Problem installing SCT 4.2.2

SCT
1

Hi,

i got a problem installing SCT version 4.2.2. I got the same issue with installing 4.20 and 4.2.1.
The OS is Ubuntu 16.04.
I guess the problem is caused by conda not creating an environment due to an url that cannot be resolved.

Maybe you can help me.

Here is the installation log:

*******************************
* Welcome to SCT installation *
*******************************



Checking OS type and version...

Linux Ubunt308001 4.13.0-31-generic #34~16.04.1-Ubuntu SMP Fri Jan 19 17:11:01 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...


OK!


SCT version ......... 4.2.2
Installation type ... package
Operating system .... linux (unknown)
Shell config ........ /home/admin-123/.bashrc

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: n

--> Crash reports will not be sent.


SCT will be installed here: [/home/admin-123/sct_4.2.2]

Do you agree? [y]es/[n]o: y

Copying source files from /media/admin-123/Daten/Software/Spinalcord/spinalcordtoolbox-4.2.2 to /home/admin-123/sct_4.2.2

...................................................................................................................................................................................................................................................................................................................................................
Installing conda...


rm -rf /home/admin-123/sct_4.2.2/python


mkdir -p /home/admin-123/sct_4.2.2/python


wget -O /tmp/tmp.8gONaUckvE/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2020-03-10 10:04:50--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Auflösen des Hostnamen »repo.continuum.io (repo.continuum.io)«... 104.18.201.79, 104.18.200.79, 2606:4700::6812:c94f, ...
Verbindungsaufbau zu repo.continuum.io (repo.continuum.io)|104.18.201.79|:443... verbunden.
HTTP-Anforderung gesendet, warte auf Antwort... 200 OK
Länge: 71785000 (68M) [application/x-sh]
In »»/tmp/tmp.8gONaUckvE/miniconda.sh«« speichern.

/tmp/tmp.8gONaUckvE/miniconda.sh                                     100%[=====================================================================================================================================================================>]  68,46M  1,27MB/s    in 52s     

2020-03-10 10:05:42 (1,32 MB/s) - »/tmp/tmp.8gONaUckvE/miniconda.sh« gespeichert [71785000/71785000]

exit status is 0

bash /tmp/tmp.8gONaUckvE/miniconda.sh -p /home/admin-123/sct_4.2.2/python -b -f

PREFIX=/home/admin-123/sct_4.2.2/python
Unpacking payload ...
Collecting package metadata (current_repodata.json): done                                                                                                                                                                                                                          
Solving environment: done

## Package Plan ##

  environment location: /home/admin-123/sct_4.2.2/python

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - asn1crypto==1.2.0=py37_0
    - ca-certificates==2019.10.16=0
    - certifi==2019.9.11=py37_0
    - cffi==1.13.0=py37h2e261b9_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h7b6447c_0
    - conda==4.7.12=py37_0
    - cryptography==2.8=py37h1ba5d50_0
    - idna==2.8=py37_0
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.2.1=hd88cf55_4
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.1=he6710b0_1
    - openssl==1.1.1d=h7b6447c_3
    - pip==19.3.1=py37_0
    - pycosat==0.6.3=py37h14c3975_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.0.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.4=h265db76_1
    - readline==7.0=h7b6447c_5
    - requests==2.22.0=py37_0
    - ruamel_yaml==0.15.46=py37h14c3975_0
    - setuptools==41.4.0=py37_0
    - six==1.12.0=py37_0
    - sqlite==3.30.0=h7b6447c_0
    - tk==8.6.8=hbc83047_0
    - tqdm==4.36.1=py_0
    - urllib3==1.24.2=py37_0
    - wheel==0.33.6=py37_0
    - xz==5.2.4=h14c3975_4
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  cffi               pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.7.12-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  idna               pkgs/main/linux-64::idna-2.8-py37_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
  pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  requests           pkgs/main/linux-64::requests-2.22.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  six                pkgs/main/linux-64::six-1.12.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.36.1-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.24.2-py37_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Preparing transaction: done
Executing transaction: done
installation finished.
**Collecting package metadata (current_repodata.json): failed**

**CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://your.repo/binstar_username/linux-64/current_repodata.json>**
**Elapsed: -**

**An HTTP error occurred when trying to retrieve this URL.**
**HTTP errors are often intermittent, and a simple retry will get you on your way.**
**ConnectionError(MaxRetryError("HTTPSConnectionPool(host='your.repo', port=443): Max retries exceeded with url: /binstar_username/linux-64/current_repodata.json (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f9374098290>: Failed to establish a new connection: [Errno -2] Name or service not known'))"))**


**Could not find conda environment: venv_sct**
You can list all discoverable environments with `conda info --envs`.


Installing Python dependencies...

