alfoi/code/spinalcordtoolbox/python/include/python2.7 -c test.c -o test.o -msse2 -mfpmath=sse
  gcc -bundle -undefined dynamic_lookup -L/Users/alfoi/code/spinalcordtoolbox/python/lib -arch x86_64 -arch x86_64 test.o -o libtestlib.so
  ld: library not found for -lgcc_s.10.5
  clang: error: linker command failed with exit code 1 (use -v to see invocation)
  Flags ['-msse2', '-mfpmath=sse'] omitted because of compile or link error
  gcc -fno-strict-aliasing -I/Users/alfoi/code/spinalcordtoolbox/python/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/alfoi/code/spinalcordtoolbox/python/include/python2.7 -c test.c -o test.o -fopenmp
  clang: error: unsupported option '-fopenmp'
  Flags ['-fopenmp', '-fopenmp'] omitted because of compile or link error
  building 'dipy.direction.pmf' extension
  creating build/temp.macosx-10.5-x86_64-2.7
  creating build/temp.macosx-10.5-x86_64-2.7/dipy
  creating build/temp.macosx-10.5-x86_64-2.7/dipy/direction
  gcc -fno-strict-aliasing -I/Users/alfoi/code/spinalcordtoolbox/python/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isrc -I/Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include -Ibuild -I/Users/alfoi/code/spinalcordtoolbox/python/include/python2.7 -c dipy/direction/pmf.c -o build/temp.macosx-10.5-x86_64-2.7/dipy/direction/pmf.o
  In file included from dipy/direction/pmf.c:613:
  In file included from /Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
  In file included from /Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
  In file included from /Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:
  /Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
  #warning "Using deprecated NumPy API, disable it by " \
   ^
  1 warning generated.
  gcc -bundle -undefined dynamic_lookup -L/Users/alfoi/code/spinalcordtoolbox/python/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/dipy/direction/pmf.o -o build/lib.macosx-10.5-x86_64-2.7/dipy/direction/pmf.so
  ld: library not found for -lgcc_s.10.5
  clang: error: linker command failed with exit code 1 (use -v to see invocation)
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for dipy
  Running setup.py clean for dipy
Failed to build dipy
ERROR: traitlets 4.3.2 requires ipython_genutils, which is not installed.
Installing collected packages: h5py, keras-applications, keras-preprocessing, Keras, bz2file, nibabel, dipy, mpmath, sympy, nipy, contextlib2, raven, tqdm, transforms3d, portalocker, spinalcordtoolbox, python-dateutil, pytz, tensorflow-tensorboard, ipaddress, decorator
  Running setup.py install for dipy ... error
    ERROR: Complete output from command /Users/alfoi/code/spinalcordtoolbox/python/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/pip-install-7BVjgf/dipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/pip-record-K6MzmP/install-record.txt --single-version-externally-managed --compile:
    ERROR: running install
    running build
    running build_py
    creating build/lib.macosx-10.5-x86_64-2.7
    creating build/lib.macosx-10.5-x86_64-2.7/dipy
    copying dipy/conftest.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
    copying dipy/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
    copying dipy/__config__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
    copying dipy/pkg_info.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
    copying dipy/info.py -> build/lib.macosx-10.5-x86_64-2.7/dipy
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/tests
    copying dipy/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tests
    copying dipy/tests/scriptrunner.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tests
    copying dipy/tests/test_scripts.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tests
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/align
    copying dipy/align/streamlinear.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
    copying dipy/align/metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
    copying dipy/align/scalespace.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
    copying dipy/align/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
    copying dipy/align/imaffine.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
    copying dipy/align/imwarp.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
    copying dipy/align/reslice.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_expectmax.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_imwarp.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_vector_fields.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_sumsqdiff.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_whole_brain_slr.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_transforms.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_scalespace.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_streamlinear.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_imaffine.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_crosscorr.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_parzenhist.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    copying dipy/align/tests/test_reslice.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/align/tests
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/optimize.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/rng.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/gradients.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/profile.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/graph.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/subdivide_octahedron.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/ndindex.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/wavelet.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/geometry.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/onetime.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/sphere.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/histeq.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    copying dipy/core/sphere_stats.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    copying dipy/core/tests/test_ndindex.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    copying dipy/core/tests/test_optimize.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    copying dipy/core/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    copying dipy/core/tests/test_sphere.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    copying dipy/core/tests/test_graph.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    copying dipy/core/tests/test_geometry.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    copying dipy/core/tests/test_gradients.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    copying dipy/core/tests/test_subdivide_octahedron.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/core/tests
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/direction
    copying dipy/direction/peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction
    copying dipy/direction/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
