[REVIEW]: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T" #25

roboneuro · 2024-02-15T10:19:18Z

Submitting author: @mathieuboudreau (Mathieu Boudreau)
Repository: https://github.com/shimming-toolbox/rf-shimming-7t
Branch with paper.md (empty if default branch): main
Version: r20240214
Editor: @pbellec
Reviewers: @agahkarakuzu
Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00025
Repository archive: 10.5281/zenodo.10844540
Data archive: 10.5281/zenodo.10844542
Book archive: 10.5281/zenodo.10844538
Docker archive: 10.5281/zenodo.10844544

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a"><img src="https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg)](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@agahkarakuzu, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@roboneuro generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @pbellec know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

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The text was updated successfully, but these errors were encountered:

roboneuro · 2024-02-15T10:19:21Z

Hello humans, I'm @roboneuro, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@roboneuro commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@roboneuro generate pdf

roboneuro · 2024-02-15T10:19:23Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1002/mrm.29528 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuroimage.2016.10.009 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/nrneurol.2015.80 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41582-019-0270-5 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0730-725X(01)00300-9 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/jmri.20245 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1118/1.595995 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.10137 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuroimage.2017.10.041 is INVALID because of 'https://doi.org/' prefix

roboneuro · 2024-02-15T10:19:23Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (261.5 files/s, 52371.4 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Jupyter Notebook                  1              0           1013            601
TeX                               1             13              5            237
Markdown                          2             43              0            117
YAML                              4             13             17             62
CSS                               1              6              0             46
Bourne Again Shell                1              7              0             18
JSON                              1              0              0              5
--------------------------------------------------------------------------------
SUM:                             11             82           1035           1086
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

roboneuro · 2024-02-15T10:19:25Z

Wordcount for paper.md is 736

agahkarakuzu · 2024-02-15T10:20:39Z

@roboneuro build book

roboneuro · 2024-02-15T10:20:42Z

🔴 Binder build has failed 🥀

Status: Failed b5ac4850
Last updated: 2024-02-15 02:42:19 PST

ℹ️ See details

The next comment will forward the logs

roboneuro · 2024-02-15T10:21:11Z

⚠️ An error happened when generating the pdf.

roboneuro · 2024-02-15T10:42:22Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockergv7psj34'...
HEAD is now at 3116b16 Update data to release in this repo instead of depricated repo
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
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Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
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Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
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Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
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Step 5/53 : ENV LC_ALL en_US.UTF-8
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Step 6/53 : ENV LANG en_US.UTF-8
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Step 7/53 : ENV LANGUAGE en_US.UTF-8
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Step 8/53 : ENV SHELL /bin/bash
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Step 10/53 : ARG NB_UID
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Step 11/53 : ENV USER ${NB_USER}
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Step 12/53 : ENV HOME /home/${NB_USER}
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Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
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Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
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Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
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Step 16/53 : EXPOSE 8888
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Step 17/53 : ENV APP_BASE /srv
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Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
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Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
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Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
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Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
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Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
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Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
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Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
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Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
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Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
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Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
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Step 29/53 : USER ${NB_USER}
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Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
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Step 31/53 : USER root
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Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
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Step 33/53 : ARG REPO_DIR=${HOME}
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Step 35/53 : WORKDIR ${REPO_DIR}
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Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
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Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
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Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
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Step 40/53 : USER ${NB_USER}
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Collecting nbdime
  Downloading nbdime-4.0.1-py3-none-any.whl (5.9 MB)
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Requirement already satisfied: pycparser in /srv/conda/envs/notebook/lib/python3.8/site-packages (from cffi>=1.12->cryptography>=2.0->SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (2.20)
Collecting alabaster<0.8,>=0.7
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Collecting snowballstemmer>=1.1
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Requirement already satisfied: babel>=1.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sphinx<5,>=4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.9.1)
Collecting sphinxcontrib-serializinghtml>=1.1.5
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Collecting pydata-sphinx-theme~=0.8.0
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  Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
Requirement already satisfied: wheel in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sphinx_togglebutton->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.36.2)
Collecting pybtex-docutils>=1.0.0
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Requirement already satisfied: greenlet!=0.4.17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sqlalchemy<1.5,>=1.3.12->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.1.0)
Collecting s3transfer<0.11.0,>=0.10.0
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Collecting colorama<0.4.5,>=0.2.5
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Collecting botocore==1.34.42
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Requirement already satisfied: webencodings in /srv/conda/envs/notebook/lib/python3.8/site-packages (from bleach->nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.5.1)
Collecting filelock
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Collecting more-itertools
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Collecting jupyter-server-mathjax>=0.2.2
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Collecting gitpython!=2.1.4,!=2.1.5,!=2.1.6
  Downloading GitPython-3.1.41-py3-none-any.whl (196 kB)
Requirement already satisfied: jupyter-server in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.10.1)
Collecting gitdb<5,>=4.0.1
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Collecting smmap<6,>=3.0.1
  Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Requirement already satisfied: websocket-client in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.57.0)
Requirement already satisfied: anyio<4,>=3.1.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.3.0)
Requirement already satisfied: requests-unixsocket in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.0)
Requirement already satisfied: sniffio>=1.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from anyio<4,>=3.1.0->jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.2.0)
Collecting requests-toolbelt>=0.10.1
  Downloading requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB)
Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (1.7.1)
Collecting wget
  Downloading wget-3.2.zip (10 kB)
Building wheels for collected packages: wget
  Building wheel for wget (setup.py): started
  Building wheel for wget (setup.py): finished with status 'done'
  Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9680 sha256=bebd666d278899563178ddceffae86e1b5bf29fd9fc810c42a51ffc016018c16
  Stored in directory: /tmp/pip-ephem-wheel-cache-bdho_ldd/wheels/bd/a8/c3/3cf2c14a1837a4e04bd98631724e81f33f462d86a1d895fae0
Successfully built wget
Installing collected packages: packaging, smmap, gitdb, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, more-itertools, markdown-it-py, latexcodec, jupyter-server-mathjax, jmespath, jeepney, importlib-metadata, imagesize, gitpython, docutils, colorama, alabaster, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, numpy, nbdime, mdit-py-plugins, jaraco.classes, importlib-resources, botocore, beautifulsoup4, wget, uc-micro-py, tzdata, typing-extensions, tqdm, sphinx-togglebutton, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, pillow, patool, myst-parser, msgpack, looseversion, kiwisolver, keyrings.alt, keyring, jupyter-sphinx, jupyter-cache, iso8601, humanize, fonttools, filelock, fasteners, distro, cycler, contourpy, click, boto, annexremote, zenodo-get, tenacity, sphinxcontrib-bibtex, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, scipy, patsy, pandas, osfclient, myst-nb, matplotlib, linkify-it-py, gdown, datalad, awscli, statsmodels, seaborn, repo2data, plotly, nibabel, markdown, jupyter-book
  Attempting uninstall: packaging
    Found existing installation: packaging 21.0
    Uninstalling packaging-21.0:
      Successfully uninstalled packaging-21.0
  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 4.6.3
    Uninstalling importlib-metadata-4.6.3:
      Successfully uninstalled importlib-metadata-4.6.3
Successfully installed SecretStorage-3.3.3 alabaster-0.7.13 annexremote-1.6.4 awscli-1.32.42 beautifulsoup4-4.12.3 boto-2.49.0 botocore-1.34.42 click-8.1.7 colorama-0.4.4 contourpy-1.1.1 cycler-0.12.1 datalad-0.19.6 distro-1.9.0 docutils-0.16 fasteners-0.19 filelock-3.13.1 fonttools-4.48.1 gdown-5.1.0 gitdb-4.0.11 gitpython-3.1.41 humanize-4.9.0 imagesize-1.4.1 importlib-metadata-7.0.1 importlib-resources-6.1.1 iso8601-2.1.0 jaraco.classes-3.3.1 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.13.0 jupyter-cache-0.4.3 jupyter-server-mathjax-0.2.6 jupyter-sphinx-0.3.2 keyring-24.3.0 keyrings.alt-5.0.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-1.0.3 looseversion-1.3.0 markdown-3.5.2 markdown-it-py-1.1.0 matplotlib-3.7.4 mdit-py-plugins-0.2.8 more-itertools-10.2.0 msgpack-1.0.7 myst-nb-0.13.2 myst-parser-0.15.2 nbdime-4.0.1 nibabel-5.2.0 numpy-1.24.4 osfclient-0.0.5 packaging-23.2 pandas-2.0.3 patool-1.12 patsy-0.5.6 pillow-10.2.0 platformdirs-4.2.0 plotly-5.18.0 pyasn1-0.5.1 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.8.1 python-gitlab-4.4.0 pyyaml-6.0.1 repo2data-2.9.1 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.10.0 scipy-1.10.1 seaborn-0.13.2 smmap-5.0.1 snowballstemmer-2.2.0 soupsieve-2.5 sphinx-4.5.0 sphinx-book-theme-0.3.3 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.1.0 sphinx-external-toc-0.2.4 sphinx-jupyterbook-latex-0.4.7 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.1.2 sphinx-togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-bibtex-2.5.0 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 statsmodels-0.14.1 tenacity-8.2.3 tqdm-4.66.2 typing-extensions-4.9.0 tzdata-2024.1 uc-micro-py-1.0.3 wget-3.2 zenodo-get-1.5.1
Removing intermediate container 6f905bf80fc9
 ---> 48f0784fcf61
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> fd4fd6dbe67b
Step 43/53 : LABEL repo2docker.ref="3116b16edcc00fcb465831d8d8a51f98805d6374"
 ---> Running in 2d9ff712f48f
Removing intermediate container 2d9ff712f48f
 ---> d4b6931a1e3c
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in f59fc4511ca0
Removing intermediate container f59fc4511ca0
 ---> 30d80299ea5e
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 71d6756eccbc
Removing intermediate container 71d6756eccbc
 ---> e6a165621857
Step 46/53 : USER ${NB_USER}
 ---> Running in 719c78712a9a
Removing intermediate container 719c78712a9a
 ---> 84fd1c625d00
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 5a70d4006e71
Removing intermediate container 5a70d4006e71
 ---> 35d6c33e0f6e
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 4d785d5b87a6
---- repo2data starting ----
/srv/conda/envs/notebook/lib/python3.8/site-packages/repo2data
Config from file :
../binder/data_requirement.json
Destination:
../data/rf-shimming-7t
File downloaded to: ../data/rf-shimming-7t/ds004906.zip

patool: Extracting ../data/rf-shimming-7t/ds004906.zip ...

patool: ... ../data/rf-shimming-7t/ds004906.zip extracted to `../data/rf-shimming-7t'.