Collecting numpy
  Downloading https://files.pythonhosted.org/packages/63/0c/0261693cc3ad8e2b66e66dc2d2676a2cc17d3efb1c58a70db73754320e47/numpy-1.18.1-cp37-cp37m-manylinux1_x86_64.whl (20.1MB)
     |████████████████████████████████| 20.1MB 1.5MB/s 
Installing collected packages: numpy
Successfully installed numpy-1.18.1

Using requirements-freeze.txt (release installation)

Processing /home/admin-123/.cache/pip/wheels/8e/28/49/fad4e7f0b9a1227708cbbee4487ac8558a7334849cb81c813d/absl_py-0.9.0-cp37-none-any.whl
Collecting astor==0.8.1
  Downloading https://files.pythonhosted.org/packages/c3/88/97eef84f48fa04fbd6750e62dcceafba6c63c81b7ac1420856c8dcc0a3f9/astor-0.8.1-py2.py3-none-any.whl
Collecting attrs==19.3.0
  Downloading https://files.pythonhosted.org/packages/a2/db/4313ab3be961f7a763066401fb77f7748373b6094076ae2bda2806988af6/attrs-19.3.0-py2.py3-none-any.whl
Collecting cachetools==4.0.0
  Downloading https://files.pythonhosted.org/packages/08/6a/abf83cb951617793fd49c98cb9456860f5df66ff89883c8660aa0672d425/cachetools-4.0.0-py3-none-any.whl
Collecting certifi==2019.11.28
  Downloading https://files.pythonhosted.org/packages/b9/63/df50cac98ea0d5b006c55a399c3bf1db9da7b5a24de7890bc9cfd5dd9e99/certifi-2019.11.28-py2.py3-none-any.whl (156kB)
     |████████████████████████████████| 163kB 1.5MB/s 
Collecting cffi==1.13.2
  Downloading https://files.pythonhosted.org/packages/16/cd/1f4ddf6be8300713c676bb9f3a2d3b8eb8accc0a6a24f57d4f6c4cd59d34/cffi-1.13.2-cp37-cp37m-manylinux1_x86_64.whl (398kB)
     |████████████████████████████████| 399kB 1.5MB/s 
Requirement already satisfied: chardet==3.0.4 in ./python/lib/python3.7/site-packages (from -r requirements-freeze.txt (line 7)) (3.0.4)
Collecting coverage==5.0
  Downloading https://files.pythonhosted.org/packages/b6/d8/cb3f8bbae33db7f24027721d61f73145f25bfbcf078a23b2998478e5258c/coverage-5.0-cp37-cp37m-manylinux1_x86_64.whl (226kB)
     |████████████████████████████████| 235kB 1.5MB/s 
Requirement already satisfied: cryptography==2.8 in ./python/lib/python3.7/site-packages (from -r requirements-freeze.txt (line 9)) (2.8)
Collecting cycler==0.10.0
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting decorator==4.4.1
  Downloading https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
Collecting dipy==1.0.0
  Downloading https://files.pythonhosted.org/packages/85/72/c54ea65a945d6c8d23b5308c67c64384807307963f4c6febabec73b75909/dipy-1.0.0-cp37-cp37m-manylinux1_x86_64.whl (8.1MB)
     |████████████████████████████████| 8.1MB 1.3MB/s 
Collecting futures==3.1.1
  Downloading https://files.pythonhosted.org/packages/05/80/f41cca0ea1ff69bce7e7a7d76182b47bb4e1a494380a532af3e8ee70b9ec/futures-3.1.1-py3-none-any.whl
Processing /home/admin-123/.cache/pip/wheels/5c/2e/7e/a1d4d4fcebe6c381f378ce7743a3ced3699feb89bcfbdadadd/gast-0.2.2-cp37-none-any.whl
Collecting google-auth==1.10.0
  Downloading https://files.pythonhosted.org/packages/36/f8/84b5771faec3eba9fe0c91c8c5896364a8ba08852c0dea5ad2025026dd95/google_auth-1.10.0-py2.py3-none-any.whl (76kB)
     |████████████████████████████████| 81kB 2.0MB/s 
Collecting google-auth-oauthlib==0.4.1
  Downloading https://files.pythonhosted.org/packages/7b/b8/88def36e74bee9fce511c9519571f4e485e890093ab7442284f4ffaef60b/google_auth_oauthlib-0.4.1-py2.py3-none-any.whl
Collecting google-pasta==0.1.8
  Downloading https://files.pythonhosted.org/packages/c3/fd/1e86bc4837cc9a3a5faf3db9b1854aa04ad35b5f381f9648fbe81a6f94e4/google_pasta-0.1.8-py3-none-any.whl (57kB)
     |████████████████████████████████| 61kB 2.2MB/s 
Collecting grpcio==1.26.0
  Downloading https://files.pythonhosted.org/packages/bc/b3/0052e38c640d52b710e235b15821cc3c61d0065bf54e70a44550ef127349/grpcio-1.26.0-cp37-cp37m-manylinux2010_x86_64.whl (2.4MB)
     |████████████████████████████████| 2.4MB 1.5MB/s 
Collecting h5py==2.10.0