    copying dipy/direction/tests/test_prob_direction_getter.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
    copying dipy/direction/tests/test_bootstrap_direction_getter.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
    copying dipy/direction/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
    copying dipy/direction/tests/test_peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
    copying dipy/direction/tests/test_pmf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/direction/tests
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    copying dipy/tracking/metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    copying dipy/tracking/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    copying dipy/tracking/streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    copying dipy/tracking/eudx.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    copying dipy/tracking/life.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    copying dipy/tracking/utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    copying dipy/tracking/learning.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    copying dipy/tracking/_utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local
    copying dipy/tracking/local/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local
    copying dipy/tracking/local/localtracking.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
    copying dipy/tracking/local/tests/test_interpolation.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
    copying dipy/tracking/local/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
    copying dipy/tracking/local/tests/test_tissue_classifier.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
    copying dipy/tracking/local/tests/test_tracking.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/local/tests
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_track_volumes.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_learning.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_distances.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_life.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_fbc.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    copying dipy/tracking/tests/test_propagation.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/tests
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/benchmarks
    copying dipy/tracking/benchmarks/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/benchmarks
    copying dipy/tracking/benchmarks/bench_streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/tracking/benchmarks
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/fwdti.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/qtdmri.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/dti.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/shm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/odf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/forecast.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/mapmri.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/dsi.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/multi_voxel.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/cache.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/shore.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/dki_micro.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/interpolate.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/csdeconv.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/ivim.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/gqi.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/dki.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/base.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/sfm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    copying dipy/reconst/cross_validation.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
    copying dipy/reconst/benchmarks/bench_csd.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
    copying dipy/reconst/benchmarks/bench_bounding_box.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
    copying dipy/reconst/benchmarks/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
    copying dipy/reconst/benchmarks/bench_squash.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
    copying dipy/reconst/benchmarks/bench_vec_val_sum.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
    copying dipy/reconst/benchmarks/bench_peaks.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/benchmarks
    creating build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_dki_micro.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_peakdf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_multi_voxel.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_cross_validation.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_dti.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_shm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_shore_odf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_odf.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_forecast.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_shore_metrics.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
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    copying dipy/reconst/tests/test_sfm.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
    copying dipy/reconst/tests/test_peak_finding.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
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    copying dipy/reconst/tests/test_cache.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
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    copying dipy/reconst/tests/test_dsi_deconv.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/reconst/tests
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    copying dipy/io/trackvis.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
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    copying dipy/io/gradients.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
    copying dipy/io/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
    copying dipy/io/streamline.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
    copying dipy/io/utils.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
    copying dipy/io/vtk.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io
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    creating build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
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    copying dipy/io/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
    copying dipy/io/tests/test_io.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/io/tests
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    copying dipy/viz/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/viz/tests
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    creating build/lib.macosx-10.5-x86_64-2.7/dipy/stats/tests