Info : ds004906.zip Decompressed

�[91mCloning into '/home/jovyan/content/sct'...

�[0m

�[0;32m


Welcome to SCT installation *


�[0m
�[0;32mChecking OS type and version...�[0m
Linux 4d785d5b87a6 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
�[0;32mChecking requirements...�[0m
�[0;32mOK!�[0m
SCT version ......... 6.2.dev0

Installation type ... in-place

Operating system .... linux (unknown)

Shell config ........ /home/jovyan/.bashrc
�[0;32mSCT will be installed here: [/home/jovyan/content/sct]�[0m
�[0;92m

Do you agree? [y]es/[n]o: �[0m

�[0;32mSkipping copy of source files (source and destination folders are the same)�[0m
�[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: �[0m

�[0;32mDownloading Miniconda...�[0m
�[0;34mwget -nv -O /tmp/tmp.Fd9nSqpTBQ/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh�[0m
2024-02-15 10:25:56 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.Fd9nSqpTBQ/miniconda.sh" [1]
�[0;32mInstalling Miniconda...�[0m
�[0;34mbash /tmp/tmp.Fd9nSqpTBQ/miniconda.sh -p /home/jovyan/content/sct/python -b -f�[0m
PREFIX=/home/jovyan/content/sct/python

Unpacking payload ...
0%|          | 0/73 [00:00<?, ?it/s]

Extracting : tqdm-4.65.0-py311h92b7b1e_0.conda:   0%|          | 0/73 [00:00<?, ?it/s]

Extracting : tk-8.6.12-h1ccaba5_0.conda:   1%|▏         | 1/73 [00:00<00:17,  4.00it/s]

Extracting : tk-8.6.12-h1ccaba5_0.conda:   3%|▎         | 2/73 [00:00<00:08,  8.00it/s]

Extracting : reproc-cpp-14.2.4-h295c915_1.conda:   3%|▎         | 2/73 [00:00<00:08,  8.00it/s]

Extracting : zlib-1.2.13-h5eee18b_0.conda:   4%|▍         | 3/73 [00:00<00:08,  8.00it/s]

Extracting : conda-content-trust-0.2.0-py311h06a4308_0.conda:   5%|▌         | 4/73 [00:00<00:08,  8.00it/s]

Extracting : icu-73.1-h6a678d5_0.conda:   7%|▋         | 5/73 [00:00<00:08,  8.00it/s]

Extracting : icu-73.1-h6a678d5_0.conda:   8%|▊         | 6/73 [00:00<00:06, 10.01it/s]

Extracting : archspec-0.2.1-pyhd3eb1b0_0.conda:   8%|▊         | 6/73 [00:00<00:06, 10.01it/s]

Extracting : pyopenssl-23.2.0-py311h06a4308_0.conda:  10%|▉         | 7/73 [00:00<00:06, 10.01it/s]

Extracting : libstdcxx-ng-11.2.0-h1234567_1.conda:  11%|█         | 8/73 [00:00<00:06, 10.01it/s]

Extracting : platformdirs-3.10.0-py311h06a4308_0.conda:  12%|█▏        | 9/73 [00:00<00:06, 10.01it/s]

Extracting : boltons-23.0.0-py311h06a4308_0.conda:  14%|█▎        | 10/73 [00:00<00:06, 10.01it/s]

Extracting : lz4-c-1.9.4-h6a678d5_0.conda:  15%|█▌        | 11/73 [00:00<00:06, 10.01it/s]

Extracting : python-3.11.5-h955ad1f_0.conda:  16%|█▋        | 12/73 [00:02<00:06, 10.01it/s]

Extracting : python-3.11.5-h955ad1f_0.conda:  18%|█▊        | 13/73 [00:02<00:10,  5.76it/s]

Extracting : openssl-3.0.12-h7f8727e_0.conda:  18%|█▊        | 13/73 [00:02<00:10,  5.76it/s]

Extracting : cryptography-41.0.7-py311hdda0065_0.conda:  19%|█▉        | 14/73 [00:02<00:10,  5.76it/s]

Extracting : xz-5.4.5-h5eee18b_0.conda:  21%|██        | 15/73 [00:02<00:10,  5.76it/s]

Extracting : packaging-23.1-py311h06a4308_0.conda:  22%|██▏       | 16/73 [00:02<00:09,  5.76it/s]

Extracting : fmt-9.1.0-hdb19cb5_0.conda:  23%|██▎       | 17/73 [00:02<00:09,  5.76it/s]

Extracting : bzip2-1.0.8-h7b6447c_0.conda:  25%|██▍       | 18/73 [00:02<00:09,  5.76it/s]

Extracting : conda-package-streaming-0.9.0-py311h06a4308_0.conda:  26%|██▌       | 19/73 [00:02<00:09,  5.76it/s]

Extracting : libssh2-1.10.0-hdbd6064_2.conda:  27%|██▋       | 20/73 [00:02<00:09,  5.76it/s]

Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda:  29%|██▉       | 21/73 [00:02<00:09,  5.76it/s]

Extracting : wheel-0.41.2-py311h06a4308_0.conda:  30%|███       | 22/73 [00:02<00:08,  5.76it/s]

Extracting : tzdata-2023c-h04d1e81_0.conda:  32%|███▏      | 23/73 [00:02<00:08,  5.76it/s]

Extracting : jsonpatch-1.32-pyhd3eb1b0_0.conda:  33%|███▎      | 24/73 [00:02<00:08,  5.76it/s]

Extracting : libffi-3.4.4-h6a678d5_0.conda:  34%|███▍      | 25/73 [00:02<00:08,  5.76it/s]

Extracting : libcurl-8.4.0-h251f7ec_1.conda:  36%|███▌      | 26/73 [00:02<00:08,  5.76it/s]

Extracting : zstd-1.5.5-hc292b87_0.conda:  37%|███▋      | 27/73 [00:02<00:07,  5.76it/s]

Extracting : pluggy-1.0.0-py311h06a4308_1.conda:  38%|███▊      | 28/73 [00:02<00:07,  5.76it/s]

Extracting : menuinst-2.0.1-py311h06a4308_1.conda:  40%|███▉      | 29/73 [00:02<00:07,  5.76it/s]

Extracting : ncurses-6.4-h6a678d5_0.conda:  41%|████      | 30/73 [00:02<00:07,  5.76it/s]

Extracting : ncurses-6.4-h6a678d5_0.conda:  42%|████▏     | 31/73 [00:02<00:02, 16.24it/s]

Extracting : readline-8.2-h5eee18b_0.conda:  42%|████▏     | 31/73 [00:02<00:02, 16.24it/s]

Extracting : yaml-cpp-0.8.0-h6a678d5_0.conda:  44%|████▍     | 32/73 [00:02<00:02, 16.24it/s]

Extracting : zstandard-0.19.0-py311h5eee18b_0.conda:  45%|████▌     | 33/73 [00:02<00:02, 16.24it/s]

Extracting : pycosat-0.6.6-py311h5eee18b_0.conda:  47%|████▋     | 34/73 [00:02<00:02, 16.24it/s]

Extracting : pip-23.3.1-py311h06a4308_0.conda:  48%|████▊     | 35/73 [00:02<00:02, 16.24it/s]

Extracting : ca-certificates-2023.12.12-h06a4308_0.conda:  49%|████▉     | 36/73 [00:02<00:02, 16.24it/s]

Extracting : libgcc-ng-11.2.0-h1234567_1.conda:  51%|█████     | 37/73 [00:02<00:02, 16.24it/s]

Extracting : pysocks-1.7.1-py311h06a4308_0.conda:  52%|█████▏    | 38/73 [00:02<00:02, 16.24it/s]

Extracting : conda-package-handling-2.2.0-py311h06a4308_0.conda:  53%|█████▎    | 39/73 [00:02<00:02, 16.24it/s]

Extracting : idna-3.4-py311h06a4308_0.conda:  55%|█████▍    | 40/73 [00:02<00:02, 16.24it/s]