  Downloading https://files.pythonhosted.org/packages/3f/c0/abde58b837e066bca19a3f7332d9d0493521d7dd6b48248451a9e3fe2214/h5py-2.10.0-cp37-cp37m-manylinux1_x86_64.whl (2.9MB)
     |████████████████████████████████| 2.9MB 1.5MB/s 
Requirement already satisfied: idna==2.8 in ./python/lib/python3.7/site-packages (from -r requirements-freeze.txt (line 20)) (2.8)
Collecting imageio==2.6.1
  Downloading https://files.pythonhosted.org/packages/1a/de/f7f985018f462ceeffada7f6e609919fbcc934acd9301929cba14bc2c24a/imageio-2.6.1-py3-none-any.whl (3.3MB)
     |████████████████████████████████| 3.3MB 1.5MB/s 
Collecting importlib-metadata==1.3.0
  Downloading https://files.pythonhosted.org/packages/e9/71/1a1e0ed0981bb6a67bce55a210f168126b7ebd2065958673797ea66489ca/importlib_metadata-1.3.0-py2.py3-none-any.whl
Collecting joblib==0.14.1
  Downloading https://files.pythonhosted.org/packages/28/5c/cf6a2b65a321c4a209efcdf64c2689efae2cb62661f8f6f4bb28547cf1bf/joblib-0.14.1-py2.py3-none-any.whl (294kB)
     |████████████████████████████████| 296kB 1.5MB/s 
Collecting Keras==2.3.1
  Downloading https://files.pythonhosted.org/packages/ad/fd/6bfe87920d7f4fd475acd28500a42482b6b84479832bdc0fe9e589a60ceb/Keras-2.3.1-py2.py3-none-any.whl (377kB)
     |████████████████████████████████| 378kB 1.5MB/s 
Collecting Keras-Applications==1.0.8
  Downloading https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl (50kB)
     |████████████████████████████████| 51kB 2.2MB/s 
Collecting Keras-Preprocessing==1.1.0
  Downloading https://files.pythonhosted.org/packages/28/6a/8c1f62c37212d9fc441a7e26736df51ce6f0e38455816445471f10da4f0a/Keras_Preprocessing-1.1.0-py2.py3-none-any.whl (41kB)
     |████████████████████████████████| 51kB 2.8MB/s 
Collecting kiwisolver==1.1.0
  Downloading https://files.pythonhosted.org/packages/93/f8/518fb0bb89860eea6ff1b96483fbd9236d5ee991485d0f3eceff1770f654/kiwisolver-1.1.0-cp37-cp37m-manylinux1_x86_64.whl (90kB)
     |████████████████████████████████| 92kB 1.8MB/s 
Collecting Markdown==3.1.1
  Downloading https://files.pythonhosted.org/packages/c0/4e/fd492e91abdc2d2fcb70ef453064d980688762079397f779758e055f6575/Markdown-3.1.1-py2.py3-none-any.whl (87kB)
     |████████████████████████████████| 92kB 1.9MB/s 
Collecting matplotlib==3.1.2
  Downloading https://files.pythonhosted.org/packages/61/42/3e92d7aa64295483fbca20a86c89b34d0cb43cffaadaffe028793902d790/matplotlib-3.1.2-cp37-cp37m-manylinux1_x86_64.whl (13.1MB)
     |████████████████████████████████| 13.1MB 1.5MB/s 
Collecting more-itertools==8.0.2
  Downloading https://files.pythonhosted.org/packages/68/03/0604cec1ea13c9f063dd50f900d1a36160334dd3cfb01fd0e638f61b46ba/more_itertools-8.0.2-py3-none-any.whl (40kB)
     |████████████████████████████████| 40kB 2.5MB/s 
Collecting networkx==2.4
  Downloading https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl (1.6MB)
     |████████████████████████████████| 1.6MB 1.5MB/s 
Collecting nibabel==3.0.0
  Downloading https://files.pythonhosted.org/packages/0d/fc/2efb2a7c5d117c761b72f6bc00bf057294e9ccdf0a737957c65fa89ecc6f/nibabel-3.0.0-py3-none-any.whl (3.3MB)
     |████████████████████████████████| 3.3MB 1.3MB/s 
Collecting numpy==1.17.4
  Downloading https://files.pythonhosted.org/packages/9b/af/4fc72f9d38e43b092e91e5b8cb9956d25b2e3ff8c75aed95df5569e4734e/numpy-1.17.4-cp37-cp37m-manylinux1_x86_64.whl (20.0MB)
     |████████████████████████████████| 20.0MB 1.3MB/s 
Collecting oauthlib==3.1.0
  Downloading https://files.pythonhosted.org/packages/05/57/ce2e7a8fa7c0afb54a0581b14a65b56e62b5759dbc98e80627142b8a3704/oauthlib-3.1.0-py2.py3-none-any.whl (147kB)
     |████████████████████████████████| 153kB 1.3MB/s 
Processing /home/admin-123/.cache/pip/wheels/2c/b1/94/43d03e130b929aae7ba3f8d15cbd7bc0d1cb5bb38a5c721833/opt_einsum-3.1.0-cp37-none-any.whl
Collecting packaging==19.2
  Downloading https://files.pythonhosted.org/packages/cf/94/9672c2d4b126e74c4496c6b3c58a8b51d6419267be9e70660ba23374c875/packaging-19.2-py2.py3-none-any.whl