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    copying dipy/denoise/noise_estimate.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
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    copying dipy/denoise/adaptive_soft_matching.py -> build/lib.macosx-10.5-x86_64-2.7/dipy/denoise
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    creating build/lib.macosx-10.5-x86_64-2.7/dipy/denoise/tests
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    copying dipy/data/files/ScannerVectors_GQI101.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
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    copying dipy/data/files/fib1.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/func_discrete.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/grad_514.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/dsi4169_b_table.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/life_matlab_weights.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/evenly_distributed_sphere_724.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/dipy_colormaps.json -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_101D.bvec -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/tracks300.trk -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/C.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/life_matlab_rmse.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_64D.gradients.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_101D.bval -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/gtab_3shell.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/repulsion724.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_25.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/55dir_grad.bval -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/test_piesno.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/cb_2.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/gtab_isbi2013_2shell.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/fib2.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/C3.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_64D.bval -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/func_coef.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/repulsion100.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_101D.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/eg_3voxels.pkl -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/C1.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/evenly_distributed_sphere_362.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_64D.nii -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_25.bvec -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/t1_coronal_slice.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/fib0.pkl.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/gtab_taiwan_dsi.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_64D.bvec -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/S0_10slices.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/small_25.bval -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/sphere_grad.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/dsi515_b_table.txt -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/repulsion200.npz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/circle.npy -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    copying dipy/data/files/ascm_out_test.nii.gz -> build/lib.macosx-10.5-x86_64-2.7/dipy/data/files
    package init file 'dipy/data/tests/__init__.py' not found (or not a regular file)
    package init file 'dipy/stats/tests/__init__.py' not found (or not a regular file)
    running build_ext
    gcc -fno-strict-aliasing -I/Users/alfoi/code/spinalcordtoolbox/python/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/alfoi/code/spinalcordtoolbox/python/include/python2.7 -c test.c -o test.o -msse2 -mfpmath=sse
    gcc -bundle -undefined dynamic_lookup -L/Users/alfoi/code/spinalcordtoolbox/python/lib -arch x86_64 -arch x86_64 test.o -o libtestlib.so
    ld: library not found for -lgcc_s.10.5
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    Flags ['-msse2', '-mfpmath=sse'] omitted because of compile or link error
    gcc -fno-strict-aliasing -I/Users/alfoi/code/spinalcordtoolbox/python/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/alfoi/code/spinalcordtoolbox/python/include/python2.7 -c test.c -o test.o -fopenmp
    clang: error: unsupported option '-fopenmp'
    Flags ['-fopenmp', '-fopenmp'] omitted because of compile or link error
    building 'dipy.direction.pmf' extension
    creating build/temp.macosx-10.5-x86_64-2.7
    creating build/temp.macosx-10.5-x86_64-2.7/dipy
    creating build/temp.macosx-10.5-x86_64-2.7/dipy/direction
    gcc -fno-strict-aliasing -I/Users/alfoi/code/spinalcordtoolbox/python/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isrc -I/Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include -Ibuild -I/Users/alfoi/code/spinalcordtoolbox/python/include/python2.7 -c dipy/direction/pmf.c -o build/temp.macosx-10.5-x86_64-2.7/dipy/direction/pmf.o
    In file included from dipy/direction/pmf.c:613:
    In file included from /Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
    In file included from /Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
    In file included from /Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:
    /Users/alfoi/code/spinalcordtoolbox/python/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
    #warning "Using deprecated NumPy API, disable it by " \
     ^
    1 warning generated.
    gcc -bundle -undefined dynamic_lookup -L/Users/alfoi/code/spinalcordtoolbox/python/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/dipy/direction/pmf.o -o build/lib.macosx-10.5-x86_64-2.7/dipy/direction/pmf.so
    ld: library not found for -lgcc_s.10.5
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command "/Users/alfoi/code/spinalcordtoolbox/python/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/pip-install-7BVjgf/dipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/pip-record-K6MzmP/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/pip-install-7BVjgf/dipy/
Failed to pip install sct, which is quite unexpected.
Installation failed

@jcohenadad
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ok-- py2k issue then. Let's merge the py3k asap

@Nicolas-Pinon
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@alexfoias can you try please?

i suspect this is a py2k compatibility issue, which means we should merge #2238 asap. @Nicolas-Pinon do you get an error when installing the jca/py3k branch?

Installations went fine on the 3 setups with jca/py3k branch
So the problem is indeed comming from py2k

@jcohenadad jcohenadad mentioned this issue May 1, 2019
Merged
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bug category: fixes an error in the code installation category: install_sct or pip/setup.py
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Using Python 3.x for default installation spinalcordtoolbox/spinalcordtoolbox
3 participants
@jcohenadad @alexfoias @Nicolas-Pinon