Extracting : setuptools-68.2.2-py311h06a4308_0.conda:  56%|█████▌    | 41/73 [00:02<00:01, 16.24it/s]

Extracting : setuptools-68.2.2-py311h06a4308_0.conda:  58%|█████▊    | 42/73 [00:02<00:01, 21.88it/s]

Extracting : libarchive-3.6.2-h6ac8c49_2.conda:  58%|█████▊    | 42/73 [00:02<00:01, 21.88it/s]

Extracting : urllib3-1.26.18-py311h06a4308_0.conda:  59%|█████▉    | 43/73 [00:02<00:01, 21.88it/s]

Extracting : libuuid-1.41.5-h5eee18b_0.conda:  60%|██████    | 44/73 [00:02<00:01, 21.88it/s]

Extracting : requests-2.31.0-py311h06a4308_0.conda:  62%|██████▏   | 45/73 [00:02<00:01, 21.88it/s]

Extracting : pycparser-2.21-pyhd3eb1b0_0.conda:  63%|██████▎   | 46/73 [00:02<00:01, 21.88it/s]

Extracting : pcre2-10.42-hebb0a14_0.conda:  64%|██████▍   | 47/73 [00:02<00:01, 21.88it/s]

Extracting : libmambapy-1.5.3-py311h2dafd23_0.conda:  66%|██████▌   | 48/73 [00:02<00:01, 21.88it/s]

Extracting : conda-23.11.0-py311h06a4308_0.conda:  67%|██████▋   | 49/73 [00:02<00:01, 21.88it/s]

Extracting : conda-23.11.0-py311h06a4308_0.conda:  68%|██████▊   | 50/73 [00:02<00:00, 24.25it/s]

Extracting : jsonpointer-2.1-pyhd3eb1b0_0.conda:  68%|██████▊   | 50/73 [00:02<00:00, 24.25it/s]

Extracting : libnghttp2-1.57.0-h2d74bed_0.conda:  70%|██████▉   | 51/73 [00:02<00:00, 24.25it/s]

Extracting : libxml2-2.10.4-hf1b16e4_1.conda:  71%|███████   | 52/73 [00:02<00:00, 24.25it/s]

Extracting : libsolv-0.7.24-he621ea3_0.conda:  73%|███████▎  | 53/73 [00:02<00:00, 24.25it/s]

Extracting : libgomp-11.2.0-h1234567_1.conda:  74%|███████▍  | 54/73 [00:02<00:00, 24.25it/s]

Extracting : libev-4.33-h7f8727e_1.conda:  75%|███████▌  | 55/73 [00:02<00:00, 24.25it/s]

Extracting : ld_impl_linux-64-2.38-h1181459_1.conda:  77%|███████▋  | 56/73 [00:02<00:00, 24.25it/s]

Extracting : libedit-3.1.20230828-h5eee18b_0.conda:  78%|███████▊  | 57/73 [00:02<00:00, 24.25it/s]

Extracting : pybind11-abi-4-hd3eb1b0_1.conda:  79%|███████▉  | 58/73 [00:02<00:00, 24.25it/s]

Extracting : _libgcc_mutex-0.1-main.conda:  81%|████████  | 59/73 [00:02<00:00, 24.25it/s]

Extracting : sqlite-3.41.2-h5eee18b_0.conda:  82%|████████▏ | 60/73 [00:02<00:00, 24.25it/s]

Extracting : reproc-14.2.4-h295c915_1.conda:  84%|████████▎ | 61/73 [00:02<00:00, 24.25it/s]

Extracting : certifi-2023.11.17-py311h06a4308_0.conda:  85%|████████▍ | 62/73 [00:02<00:00, 24.25it/s]

Extracting : _openmp_mutex-5.1-1_gnu.conda:  86%|████████▋ | 63/73 [00:02<00:00, 24.25it/s]

Extracting : distro-1.8.0-py311h06a4308_0.conda:  88%|████████▊ | 64/73 [00:02<00:00, 24.25it/s]

Extracting : ruamel.yaml-0.17.21-py311h5eee18b_0.conda:  89%|████████▉ | 65/73 [00:02<00:00, 24.25it/s]

Extracting : brotli-python-1.0.9-py311h6a678d5_7.conda:  90%|█████████ | 66/73 [00:02<00:00, 24.25it/s]

Extracting : conda-libmamba-solver-23.12.0-pyhd3eb1b0_1.conda:  92%|█████████▏| 67/73 [00:02<00:00, 24.25it/s]

Extracting : krb5-1.20.1-h143b758_1.conda:  93%|█████████▎| 68/73 [00:02<00:00, 24.25it/s]

Extracting : krb5-1.20.1-h143b758_1.conda:  95%|█████████▍| 69/73 [00:02<00:00, 39.90it/s]

Extracting : truststore-0.8.0-py311h06a4308_0.conda:  95%|█████████▍| 69/73 [00:02<00:00, 39.90it/s]

Extracting : c-ares-1.19.1-h5eee18b_0.conda:  96%|█████████▌| 70/73 [00:02<00:00, 39.90it/s]

Extracting : libmamba-1.5.3-haf1ee3a_0.conda:  97%|█████████▋| 71/73 [00:02<00:00, 39.90it/s]

Extracting : cffi-1.16.0-py311h5eee18b_0.conda:  99%|█████████▊| 72/73 [00:02<00:00, 39.90it/s]
Installing base environment...
Downloading and Extracting Packages: ...working... done
Downloading and Extracting Packages: ...working... done

Preparing transaction: ...working... done

Executing transaction: ...working... done

installation finished.
�[0;32mCreating conda environment...�[0m
Channels:

defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

Package Plan
environment location: /home/jovyan/content/sct/python/envs/venv_sct
added / updated specs:

- python=3.9
The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
openssl-3.0.13             |       h7f8727e_0         5.2 MB
pip-23.3.1                 |   py39h06a4308_0         2.6 MB
python-3.9.18              |       h955ad1f_0        25.1 MB
setuptools-68.2.2          |   py39h06a4308_0         948 KB
tzdata-2023d               |       h04d1e81_0         117 KB
wheel-0.41.2               |   py39h06a4308_0         108 KB
------------------------------------------------------------
                                       Total:        34.0 MB

The following NEW packages will be INSTALLED:
_libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main

_openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu

ca-certificates    pkgs/main/linux-64::ca-certificates-2023.12.12-h06a4308_0

ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1

libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0

libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1

libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1

libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1

ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0

openssl            pkgs/main/linux-64::openssl-3.0.13-h7f8727e_0

pip                pkgs/main/linux-64::pip-23.3.1-py39h06a4308_0

python             pkgs/main/linux-64::python-3.9.18-h955ad1f_0

readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0

setuptools         pkgs/main/linux-64::setuptools-68.2.2-py39h06a4308_0

sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0

tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0

tzdata             pkgs/main/noarch::tzdata-2023d-h04d1e81_0

wheel              pkgs/main/linux-64::wheel-0.41.2-py39h06a4308_0

xz                 pkgs/main/linux-64::xz-5.4.5-h5eee18b_0

zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0
Downloading and Extracting Packages: ...working... done

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

To activate this environment, use

$ conda activate /home/jovyan/content/sct/python/envs/venv_sct

To deactivate an active environment, use

$ conda deactivate
Channels:

conda-forge
defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

Package Plan
environment location: /home/jovyan/content/sct/python/envs/venv_sct
added / updated specs:

- libstdcxx-ng
The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
_libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
_openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
ca-certificates-2024.2.2   |       hbcca054_0         152 KB  conda-forge
libgcc-ng-13.2.0           |       h807b86a_5         752 KB  conda-forge
libgomp-13.2.0             |       h807b86a_5         410 KB  conda-forge
libstdcxx-ng-13.2.0        |       h7e041cc_5         3.7 MB  conda-forge
openssl-3.2.1              |       hd590300_0         2.7 MB  conda-forge
------------------------------------------------------------
                                       Total:         7.7 MB

The following packages will be UPDATED:
ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-hbcca054_0

libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5

libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5

libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5

openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0
The following packages will be SUPERSEDED by a higher-priority channel:
_libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge

_openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu
Downloading and Extracting Packages: ...working... done

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Channels:

conda-forge
defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

All requested packages already installed.
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)

Collecting pip!=21.2.*

Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)

Downloading pip-24.0-py3-none-any.whl (2.1 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 10.7 MB/s eta 0:00:00

Installing collected packages: pip

Attempting uninstall: pip

Found existing installation: pip 23.3.1

Uninstalling pip-23.3.1:

Successfully uninstalled pip-23.3.1

Successfully installed pip-24.0
�[0;32mInstalling Python dependencies...�[0m
�[0;32mUsing requirements.txt (git installation)�[0m
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu

Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment

Collecting certifi

Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)

Collecting dipy!=1.6.,!=1.7.,!=1.8.* (from -r requirements.txt (line 7))

Downloading dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 4.2 MB/s eta 0:00:00

Collecting ivadomed (from -r requirements.txt (line 11))

Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)

Collecting matplotlib (from -r requirements.txt (line 12))

Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)

Collecting nibabel (from -r requirements.txt (line 21))

Downloading nibabel-5.2.0-py3-none-any.whl.metadata (8.8 kB)

Collecting nilearn (from -r requirements.txt (line 22))

Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB)

Collecting nnunetv2 (from -r requirements.txt (line 23))