Collecting pandas==0.25.3
  Downloading https://files.pythonhosted.org/packages/63/e0/a1b39cdcb2c391f087a1538bc8a6d62a82d0439693192aef541d7b123769/pandas-0.25.3-cp37-cp37m-manylinux1_x86_64.whl (10.4MB)
     |████████████████████████████████| 10.4MB 1.5MB/s 
Collecting Pillow==6.2.1
  Downloading https://files.pythonhosted.org/packages/89/3e/31c2e5385d7588016c6f7ac552e81c3fff2bef4bc61b6f82f8177752405c/Pillow-6.2.1-cp37-cp37m-manylinux1_x86_64.whl (2.1MB)
     |████████████████████████████████| 2.1MB 1.5MB/s 
Collecting pluggy==0.13.1
  Downloading https://files.pythonhosted.org/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl
Collecting protobuf==3.11.1
  Downloading https://files.pythonhosted.org/packages/c8/bd/9609c681f655c4b85f4e4f4c99d42b68bca63ad8891c6924ba6696dee0bb/protobuf-3.11.1-cp37-cp37m-manylinux1_x86_64.whl (1.3MB)
     |████████████████████████████████| 1.3MB 1.5MB/s 
Processing /home/admin-123/.cache/pip/wheels/52/41/b0/bf50409fe2b1d3b79afa3eed71b54b3e30fe5b695db2c7ba2e/psutil-5.6.7-cp37-cp37m-linux_x86_64.whl
Collecting py==1.8.0
  Downloading https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl (83kB)
     |████████████████████████████████| 92kB 1.9MB/s 
Collecting pyasn1==0.4.8
  Downloading https://files.pythonhosted.org/packages/62/1e/a94a8d635fa3ce4cfc7f506003548d0a2447ae76fd5ca53932970fe3053f/pyasn1-0.4.8-py2.py3-none-any.whl (77kB)
     |████████████████████████████████| 81kB 2.0MB/s 
Collecting pyasn1-modules==0.2.7
  Downloading https://files.pythonhosted.org/packages/52/50/bb4cefca37da63a0c52218ba2cb1b1c36110d84dcbae8aa48cd67c5e95c2/pyasn1_modules-0.2.7-py2.py3-none-any.whl (131kB)
     |████████████████████████████████| 133kB 1.5MB/s 
Requirement already satisfied: pycparser==2.19 in ./python/lib/python3.7/site-packages (from -r requirements-freeze.txt (line 45)) (2.19)
Collecting pyOpenSSL==19.1.0
  Downloading https://files.pythonhosted.org/packages/9e/de/f8342b68fa9e981d348039954657bdf681b2ab93de27443be51865ffa310/pyOpenSSL-19.1.0-py2.py3-none-any.whl (53kB)
     |████████████████████████████████| 61kB 2.4MB/s 
Collecting pyparsing==2.4.5
  Downloading https://files.pythonhosted.org/packages/c0/0c/fc2e007d9a992d997f04a80125b0f183da7fb554f1de701bbb70a8e7d479/pyparsing-2.4.5-py2.py3-none-any.whl (67kB)
     |████████████████████████████████| 71kB 2.0MB/s 
Collecting PyQt5==5.11.3
  Downloading https://files.pythonhosted.org/packages/d4/bf/d884da8e2f7096d201c891d515eb6813a8e85df5eb6f5e12e867bf1d831c/PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8MB)
     |████████████████████████████████| 117.8MB 1.5MB/s 
Collecting PyQt5-sip==4.19.19
  Downloading https://files.pythonhosted.org/packages/bf/63/d363b567237375235d270049fd6416c83949f470bb51539458966cd7a38c/PyQt5_sip-4.19.19-cp37-cp37m-manylinux1_x86_64.whl (67kB)
     |████████████████████████████████| 71kB 1.5MB/s 
Collecting pytest==5.3.2
  Downloading https://files.pythonhosted.org/packages/19/cf/711f1d887cb92c5155c9a1eb338f1b5d2411b50e4492a3b20e4a188a22b2/pytest-5.3.2-py3-none-any.whl (234kB)
     |████████████████████████████████| 235kB 1.5MB/s 
Collecting pytest-cov==2.8.1
  Downloading https://files.pythonhosted.org/packages/b9/54/3673ee8be482f81527678ac894276223b9814bb7262e4f730469bb7bf70e/pytest_cov-2.8.1-py2.py3-none-any.whl
Collecting python-dateutil==2.8.1
  Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
     |████████████████████████████████| 235kB 1.5MB/s 
Collecting pytz==2019.3
  Downloading https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl (509kB)
     |████████████████████████████████| 512kB 1.5MB/s 
Collecting PyWavelets==1.1.1
  Downloading https://files.pythonhosted.org/packages/62/bd/592c7242fdd1218a96431512e77265c50812315ef72570ace85e1cfae298/PyWavelets-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (4.4MB)
     |████████████████████████████████| 4.4MB 1.4MB/s 