Downloading nnunetv2-2.2.1.tar.gz (178 kB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.6/178.6 kB 1.4 MB/s eta 0:00:00

Installing build dependencies: started

Installing build dependencies: finished with status 'done'

Getting requirements to build wheel: started

Getting requirements to build wheel: finished with status 'done'

Installing backend dependencies: started

Installing backend dependencies: finished with status 'done'

Preparing metadata (pyproject.toml): started

Preparing metadata (pyproject.toml): finished with status 'done'

Collecting numpy<1.24 (from -r requirements.txt (line 27))

Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 23.4 MB/s eta 0:00:00

Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))

Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)

Collecting pandas (from -r requirements.txt (line 32))

Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)

Collecting portalocker (from -r requirements.txt (line 33))

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Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt

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Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt

Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tf-keras, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, PyQt5_sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed

Successfully installed Deprecated-1.2.14 GitPython-3.1.41 MarkupSafe-2.1.5 PyQt5_sip-12.13.0 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.48.1 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.2 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pystrum-0.4 pytest-8.0.0 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.0 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.1 tensorboard-data-server-0.7.2 tf-keras-2.15.0 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240215 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.0 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0
�[0;32mInstalling spinalcordtoolbox...�[0m
Obtaining file:///home/jovyan/content/sct

Preparing metadata (setup.py): started

Preparing metadata (setup.py): finished with status 'done'

Installing collected packages: spinalcordtoolbox

Running setup.py develop for spinalcordtoolbox

Successfully installed spinalcordtoolbox-6.2.dev0
�[0;32mCreating launchers for Python scripts...�[0m
�[0;32mInstalling binaries...�[0m
�[0;34msct_download_data -d binaries_linux -k�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d binaries_linux -k
Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz

Downloading: spinalcordtoolbox-binaries_linux.tar.gz
Status:   0%|          | 0.00/83.7M [00:00<?, ?B/s]

Status:   1%|          | 967k/83.7M [00:00<00:08, 9.21MB/s]

Status:   4%|▍         | 3.24M/83.7M [00:00<00:04, 17.0MB/s]

Status:  10%|█         | 8.42M/83.7M [00:00<00:02, 32.7MB/s]

Status:  20%|██        | 16.8M/83.7M [00:00<00:01, 52.7MB/s]

Status:  28%|██▊       | 23.2M/83.7M [00:00<00:01, 56.6MB/s]

Status:  37%|███▋      | 30.7M/83.7M [00:00<00:00, 62.8MB/s]

Status:  45%|████▍     | 37.2M/83.7M [00:00<00:00, 63.7MB/s]

Status:  53%|█████▎    | 44.5M/83.7M [00:00<00:00, 66.6MB/s]

Status:  61%|██████▏   | 51.3M/83.7M [00:00<00:00, 67.1MB/s]

Status:  69%|██████▉   | 58.1M/83.7M [00:01<00:00, 67.0MB/s]

Status:  77%|███████▋  | 64.8M/83.7M [00:01<00:00, 67.2MB/s]

Status:  86%|████████▌ | 71.6M/83.7M [00:01<00:00, 66.8MB/s]

Status:  94%|█████████▍| 78.6M/83.7M [00:01<00:00, 67.7MB/s]

Status: 100%|██████████| 83.7M/83.7M [00:01<00:00, 61.0MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_10-32-37_install-data_anlp0xu8)

Unzip data to: /tmp/sct_2024-02-15_10-32-37_install-data_anlp0xu8

Copying data to: /home/jovyan/content/sct/bin

Removing temporary folders...

Done!
�[0;32mAll requirements installed!�[0m
�[0;32mInstalling data...�[0m
�[0;34mmkdir -p /home/jovyan/content/sct/data�[0m
�[0;34msct_download_data -d PAM50�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d PAM50
Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20231024/PAM50-r20231024.zip

Downloading: PAM50-r20231024.zip
Status:   0%|          | 0.00/104M [00:00<?, ?B/s]

Status:   3%|▎         | 2.75M/104M [00:00<00:03, 27.4MB/s]

Status:  10%|█         | 10.6M/104M [00:00<00:01, 57.2MB/s]

Status:  21%|██▏       | 22.2M/104M [00:00<00:00, 84.1MB/s]

Status:  29%|██▉       | 30.6M/104M [00:00<00:00, 82.1MB/s]

Status:  37%|███▋      | 38.8M/104M [00:00<00:00, 79.3MB/s]

Status:  45%|████▌     | 47.1M/104M [00:00<00:00, 80.5MB/s]

Status:  53%|█████▎    | 55.2M/104M [00:00<00:00, 77.6MB/s]

Status:  61%|██████    | 63.1M/104M [00:00<00:00, 78.0MB/s]

Status:  68%|██████▊   | 70.9M/104M [00:00<00:00, 77.3MB/s]

Status:  76%|███████▌  | 78.7M/104M [00:01<00:00, 76.3MB/s]

Status:  83%|████████▎ | 86.3M/104M [00:01<00:00, 75.1MB/s]

Status:  91%|█████████▏| 94.8M/104M [00:01<00:00, 78.1MB/s]

Status:  99%|█████████▉| 103M/104M [00:01<00:00, 76.6MB/s]

Status: 100%|██████████| 104M/104M [00:01<00:00, 76.3MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_10-32-43_install-data_az4tnus1)

Unzip data to: /tmp/sct_2024-02-15_10-32-43_install-data_az4tnus1

Copying data to: /home/jovyan/content/sct/data/PAM50

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_sc_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_sc_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip

Downloading: 20220325_deepseg_sc_models_onnx.zip
Status:   0%|          | 0.00/19.5M [00:00<?, ?B/s]

Status:   5%|▌         | 1.04M/19.5M [00:00<00:03, 4.69MB/s]

Status:   8%|▊         | 1.52M/19.5M [00:00<00:04, 4.19MB/s]

Status:  21%|██▏       | 4.17M/19.5M [00:00<00:01, 11.5MB/s]

Status:  55%|█████▌    | 10.7M/19.5M [00:00<00:00, 28.9MB/s]

Status:  92%|█████████▏| 17.9M/19.5M [00:00<00:00, 42.4MB/s]

Status: 100%|██████████| 19.5M/19.5M [00:00<00:00, 28.6MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_10-32-45_install-data_xi88yjsg)

Unzip data to: /tmp/sct_2024-02-15_10-32-45_install-data_xi88yjsg

Copying data to: /home/jovyan/content/sct/data/deepseg_sc_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_gm_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_gm_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip

Downloading: 20220325_deepseg_gm_models_onnx.zip
Status:   0%|          | 0.00/2.24M [00:00<?, ?B/s]

Status: 100%|██████████| 2.24M/2.24M [00:00<00:00, 65.5MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_10-32-46_install-data_7tbqy014)

Unzip data to: /tmp/sct_2024-02-15_10-32-46_install-data_7tbqy014

Copying data to: /home/jovyan/content/sct/data/deepseg_gm_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_lesion_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_lesion_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip

Downloading: 20220325_deepseg_lesion_models_onnx.zip
Status:   0%|          | 0.00/5.35M [00:00<?, ?B/s]

Status:  50%|████▉     | 2.67M/5.35M [00:00<00:00, 26.6MB/s]

Status: 100%|█████████▉| 5.33M/5.35M [00:00<00:00, 16.5MB/s]

Status: 100%|██████████| 5.35M/5.35M [00:00<00:00, 17.5MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_10-32-48_install-data_jv5v5ynb)

Unzip data to: /tmp/sct_2024-02-15_10-32-48_install-data_jv5v5ynb

Copying data to: /home/jovyan/content/sct/data/deepseg_lesion_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepreg_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepreg_models
Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip

Downloading: models.zip
Status:   0%|          | 0.00/158M [00:00<?, ?B/s]

Status:   5%|▌         | 8.44M/158M [00:00<00:01, 75.7MB/s]

Status:  10%|█         | 16.0M/158M [00:00<00:01, 75.8MB/s]

Status:  15%|█▍        | 23.6M/158M [00:00<00:01, 70.3MB/s]

Status:  19%|█▉        | 30.7M/158M [00:00<00:01, 65.2MB/s]

Status:  24%|██▍       | 37.6M/158M [00:00<00:01, 66.6MB/s]

Status:  28%|██▊       | 44.3M/158M [00:00<00:01, 66.8MB/s]

Status:  32%|███▏      | 51.1M/158M [00:00<00:01, 65.5MB/s]

Status:  38%|███▊      | 60.0M/158M [00:00<00:01, 72.7MB/s]

Status:  43%|████▎     | 67.3M/158M [00:00<00:01, 68.4MB/s]

Status:  47%|████▋     | 74.2M/158M [00:01<00:01, 66.9MB/s]

Status:  52%|█████▏    | 82.4M/158M [00:01<00:01, 71.0MB/s]

Status:  57%|█████▋    | 89.5M/158M [00:01<00:01, 67.0MB/s]

Status:  62%|██████▏   | 97.6M/158M [00:01<00:00, 71.0MB/s]

Status:  66%|██████▌   | 105M/158M [00:01<00:00, 70.2MB/s]

Status:  71%|███████   | 112M/158M [00:01<00:00, 69.3MB/s]

Status:  75%|███████▌  | 119M/158M [00:01<00:00, 69.3MB/s]

Status:  80%|███████▉  | 126M/158M [00:01<00:00, 71.0MB/s]

Status:  84%|████████▍ | 134M/158M [00:01<00:00, 70.3MB/s]

Status:  89%|████████▉ | 141M/158M [00:02<00:00, 69.1MB/s]

Status:  94%|█████████▍| 149M/158M [00:02<00:00, 74.2MB/s]

Status:  99%|█████████▉| 157M/158M [00:02<00:00, 74.8MB/s]

Status: 100%|██████████| 158M/158M [00:02<00:00, 70.3MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_10-32-51_install-data_7wtf1uz_)

Unzip data to: /tmp/sct_2024-02-15_10-32-51_install-data_7wtf1uz_

Copying data to: /home/jovyan/content/sct/data/deepreg_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d PAM50_normalized_metrics�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d PAM50_normalized_metrics
Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20230222.zip

Downloading: PAM50-normalized-metrics-r20230222.zip
Status:   0%|          | 0.00/1.00 [00:00<?, ?B/s]

Status: 47.3kB [00:00, 360kB/s]

Status: 213kB [00:00, 844kB/s]

Status: 884kB [00:00, 2.63MB/s]

Status: 3.62MB [00:00, 9.18MB/s]

Status: 5.15MB [00:00, 10.9MB/s]

Status: 6.28MB [00:00, 9.67MB/s]

Status: 6.92MB [00:00, 7.78MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_10-32-55_install-data_3cdx0eo0)

Unzip data to: /tmp/sct_2024-02-15_10-32-55_install-data_3cdx0eo0

Copying data to: /home/jovyan/content/sct/data/PAM50_normalized_metrics

Removing temporary folders...

Done!
Status:   0%|          | 0.00/18.0M [00:00<?, ?B/s]

Status:  47%|████▋     | 8.41M/18.0M [00:00<00:00, 82.5MB/s]

Status:  93%|█████████▎| 16.7M/18.0M [00:00<00:00, 82.2MB/s]

Status: 100%|██████████| 18.0M/18.0M [00:00<00:00, 80.3MB/s]
�[0;32mValidate installation...�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_check_dependencies
SYSTEM INFORMATION
SCT info:

version: git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9
path: /home/jovyan/content/sct

OS: linux (Linux-5.4.0-139-generic-x86_64-with-glibc2.27)

CPU cores: Available: 16, Used by ITK functions: 16

RAM: Total: 60286MB, Used: 1480MB, Available: 58423MB

OPTIONAL DEPENDENCIES
Check FSLeyes version...............................[  ]

(127, '/bin/sh: 1: fsleyes: not found')
MANDATORY DEPENDENCIES
Check Python executable.............................[�[92mOK�[0m]

Using bundled python 3.9.18 (main, Sep 11 2023, 13:41:44)

[GCC 11.2.0] at /home/jovyan/content/sct/python/envs/venv_sct/bin/python

Check if data are installed.........................[�[92mOK�[0m]

Check if dipy is installed..........................[�[92mOK�[0m] (1.5.0)

Check if ivadomed is installed......................[�[92mOK�[0m] (2.9.9)

Check if matplotlib is installed....................[�[92mOK�[0m] (3.8.3)

Check if monai is installed.........................[�[92mOK�[0m] (1.3.0)

Check if nibabel is installed.......................[�[92mOK�[0m] (3.2.2)

Check if nilearn is installed.......................[�[92mOK�[0m] (0.10.2)

Check if nnunetv2 is installed......................[�[92mOK�[0m]

Check if numpy is installed.........................[�[92mOK�[0m] (1.23.5)

Check if onnxruntime is installed...................[�[92mOK�[0m] (1.17.0)

Check if pandas is installed........................[�[92mOK�[0m] (1.4.4)

Check if portalocker is installed...................[�[92mOK�[0m] (2.8.2)

Check if psutil is installed........................[�[92mOK�[0m] (5.9.8)

Check if pyqt5 (5.12.3) is installed................[�[92mOK�[0m] (5.12.3)

Check if pytest is installed........................[�[92mOK�[0m] (8.0.0)

Check if pytest-cov is installed....................[�[92mOK�[0m] (4.1.0)

Check if requests is installed......................[�[92mOK�[0m] (2.31.0)

Check if requirements-parser is installed...........[�[92mOK�[0m]

Check if scipy is installed.........................[�[92mOK�[0m] (1.12.0)

Check if scikit-image is installed..................[�[92mOK�[0m] (0.22.0)

Check if scikit-learn is installed..................[�[92mOK�[0m] (1.4.0)

Check if xlwt is installed..........................[�[92mOK�[0m] (1.3.0)

Check if tqdm is installed..........................[�[92mOK�[0m] (4.66.2)

Check if transforms3d is installed..................[�[92mOK�[0m] (0.4.1)

Check if urllib3 is installed.......................[�[92mOK�[0m] (2.2.0)

Check if pytest_console_scripts is installed........[�[92mOK�[0m]

Check if pyyaml is installed........................[�[92mOK�[0m] (6.0.1)

Check if voxelmorph is installed....................[�[92mOK�[0m] (0.2)

Check if wquantiles is installed....................[�[92mOK�[0m] (0.4)

Check if xlsxwriter is installed....................[�[92mOK�[0m] (3.1.9)

Check if spinalcordtoolbox is installed.............[�[92mOK�[0m]

Check ANTs compatibility with OS ...................[�[92mOK�[0m]

Check PropSeg compatibility with OS ................[�[92mOK�[0m]

Check if figure can be opened with PyQt.............[�[91mFAIL�[0m] ($DISPLAY not set on X11-supporting system)

Check if figure can be opened with matplotlib.......[�[91mFAIL�[0m] (Using non-GUI backend 'agg')
�[0;32mOpen a new Terminal window to load environment variables, or run:

source /home/jovyan/.bashrc�[0m
�[0;32mInstallation finished successfully!�[0m
Removing intermediate container 4d785d5b87a6

---> 034b7c549c0f

Step 49/53 : ENV PYTHONUNBUFFERED=1

---> Running in a44ea4f558f4

Removing intermediate container a44ea4f558f4

---> 1fbce215a846

Step 50/53 : COPY /python3-login /usr/local/bin/python3-login

---> de81665bdba8

Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint

---> 3c0b2c1dacf0

Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]

---> Running in b2a8ac757f00

Removing intermediate container b2a8ac757f00

---> 5ad1c1370c7c

Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]

---> Running in f15fa369c30c

Removing intermediate container f15fa369c30c

---> 7cd85151c78a

{"aux": {"ID": "sha256:7cd85151c78ac2a6c5d4a1820828c41b6cecb491c2bfc4e6452c73e17697d581"}}Successfully built 7cd85151c78a

Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:3116b16edcc00fcb465831d8d8a51f98805d6374

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received unexpected HTTP status: 500 Internal Server Error

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3116b16edcc00fcb465831d8d8a51f98805d6374

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

agahkarakuzu · 2024-02-15T11:19:36Z

@mathieuboudreau this error is due to built image size, nothing on your end. I am working on it.

Update: OK, now the registry is behind nginx with a generous upload limit, let's see!