Processing /home/admin-123/.cache/pip/wheels/54/b7/c7/2ada654ee54483c9329871665aaf4a6056c3ce36f29cf66e67/PyYAML-5.2-cp37-cp37m-linux_x86_64.whl
Collecting raven==6.10.0
  Downloading https://files.pythonhosted.org/packages/bd/8e/62e26a88c0a1bbae677200baf0767c1022321a6555634f8129e6d55c5ddc/raven-6.10.0-py2.py3-none-any.whl (284kB)
     |████████████████████████████████| 286kB 1.5MB/s 
Requirement already satisfied: requests==2.22.0 in ./python/lib/python3.7/site-packages (from -r requirements-freeze.txt (line 57)) (2.22.0)
Collecting requests-oauthlib==1.3.0
  Downloading https://files.pythonhosted.org/packages/a3/12/b92740d845ab62ea4edf04d2f4164d82532b5a0b03836d4d4e71c6f3d379/requests_oauthlib-1.3.0-py2.py3-none-any.whl
Collecting rsa==4.0
  Downloading https://files.pythonhosted.org/packages/02/e5/38518af393f7c214357079ce67a317307936896e961e35450b70fad2a9cf/rsa-4.0-py2.py3-none-any.whl
Collecting scikit-image==0.16.2
  Downloading https://files.pythonhosted.org/packages/dc/48/454bf836d302465475e02bc0468b879302145b07a005174c409a5b5869c7/scikit_image-0.16.2-cp37-cp37m-manylinux1_x86_64.whl (26.5MB)
     |████████████████████████████████| 26.5MB 1.5MB/s 
Collecting scikit-learn==0.22
  Downloading https://files.pythonhosted.org/packages/19/96/8034e350d4550748277e514d0d6d91bdd36be19e6c5f40b8af0d74cb0c84/scikit_learn-0.22-cp37-cp37m-manylinux1_x86_64.whl (7.0MB)
     |████████████████████████████████| 7.0MB 1.5MB/s 
Collecting scipy==1.4.0
  Downloading https://files.pythonhosted.org/packages/37/9d/a606dc7b17ef0b7326afd128e132b7a483d5611da603334842df75d92d3c/scipy-1.4.0-cp37-cp37m-manylinux1_x86_64.whl (26.1MB)
     |████████████████████████████████| 26.1MB 1.5MB/s 
Collecting six==1.13.0
  Downloading https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl
Collecting tensorboard==2.0.2
  Downloading https://files.pythonhosted.org/packages/76/54/99b9d5d52d5cb732f099baaaf7740403e83fe6b0cedde940fabd2b13d75a/tensorboard-2.0.2-py3-none-any.whl (3.8MB)
     |████████████████████████████████| 3.8MB 1.3MB/s 
Collecting tensorflow==2.0.1
  Downloading https://files.pythonhosted.org/packages/85/65/6b9dfbbbe625863cd05879fb9e5e98083b96bb8c9c1b524e303a24b7609d/tensorflow-2.0.1-cp37-cp37m-manylinux2010_x86_64.whl (86.3MB)
     |████████████████████████████████| 86.3MB 1.3MB/s 
Collecting tensorflow-estimator==2.0.1
  Downloading https://files.pythonhosted.org/packages/fc/08/8b927337b7019c374719145d1dceba21a8bb909b93b1ad6f8fb7d22c1ca1/tensorflow_estimator-2.0.1-py2.py3-none-any.whl (449kB)
     |████████████████████████████████| 450kB 1.3MB/s 
Processing /home/admin-123/.cache/pip/wheels/7c/06/54/bc84598ba1daf8f970247f550b175aaaee85f68b4b0c5ab2c6/termcolor-1.1.0-cp37-none-any.whl
Collecting tqdm==4.40.2
  Downloading https://files.pythonhosted.org/packages/7f/32/5144caf0478b1f26bd9d97f510a47336cf4ac0f96c6bc3b5af20d4173920/tqdm-4.40.2-py2.py3-none-any.whl (55kB)
     |████████████████████████████████| 61kB 2.3MB/s 
Processing /home/admin-123/.cache/pip/wheels/3d/3c/84/28d36677f3c760c048bd02b5a547ea0c4027770cc9cdb9af1e/transforms3d-0.3.1-cp37-none-any.whl
Collecting urllib3==1.25.7
  Downloading https://files.pythonhosted.org/packages/b4/40/a9837291310ee1ccc242ceb6ebfd9eb21539649f193a7c8c86ba15b98539/urllib3-1.25.7-py2.py3-none-any.whl (125kB)
     |████████████████████████████████| 133kB 1.5MB/s 
Collecting wcwidth==0.1.7
  Downloading https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Collecting Werkzeug==0.16.0
  Downloading https://files.pythonhosted.org/packages/ce/42/3aeda98f96e85fd26180534d36570e4d18108d62ae36f87694b476b83d6f/Werkzeug-0.16.0-py2.py3-none-any.whl (327kB)
     |████████████████████████████████| 327kB 1.5MB/s 
Processing /home/admin-123/.cache/pip/wheels/d7/de/2e/efa132238792efb6459a96e85916ef8597fcb3d2ae51590dfd/wrapt-1.11.2-cp37-cp37m-linux_x86_64.whl
Collecting xlrd==1.2.0