agahkarakuzu · 2024-02-15T12:34:48Z

@roboneuro build book

roboneuro · 2024-02-15T12:34:52Z

🔴 Binder build has failed 🥀

Status: Failed 4e356305
Last updated: 2024-02-15 04:49:26 PST

ℹ️ See details

The next comment will forward the logs

roboneuro · 2024-02-15T12:49:30Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerzqkm_ub7'...
HEAD is now at 3116b16 Update data to release in this repo instead of depricated repo
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> c686d3b638a4
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 78d0bdd256b4
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> e38b8fcb0fbd
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 35dbdf6176db
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 77ef363567fb
Step 31/53 : USER root
 ---> Using cache
 ---> 9848a0cccf77
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 4e3241167052
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> fee82a54343b
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4fb91435c67e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> be3e63cb11d8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 4f20431eee2a
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 40e55985010d
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 5971166c5297
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 17d6eea84084
Step 40/53 : USER ${NB_USER}
 ---> Running in 3469264d3b66
Removing intermediate container 3469264d3b66
 ---> f7275c32720b
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in bf16a21c1a5d
Collecting jupyter-book==0.13.0
  Downloading jupyter_book-0.13.0-py3-none-any.whl (43 kB)
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  Downloading nibabel-5.2.0-py3-none-any.whl (3.3 MB)
Requirement already satisfied: notebook in /srv/conda/envs/notebook/lib/python3.8/site-packages (from -r binder/requirements.txt (line 8)) (6.3.0)
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Collecting sphinx_book_theme~=0.3.2
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Collecting sphinx-jupyterbook-latex~=0.4.6
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Collecting sphinxcontrib-bibtex<=2.5.0,>=2.2.0
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Collecting pyyaml
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Collecting sphinx-design~=0.1.0
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Collecting sphinx-multitoc-numbering~=0.1.3
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Collecting linkify-it-py~=1.0.1
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Collecting myst-nb~=0.13.1
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Collecting docutils<0.18,>=0.15
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Collecting sphinx<5,>=4
  Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB)
Collecting sphinx-thebe~=0.1.1
  Downloading sphinx_thebe-0.1.2-py3-none-any.whl (8.3 kB)
Requirement already satisfied: jsonschema<4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.2.0)
Collecting click<9,>=7.1
  Downloading click-8.1.7-py3-none-any.whl (97 kB)
Requirement already satisfied: Jinja2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.0.1)
Collecting sphinx-external-toc~=0.2.3
  Downloading sphinx_external_toc-0.2.4-py3-none-any.whl (25 kB)
Requirement already satisfied: packaging in /srv/conda/envs/notebook/lib/python3.8/site-packages (from plotly->-r binder/requirements.txt (line 2)) (21.0)
Collecting tenacity>=6.2.0
  Downloading tenacity-8.2.3-py3-none-any.whl (24 kB)
Requirement already satisfied: importlib-metadata>=4.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from markdown->-r binder/requirements.txt (line 4)) (4.6.3)
Collecting msgpack
  Downloading msgpack-1.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (534 kB)
Collecting annexremote
  Downloading annexremote-1.6.4-py3-none-any.whl (25 kB)
Collecting patool>=1.7
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Collecting looseversion
  Downloading looseversion-1.3.0-py2.py3-none-any.whl (8.2 kB)
Collecting fasteners>=0.14
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Collecting humanize
  Downloading humanize-4.9.0-py3-none-any.whl (126 kB)
Collecting importlib-resources>=3.0
  Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Collecting boto
  Downloading boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting keyring!=23.9.0,>=20.0
  Downloading keyring-24.3.0-py3-none-any.whl (38 kB)
Collecting python-gitlab
  Downloading python_gitlab-4.4.0-py3-none-any.whl (138 kB)
Collecting platformdirs
  Downloading platformdirs-4.2.0-py3-none-any.whl (17 kB)
Requirement already satisfied: chardet>=3.0.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from datalad->-r binder/requirements.txt (line 5)) (4.0.0)
Collecting keyrings.alt
  Downloading keyrings.alt-5.0.0-py3-none-any.whl (18 kB)
Collecting distro
  Downloading distro-1.9.0-py3-none-any.whl (20 kB)
Requirement already satisfied: requests>=1.2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from datalad->-r binder/requirements.txt (line 5)) (2.26.0)
Collecting tqdm>=4.32.0
  Downloading tqdm-4.66.2-py3-none-any.whl (78 kB)
Collecting iso8601
  Downloading iso8601-2.1.0-py3-none-any.whl (7.5 kB)
Collecting typing-extensions>=4.0.0
  Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.4.5-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.2 MB)
Requirement already satisfied: python-dateutil>=2.7 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from matplotlib->-r binder/requirements.txt (line 6)) (2.8.2)
Requirement already satisfied: pyparsing>=2.3.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from matplotlib->-r binder/requirements.txt (line 6)) (2.4.7)
Collecting cycler>=0.10
  Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Collecting contourpy>=1.0.1
  Downloading contourpy-1.1.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (301 kB)
Collecting pillow>=6.2.0
  Downloading pillow-10.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
Collecting fonttools>=4.22.0
  Downloading fonttools-4.48.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
Requirement already satisfied: argon2-cffi in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (20.1.0)
Requirement already satisfied: jupyter-core>=4.6.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (4.7.1)
Requirement already satisfied: pyzmq>=17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (22.1.0)
Requirement already satisfied: prometheus-client in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.11.0)
Requirement already satisfied: nbformat in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (5.1.3)
Requirement already satisfied: nbconvert in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.0.7)
Requirement already satisfied: ipython-genutils in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.2.0)
Requirement already satisfied: jupyter-client>=5.3.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.1.12)
Requirement already satisfied: ipykernel in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.0.3)
Requirement already satisfied: Send2Trash>=1.5.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (1.7.1)
Requirement already satisfied: terminado>=0.8.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.10.1)
Requirement already satisfied: tornado>=6.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.1)
Requirement already satisfied: traitlets>=4.2.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (5.0.5)
Requirement already satisfied: pytz>=2020.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from pandas->-r binder/requirements.txt (line 10)) (2021.1)
Collecting tzdata>=2022.1
  Downloading tzdata-2024.1-py2.py3-none-any.whl (345 kB)
Collecting patsy>=0.5.4
  Downloading patsy-0.5.6-py2.py3-none-any.whl (233 kB)
Collecting packaging
  Downloading packaging-23.2-py3-none-any.whl (53 kB)
Collecting osfclient
  Downloading osfclient-0.0.5-py2.py3-none-any.whl (39 kB)
Collecting gdown
  Downloading gdown-5.1.0-py3-none-any.whl (17 kB)
Collecting awscli
  Downloading awscli-1.32.42-py3-none-any.whl (4.4 MB)
Collecting zenodo-get
  Downloading zenodo_get-1.5.1-py2.py3-none-any.whl (17 kB)
Requirement already satisfied: zipp>=0.5 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from importlib-metadata>=4.4->markdown->-r binder/requirements.txt (line 4)) (3.5.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.17.3)
Requirement already satisfied: attrs>=17.4.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (21.2.0)
Requirement already satisfied: setuptools in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (49.6.0.post20210108)
Requirement already satisfied: six>=1.11.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.16.0)
Collecting jeepney>=0.4.2
  Downloading jeepney-0.8.0-py3-none-any.whl (48 kB)
Collecting SecretStorage>=3.2
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Collecting importlib-metadata>=4.4
  Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Collecting jaraco.classes
  Downloading jaraco.classes-3.3.1-py3-none-any.whl (6.8 kB)
Collecting uc-micro-py
  Downloading uc_micro_py-1.0.3-py3-none-any.whl (6.2 kB)
Requirement already satisfied: ipywidgets<8,>=7.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (7.6.3)
Collecting myst-parser~=0.15.2
  Downloading myst_parser-0.15.2-py3-none-any.whl (46 kB)
Requirement already satisfied: ipython in /srv/conda/envs/notebook/lib/python3.8/site-packages (from myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (7.26.0)
Collecting jupyter-cache~=0.4.1
  Downloading jupyter_cache-0.4.3-py3-none-any.whl (31 kB)
Collecting jupyter-sphinx~=0.3.2
  Downloading jupyter_sphinx-0.3.2-py3-none-any.whl (20 kB)
Requirement already satisfied: widgetsnbextension~=3.5.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipywidgets<8,>=7.0.0->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.5.1)
Requirement already satisfied: jupyterlab-widgets>=1.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipywidgets<8,>=7.0.0->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.0.0)
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Requirement already satisfied: backcall in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.0)
Requirement already satisfied: decorator in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (5.0.9)
Requirement already satisfied: pickleshare in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.7.5)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.0.19)
Requirement already satisfied: pygments in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.9.0)
Requirement already satisfied: pexpect>4.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (4.8.0)
Requirement already satisfied: jedi>=0.16 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.18.0)
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Collecting nbdime
  Downloading nbdime-4.0.1-py3-none-any.whl (5.9 MB)
Collecting mdit-py-plugins~=0.2.8
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Collecting markdown-it-py<2.0.0,>=1.0.0
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Requirement already satisfied: certifi>=2017.4.17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (2021.5.30)
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Requirement already satisfied: urllib3<1.27,>=1.21.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (1.26.6)
Requirement already satisfied: idna<4,>=2.5 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (3.1)
Requirement already satisfied: cryptography>=2.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (3.4.7)
Requirement already satisfied: cffi>=1.12 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from cryptography>=2.0->SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (1.14.6)
Requirement already satisfied: pycparser in /srv/conda/envs/notebook/lib/python3.8/site-packages (from cffi>=1.12->cryptography>=2.0->SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (2.20)
Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.5
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Collecting imagesize
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting alabaster<0.8,>=0.7
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Requirement already satisfied: babel>=1.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sphinx<5,>=4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.9.1)
Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.4-py3-none-any.whl (120 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0
  Downloading sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl (99 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Collecting pydata-sphinx-theme~=0.8.0
  Downloading pydata_sphinx_theme-0.8.1-py3-none-any.whl (3.3 MB)
Collecting beautifulsoup4
  Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
Requirement already satisfied: wheel in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sphinx_togglebutton->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.36.2)
Collecting pybtex>=0.24
  Downloading pybtex-0.24.0-py2.py3-none-any.whl (561 kB)
Collecting pybtex-docutils>=1.0.0
  Downloading pybtex_docutils-1.0.3-py3-none-any.whl (6.4 kB)
Collecting latexcodec>=1.0.4
  Downloading latexcodec-2.0.1-py2.py3-none-any.whl (18 kB)
Requirement already satisfied: greenlet!=0.4.17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sqlalchemy<1.5,>=1.3.12->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.1.0)
Collecting docutils<0.18,>=0.15
  Downloading docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting s3transfer<0.11.0,>=0.10.0
  Downloading s3transfer-0.10.0-py3-none-any.whl (82 kB)
Collecting colorama<0.4.5,>=0.2.5
  Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
Collecting rsa<4.8,>=3.1.2
  Downloading rsa-4.7.2-py3-none-any.whl (34 kB)
Collecting botocore==1.34.42
  Downloading botocore-1.34.42-py3-none-any.whl (12.0 MB)
Collecting jmespath<2.0.0,>=0.7.1
  Downloading jmespath-1.0.1-py3-none-any.whl (20 kB)
Collecting pyasn1>=0.1.3
  Downloading pyasn1-0.5.1-py2.py3-none-any.whl (84 kB)
Collecting soupsieve>1.2
  Downloading soupsieve-2.5-py3-none-any.whl (36 kB)
Requirement already satisfied: webencodings in /srv/conda/envs/notebook/lib/python3.8/site-packages (from bleach->nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.5.1)
Collecting filelock
  Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Collecting more-itertools
  Downloading more_itertools-10.2.0-py3-none-any.whl (57 kB)
Requirement already satisfied: jupyter-server in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.10.1)
Collecting jupyter-server-mathjax>=0.2.2
  Downloading jupyter_server_mathjax-0.2.6-py3-none-any.whl (3.1 MB)
Collecting gitpython!=2.1.4,!=2.1.5,!=2.1.6
  Downloading GitPython-3.1.41-py3-none-any.whl (196 kB)
Collecting gitdb<5,>=4.0.1
  Downloading gitdb-4.0.11-py3-none-any.whl (62 kB)
Collecting smmap<6,>=3.0.1
  Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Requirement already satisfied: requests-unixsocket in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.0)
Requirement already satisfied: anyio<4,>=3.1.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.3.0)
Requirement already satisfied: websocket-client in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.57.0)
Requirement already satisfied: sniffio>=1.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from anyio<4,>=3.1.0->jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.2.0)
Collecting requests-toolbelt>=0.10.1
  Downloading requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB)
Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (1.7.1)
Collecting wget
  Downloading wget-3.2.zip (10 kB)
Building wheels for collected packages: wget
  Building wheel for wget (setup.py): started
  Building wheel for wget (setup.py): finished with status 'done'
  Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9680 sha256=748d64a9ab54fef0bbd3173eace4639a8e8d0ace37a00765219edf5cfe00d4c3
  Stored in directory: /tmp/pip-ephem-wheel-cache-m0r69j9m/wheels/bd/a8/c3/3cf2c14a1837a4e04bd98631724e81f33f462d86a1d895fae0
Successfully built wget
Installing collected packages: packaging, smmap, gitdb, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, more-itertools, markdown-it-py, latexcodec, jupyter-server-mathjax, jmespath, jeepney, importlib-metadata, imagesize, gitpython, docutils, colorama, alabaster, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, numpy, nbdime, mdit-py-plugins, jaraco.classes, importlib-resources, botocore, beautifulsoup4, wget, uc-micro-py, tzdata, typing-extensions, tqdm, sphinx-togglebutton, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, pillow, patool, myst-parser, msgpack, looseversion, kiwisolver, keyrings.alt, keyring, jupyter-sphinx, jupyter-cache, iso8601, humanize, fonttools, filelock, fasteners, distro, cycler, contourpy, click, boto, annexremote, zenodo-get, tenacity, sphinxcontrib-bibtex, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, scipy, patsy, pandas, osfclient, myst-nb, matplotlib, linkify-it-py, gdown, datalad, awscli, statsmodels, seaborn, repo2data, plotly, nibabel, markdown, jupyter-book
  Attempting uninstall: packaging
    Found existing installation: packaging 21.0
    Uninstalling packaging-21.0:
      Successfully uninstalled packaging-21.0
  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 4.6.3
    Uninstalling importlib-metadata-4.6.3:
      Successfully uninstalled importlib-metadata-4.6.3
Successfully installed SecretStorage-3.3.3 alabaster-0.7.13 annexremote-1.6.4 awscli-1.32.42 beautifulsoup4-4.12.3 boto-2.49.0 botocore-1.34.42 click-8.1.7 colorama-0.4.4 contourpy-1.1.1 cycler-0.12.1 datalad-0.19.6 distro-1.9.0 docutils-0.16 fasteners-0.19 filelock-3.13.1 fonttools-4.48.1 gdown-5.1.0 gitdb-4.0.11 gitpython-3.1.41 humanize-4.9.0 imagesize-1.4.1 importlib-metadata-7.0.1 importlib-resources-6.1.1 iso8601-2.1.0 jaraco.classes-3.3.1 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.13.0 jupyter-cache-0.4.3 jupyter-server-mathjax-0.2.6 jupyter-sphinx-0.3.2 keyring-24.3.0 keyrings.alt-5.0.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-1.0.3 looseversion-1.3.0 markdown-3.5.2 markdown-it-py-1.1.0 matplotlib-3.7.4 mdit-py-plugins-0.2.8 more-itertools-10.2.0 msgpack-1.0.7 myst-nb-0.13.2 myst-parser-0.15.2 nbdime-4.0.1 nibabel-5.2.0 numpy-1.24.4 osfclient-0.0.5 packaging-23.2 pandas-2.0.3 patool-1.12 patsy-0.5.6 pillow-10.2.0 platformdirs-4.2.0 plotly-5.18.0 pyasn1-0.5.1 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.8.1 python-gitlab-4.4.0 pyyaml-6.0.1 repo2data-2.9.1 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.10.0 scipy-1.10.1 seaborn-0.13.2 smmap-5.0.1 snowballstemmer-2.2.0 soupsieve-2.5 sphinx-4.5.0 sphinx-book-theme-0.3.3 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.1.0 sphinx-external-toc-0.2.4 sphinx-jupyterbook-latex-0.4.7 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.1.2 sphinx-togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-bibtex-2.5.0 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 statsmodels-0.14.1 tenacity-8.2.3 tqdm-4.66.2 typing-extensions-4.9.0 tzdata-2024.1 uc-micro-py-1.0.3 wget-3.2 zenodo-get-1.5.1
Removing intermediate container bf16a21c1a5d
 ---> d1ac2e317c84
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 6d844373e9f7
Step 43/53 : LABEL repo2docker.ref="3116b16edcc00fcb465831d8d8a51f98805d6374"
 ---> Running in 0b567743cad5
Removing intermediate container 0b567743cad5
 ---> e2be33fd595b
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in e5f2fddecd39
Removing intermediate container e5f2fddecd39
 ---> b4b8e931c8d0
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 8aa62b89a846
Removing intermediate container 8aa62b89a846
 ---> dee41d5c058a
Step 46/53 : USER ${NB_USER}
 ---> Running in 0ec3ab6b5c29
Removing intermediate container 0ec3ab6b5c29
 ---> cfecd99cc710
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 786adce18938
Removing intermediate container 786adce18938
 ---> 65529961e529
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 4ed497b87397
---- repo2data starting ----
/srv/conda/envs/notebook/lib/python3.8/site-packages/repo2data
Config from file :
../binder/data_requirement.json
Destination:
../data/rf-shimming-7t
File downloaded to: ../data/rf-shimming-7t/ds004906.zip