  Downloading https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl (103kB)
     |████████████████████████████████| 112kB 1.7MB/s 
Collecting xlutils==2.0.0
  Downloading https://files.pythonhosted.org/packages/c7/55/e22ac73dbb316cabb5db28bef6c87044a95914f713a6e81b593f8a0d2f79/xlutils-2.0.0-py2.py3-none-any.whl (55kB)
     |████████████████████████████████| 61kB 2.3MB/s 
Collecting xlwt==1.3.0
  Downloading https://files.pythonhosted.org/packages/44/48/def306413b25c3d01753603b1a222a011b8621aed27cd7f89cbc27e6b0f4/xlwt-1.3.0-py2.py3-none-any.whl (99kB)
     |████████████████████████████████| 102kB 1.8MB/s 
Collecting zipp==0.6.0
  Downloading https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools>=40.3.0 in ./python/lib/python3.7/site-packages (from google-auth==1.10.0->-r requirements-freeze.txt (line 15)) (41.4.0)
Requirement already satisfied: wheel>=0.26; python_version >= "3" in ./python/lib/python3.7/site-packages (from tensorboard==2.0.2->-r requirements-freeze.txt (line 64)) (0.33.6)
Installing collected packages: six, absl-py, astor, attrs, cachetools, certifi, cffi, coverage, cycler, decorator, numpy, nibabel, h5py, scipy, dipy, futures, gast, pyasn1, pyasn1-modules, rsa, google-auth, oauthlib, requests-oauthlib, google-auth-oauthlib, google-pasta, grpcio, Pillow, imageio, more-itertools, zipp, importlib-metadata, joblib, Keras-Applications, PyYAML, Keras-Preprocessing, Keras, kiwisolver, Markdown, pyparsing, python-dateutil, matplotlib, networkx, opt-einsum, packaging, pytz, pandas, pluggy, protobuf, psutil, py, pyOpenSSL, PyQt5-sip, PyQt5, wcwidth, pytest, pytest-cov, PyWavelets, raven, scikit-image, scikit-learn, Werkzeug, tensorboard, termcolor, wrapt, tensorflow-estimator, tensorflow, tqdm, transforms3d, urllib3, xlrd, xlwt, xlutils
  Found existing installation: six 1.12.0
    Uninstalling six-1.12.0:
      Successfully uninstalled six-1.12.0
  Found existing installation: certifi 2019.9.11
    Uninstalling certifi-2019.9.11:
      Successfully uninstalled certifi-2019.9.11
  Found existing installation: cffi 1.13.0
    Uninstalling cffi-1.13.0:
      Successfully uninstalled cffi-1.13.0
  Found existing installation: numpy 1.18.1
    Uninstalling numpy-1.18.1:
      Successfully uninstalled numpy-1.18.1
  Found existing installation: pyOpenSSL 19.0.0
    Uninstalling pyOpenSSL-19.0.0:
      Successfully uninstalled pyOpenSSL-19.0.0
  Found existing installation: tqdm 4.36.1
    Uninstalling tqdm-4.36.1:
      Successfully uninstalled tqdm-4.36.1
  Found existing installation: urllib3 1.24.2
    Uninstalling urllib3-1.24.2:
      Successfully uninstalled urllib3-1.24.2
Successfully installed Keras-2.3.1 Keras-Applications-1.0.8 Keras-Preprocessing-1.1.0 Markdown-3.1.1 Pillow-6.2.1 PyQt5-5.11.3 PyQt5-sip-4.19.19 PyWavelets-1.1.1 PyYAML-5.2 Werkzeug-0.16.0 absl-py-0.9.0 astor-0.8.1 attrs-19.3.0 cachetools-4.0.0 certifi-2019.11.28 cffi-1.13.2 coverage-5.0 cycler-0.10.0 decorator-4.4.1 dipy-1.0.0 futures-3.1.1 gast-0.2.2 google-auth-1.10.0 google-auth-oauthlib-0.4.1 google-pasta-0.1.8 grpcio-1.26.0 h5py-2.10.0 imageio-2.6.1 importlib-metadata-1.3.0 joblib-0.14.1 kiwisolver-1.1.0 matplotlib-3.1.2 more-itertools-8.0.2 networkx-2.4 nibabel-3.0.0 numpy-1.17.4 oauthlib-3.1.0 opt-einsum-3.1.0 packaging-19.2 pandas-0.25.3 pluggy-0.13.1 protobuf-3.11.1 psutil-5.6.7 py-1.8.0 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.7 pyparsing-2.4.5 pytest-5.3.2 pytest-cov-2.8.1 python-dateutil-2.8.1 pytz-2019.3 raven-6.10.0 requests-oauthlib-1.3.0 rsa-4.0 scikit-image-0.16.2 scikit-learn-0.22 scipy-1.4.0 six-1.13.0 tensorboard-2.0.2 tensorflow-2.0.1 tensorflow-estimator-2.0.1 termcolor-1.1.0 tqdm-4.40.2 transforms3d-0.3.1 urllib3-1.25.7 wcwidth-0.1.7 wrapt-1.11.2 xlrd-1.2.0 xlutils-2.0.0 xlwt-1.3.0 zipp-0.6.0
Obtaining file:///home/admin-123/sct_4.2.2
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox

Creating launchers for Python scripts...

cp: Aufruf von stat für '/home/admin-123/sct_4.2.2/python/envs/venv_sct/bin/*sct*' nicht möglich: Datei oder Verzeichnis nicht gefunden

Problem creating launchers!


Installation failed!

Please copy the historic of this Terminal (starting with the command install_sct) and paste it in a new created topic on SCT's forum:

--> http://forum.spinalcordmri.org/c/sct
2

Indeed, the following message points to a connection problem:

**CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://your.repo/binstar_username/linux-64/current_repodata.json>**
**Elapsed: -**

**An HTTP error occurred when trying to retrieve this URL.**
**HTTP errors are often intermittent, and a simple retry will get you on your way.**
**ConnectionError(MaxRetryError("HTTPSConnectionPool(host='your.repo', port=443): Max retries exceeded with url: /binstar_username/linux-64/current_repodata.json (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f9374098290>: Failed to establish a new connection: [Errno -2] Name or service not known'))"))**

Have you tried to re-run the installation? If yes, have you checked if your institution’s firewall blocks this address? If this is on a laptop, have you tried running the installer from another location (e.g. from home)?

3

I tried to re-run the installation several times, but always ended up with the same error. I tried to run the installer from another location and also tried to install to a different folder, which i granted full access rights. Everything without success.

Uninstalling the virus scanning software and rebooting didn’t help either.
There is no proxy or firewall in this configuration.

Retrieving the url https://your.repo/binstar_username/linux-64/ directly in Firefox browser tells me that the page was not found.

It is not a laptop.

4

Hi,
Sorry for the delay. We are still trying to reproduce your error. Once we understand its origin we will be able to work on a fix.
Best,
Julien

5

Just to clarify: by “different location”, did you mean different source folders in your computer, or different physical location (e.g., from home, from a cafe, from work, etc.)?

It is possible that your problem is related to the proxy of your institution. See this post.

6

“different location” was a different source folder on the same computer. There is no proxy in the above configuration and install log.
We have a proxy in our insitution limiting internet access. Normally this computer is behind that proxy and during installing SCT we got the same issues as mentioned above. To eliminate the proxy as the source of error, we connected the computer to an internet connection without any proxy but we got the same error log.

1 Like
7

Hi @Jetpack, I’m working to understand and solve this issue. I notice that the miniconda download is different. Here it is 81MB:

$ LANG=de_DE wget https://repo.continuum.io/miniconda/Miniconda3-la>
--2020-03-17 13:22:32--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Aufl"osen des Hostnamens repo.continuum.io (repo.continuum.io)... 104.18.201.79, 104.18.200.79, 2606:4700::6812:c84f, ...
Verbindungsaufbau zu repo.continuum.io (repo.continuum.io)|104.18.201.79|:443 ... verbunden.
HTTP-Anforderung gesendet, auf Antwort wird gewartet ... 200 OK
L"ange: 85055499 (81M) [application/x-sh]
Wird in >>Miniconda3-latest-Linux-x86_64.sh<< gespeichert.