patool: Extracting ../data/rf-shimming-7t/ds004906.zip ...

patool: ... ../data/rf-shimming-7t/ds004906.zip extracted to `../data/rf-shimming-7t'.

Info : ds004906.zip Decompressed

�[91mCloning into '/home/jovyan/content/sct'...

�[0m

�[0;32m


Welcome to SCT installation *


�[0m
�[0;32mChecking OS type and version...�[0m
Linux 4ed497b87397 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
�[0;32mChecking requirements...�[0m
�[0;32mOK!�[0m
SCT version ......... 6.2.dev0

Installation type ... in-place

Operating system .... linux (unknown)

Shell config ........ /home/jovyan/.bashrc
�[0;32mSCT will be installed here: [/home/jovyan/content/sct]�[0m
�[0;92m

Do you agree? [y]es/[n]o: �[0m

�[0;32mSkipping copy of source files (source and destination folders are the same)�[0m
�[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: �[0m

�[0;32mDownloading Miniconda...�[0m
�[0;34mwget -nv -O /tmp/tmp.Fdc2SXT4NL/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh�[0m
2024-02-15 12:39:36 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.Fdc2SXT4NL/miniconda.sh" [1]
�[0;32mInstalling Miniconda...�[0m
�[0;34mbash /tmp/tmp.Fdc2SXT4NL/miniconda.sh -p /home/jovyan/content/sct/python -b -f�[0m
PREFIX=/home/jovyan/content/sct/python

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Installing base environment...
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installation finished.
�[0;32mCreating conda environment...�[0m
Channels:

defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

Package Plan
environment location: /home/jovyan/content/sct/python/envs/venv_sct
added / updated specs:

- python=3.9
The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
openssl-3.0.13             |       h7f8727e_0         5.2 MB
pip-23.3.1                 |   py39h06a4308_0         2.6 MB
python-3.9.18              |       h955ad1f_0        25.1 MB
setuptools-68.2.2          |   py39h06a4308_0         948 KB
tzdata-2023d               |       h04d1e81_0         117 KB
wheel-0.41.2               |   py39h06a4308_0         108 KB
------------------------------------------------------------
                                       Total:        34.0 MB

The following NEW packages will be INSTALLED:
_libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main

_openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu

ca-certificates    pkgs/main/linux-64::ca-certificates-2023.12.12-h06a4308_0

ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1

libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0

libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1

libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1

libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1

ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0

openssl            pkgs/main/linux-64::openssl-3.0.13-h7f8727e_0

pip                pkgs/main/linux-64::pip-23.3.1-py39h06a4308_0

python             pkgs/main/linux-64::python-3.9.18-h955ad1f_0

readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0

setuptools         pkgs/main/linux-64::setuptools-68.2.2-py39h06a4308_0

sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0

tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0

tzdata             pkgs/main/noarch::tzdata-2023d-h04d1e81_0

wheel              pkgs/main/linux-64::wheel-0.41.2-py39h06a4308_0

xz                 pkgs/main/linux-64::xz-5.4.5-h5eee18b_0

zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0
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Verifying transaction: ...working... done