Miniconda3-latest-Linux-x86_64.sh 100%[===========================================================>]  81.12M   458KB/s    in 3m 3s   

2020-03-17 13:25:35 (453 KB/s) - >>Miniconda3-latest-Linux-x86_64.sh<< gespeichert [85055499/85055499]

But yours is only 68M:

wget -O /tmp/tmp.8gONaUckvE/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2020-03-10 10:04:50--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Auflösen des Hostnamen »repo.continuum.io (repo.continuum.io)«... 104.18.201.79, 104.18.200.79, 2606:4700::6812:c94f, ...
Verbindungsaufbau zu repo.continuum.io (repo.continuum.io)|104.18.201.79|:443... verbunden.
HTTP-Anforderung gesendet, warte auf Antwort... 200 OK
Länge: 71785000 (68M) [application/x-sh]

The sha256 of the correct file is 957d2f0f0701c3d1335e3b39f235d197837ad69a944fa6f5d8ad2c686b69df3b, and I’ve uploaded it to for you to https://gist.github.com/kousu/f4163e66674dfece476193df0ddce1aa/raw/daf26933c4909a26d10a216a9a45a59d968700b4/Miniconda3-latest-Linux-x86_64.sh

You should be able to retrieve it manually like this:

$ wget https://gist.github.com/kousu/f4163e66674dfece476193df0ddce1aa/raw/daf26933c4909a26d10a216a9a45a59d968700b4/Miniconda3-latest-Linux-x86_64.sh 
--2020-03-17 13:38:18--  https://gist.github.com/kousu/f4163e66674dfece476193df0ddce1aa/raw/daf26933c4909a26d10a216a9a45a59d968700b4/Miniconda3-latest-Linux-x86_64.sh
Resolving gist.github.com (gist.github.com)... 192.30.253.119
Connecting to gist.github.com (gist.github.com)|192.30.253.119|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://gist.githubusercontent.com/kousu/f4163e66674dfece476193df0ddce1aa/raw/daf26933c4909a26d10a216a9a45a59d968700b4/Miniconda3-latest-Linux-x86_64.sh [following]
--2020-03-17 13:38:18--  https://gist.githubusercontent.com/kousu/f4163e66674dfece476193df0ddce1aa/raw/daf26933c4909a26d10a216a9a45a59d968700b4/Miniconda3-latest-Linux-x86_64.sh
Resolving gist.githubusercontent.com (gist.githubusercontent.com)... 151.101.124.133
Connecting to gist.githubusercontent.com (gist.githubusercontent.com)|151.101.124.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 85055499 (81M) [application/octet-stream]
Saving to: 'Miniconda3-latest-Linux-x86_64.sh'

Miniconda3-latest-Linux-x86_64.sh 100%[===========================================================>]  81.12M  1.57MB/s    in 47s     

2020-03-17 13:39:05 (1.74 MB/s) - 'Miniconda3-latest-Linux-x86_64.sh' saved [85055499/85055499]

$ sha256sum Miniconda3-latest-Linux-x86_64.sh                                                                                
957d2f0f0701c3d1335e3b39f235d197837ad69a944fa6f5d8ad2c686b69df3b  Miniconda3-latest-Linux-x86_64.sh

Perhaps your network blocks large downloads? If you’re working from home this week, can you try from there?

On our end, we could add better verification steps to the installer to catch this sort of problem sooner.

8

If you have download it manually into the the package directory, and verify the sha256sum, could you please try applying this patch to the install script?

diff --git a/install_sct b/install_sct
index d956dead..b40afec1 100755
--- a/install_sct
+++ b/install_sct
@@ -517,18 +517,8 @@ print info "Installing conda..."
 run "rm -rf $SCT_DIR/$PYTHON_DIR"
 run "mkdir -p $SCT_DIR/$PYTHON_DIR"
 
-# Download miniconda
-case $OS in
-linux*)
-  download $TMP_DIR/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  ;;
-osx)
-  download $TMP_DIR/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
-  ;;
-esac
-
 # Run conda installer
-run "bash $TMP_DIR/miniconda.sh -p $SCT_DIR/$PYTHON_DIR -b -f"
+run "bash Miniconda3-latest-Linux-x86_64.sh -p $SCT_DIR/$PYTHON_DIR -b -f"
 
 # create py3.6 venv (for Keras/TF compatibility with Centos7, see issue #2270)
 yes | python/bin/conda create -n venv_sct python=3.6

and let us know how it goes.

Thank you very much for reporting issues. We want SCT to be a trustworthy piece of software.