Executing transaction: ...working... done

To activate this environment, use

$ conda activate /home/jovyan/content/sct/python/envs/venv_sct

To deactivate an active environment, use

$ conda deactivate
Channels:

conda-forge
defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

Package Plan
environment location: /home/jovyan/content/sct/python/envs/venv_sct
added / updated specs:

- libstdcxx-ng
The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
_libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
_openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
ca-certificates-2024.2.2   |       hbcca054_0         152 KB  conda-forge
libgcc-ng-13.2.0           |       h807b86a_5         752 KB  conda-forge
libgomp-13.2.0             |       h807b86a_5         410 KB  conda-forge
libstdcxx-ng-13.2.0        |       h7e041cc_5         3.7 MB  conda-forge
openssl-3.2.1              |       hd590300_0         2.7 MB  conda-forge
------------------------------------------------------------
                                       Total:         7.7 MB

The following packages will be UPDATED:
ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-hbcca054_0

libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5

libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5

libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5

openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0
The following packages will be SUPERSEDED by a higher-priority channel:
_libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge

_openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu
Downloading and Extracting Packages: ...working... done

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Channels:

conda-forge
defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

All requested packages already installed.
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)

Collecting pip!=21.2.*

Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)

Downloading pip-24.0-py3-none-any.whl (2.1 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 3.8 MB/s eta 0:00:00

Installing collected packages: pip

Attempting uninstall: pip

Found existing installation: pip 23.3.1

Uninstalling pip-23.3.1:

Successfully uninstalled pip-23.3.1

Successfully installed pip-24.0
�[0;32mInstalling Python dependencies...�[0m
�[0;32mUsing requirements.txt (git installation)�[0m
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu

Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment

Collecting certifi

Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)

Collecting dipy!=1.6.,!=1.7.,!=1.8.* (from -r requirements.txt (line 7))

Downloading dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB)

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Collecting ivadomed (from -r requirements.txt (line 11))

Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)

Collecting matplotlib (from -r requirements.txt (line 12))

Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)

Collecting nibabel (from -r requirements.txt (line 21))

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Collecting nilearn (from -r requirements.txt (line 22))

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Downloading nnunetv2-2.2.1.tar.gz (178 kB)

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Installing build dependencies: started

Installing build dependencies: finished with status 'done'

Getting requirements to build wheel: started

Getting requirements to build wheel: finished with status 'done'

Installing backend dependencies: started

Installing backend dependencies: finished with status 'done'

Preparing metadata (pyproject.toml): started

Preparing metadata (pyproject.toml): finished with status 'done'

Collecting numpy<1.24 (from -r requirements.txt (line 27))

Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 12.7 MB/s eta 0:00:00

Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))

Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)

Collecting pandas (from -r requirements.txt (line 32))

Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)

Collecting portalocker (from -r requirements.txt (line 33))

Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)

Collecting psutil (from -r requirements.txt (line 34))

Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)

Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39))

Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (62.4 MB)

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Collecting pytest (from -r requirements.txt (line 40))

Downloading pytest-8.0.0-py3-none-any.whl.metadata (7.8 kB)

Collecting pytest-cov (from -r requirements.txt (line 41))

Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)

Collecting requests (from -r requirements.txt (line 42))

Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)

Collecting requirements-parser (from -r requirements.txt (line 43))

Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB)

Collecting scipy (from -r requirements.txt (line 44))

Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)

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Collecting scikit-image (from -r requirements.txt (line 45))

Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)

Collecting scikit-learn (from -r requirements.txt (line 46))

Downloading scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)

Collecting xlwt (from -r requirements.txt (line 47))

Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)

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Collecting tqdm (from -r requirements.txt (line 48))

Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)

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Collecting transforms3d (from -r requirements.txt (line 49))

Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB)

Collecting urllib3 (from -r requirements.txt (line 50))

Downloading urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB)

Collecting pytest_console_scripts (from -r requirements.txt (line 51))

Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB)

Collecting pyyaml (from -r requirements.txt (line 52))

Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)

Collecting voxelmorph (from -r requirements.txt (line 53))

Downloading voxelmorph-0.2-py3-none-any.whl (54 kB)

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Collecting wquantiles (from -r requirements.txt (line 54))

Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)

Collecting xlsxwriter (from -r requirements.txt (line 57))

Downloading XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB)

Collecting monai[nibabel] (from -r requirements.txt (line 13))

Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB)

Collecting PyQt5_sip<13,>=4.19.14 (from pyqt5==5.12.3->-r requirements.txt (line 39))

Downloading PyQt5_sip-12.13.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (504 bytes)

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Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt

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Stored in directory: /home/jovyan/.cache/pip/wheels/4e/c0/70/740949411012a24276008fa6e920f42701ae6fa18ce6122eb5

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Stored in directory: /home/jovyan/.cache/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea

Building wheel for future (setup.py): started

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Stored in directory: /home/jovyan/.cache/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b

Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt

Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tf-keras, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, PyQt5_sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed

Successfully installed Deprecated-1.2.14 GitPython-3.1.41 MarkupSafe-2.1.5 PyQt5_sip-12.13.0 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.48.1 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.2 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pystrum-0.4 pytest-8.0.0 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.0 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.1 tensorboard-data-server-0.7.2 tf-keras-2.15.0 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240215 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.0 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0
�[0;32mInstalling spinalcordtoolbox...�[0m
Obtaining file:///home/jovyan/content/sct

Preparing metadata (setup.py): started

Preparing metadata (setup.py): finished with status 'done'

Installing collected packages: spinalcordtoolbox

Running setup.py develop for spinalcordtoolbox

Successfully installed spinalcordtoolbox-6.2.dev0
�[0;32mCreating launchers for Python scripts...�[0m
�[0;32mInstalling binaries...�[0m
�[0;34msct_download_data -d binaries_linux -k�[0m
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Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d binaries_linux -k
Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz

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Creating temporary folder (/tmp/sct_2024-02-15_12-46-39_install-data_47p1ot6c)

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Copying data to: /home/jovyan/content/sct/bin

Removing temporary folders...

Done!
�[0;32mAll requirements installed!�[0m
�[0;32mInstalling data...�[0m
�[0;34mmkdir -p /home/jovyan/content/sct/data�[0m
�[0;34msct_download_data -d PAM50�[0m
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Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d PAM50
Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20231024/PAM50-r20231024.zip

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Done!
�[0;34msct_download_data -d deepseg_sc_models�[0m
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Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_sc_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip

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Creating temporary folder (/tmp/sct_2024-02-15_12-46-44_install-data_qk9ryutr)

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Copying data to: /home/jovyan/content/sct/data/deepseg_sc_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_gm_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_gm_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip

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Creating temporary folder (/tmp/sct_2024-02-15_12-46-45_install-data_hf_xv94b)

Unzip data to: /tmp/sct_2024-02-15_12-46-45_install-data_hf_xv94b

Copying data to: /home/jovyan/content/sct/data/deepseg_gm_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_lesion_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_lesion_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip

Downloading: 20220325_deepseg_lesion_models_onnx.zip
Status:   0%|          | 0.00/5.35M [00:00<?, ?B/s]

Status: 100%|██████████| 5.35M/5.35M [00:00<00:00, 99.0MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_12-46-46_install-data_7b90h5x0)

Unzip data to: /tmp/sct_2024-02-15_12-46-46_install-data_7b90h5x0

Copying data to: /home/jovyan/content/sct/data/deepseg_lesion_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepreg_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepreg_models
Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip

Downloading: models.zip
Status:   0%|          | 0.00/158M [00:00<?, ?B/s]

Status:   2%|▏         | 2.64M/158M [00:00<00:05, 26.3MB/s]

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Status:  15%|█▍        | 23.1M/158M [00:00<00:01, 89.0MB/s]

Status:  24%|██▍       | 37.8M/158M [00:00<00:01, 112MB/s]

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Status:  41%|████      | 65.2M/158M [00:00<00:00, 126MB/s]

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Status:  85%|████████▌ | 135M/158M [00:01<00:00, 138MB/s]

Status:  94%|█████████▍| 149M/158M [00:01<00:00, 139MB/s]

Status: 100%|██████████| 158M/158M [00:01<00:00, 125MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_12-46-49_install-data_chkt4sef)

Unzip data to: /tmp/sct_2024-02-15_12-46-49_install-data_chkt4sef

Copying data to: /home/jovyan/content/sct/data/deepreg_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d PAM50_normalized_metrics�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d PAM50_normalized_metrics
Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20230222.zip

Downloading: PAM50-normalized-metrics-r20230222.zip
Status:   0%|          | 0.00/1.00 [00:00<?, ?B/s]

Status: 47.3kB [00:00, 358kB/s]

Status: 214kB [00:00, 853kB/s]

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Status: 3.60MB [00:00, 9.72MB/s]

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Status: 6.02MB [00:00, 9.61MB/s]

Status: 6.92MB [00:00, 7.75MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_12-46-53_install-data_90xmzufb)

Unzip data to: /tmp/sct_2024-02-15_12-46-53_install-data_90xmzufb

Copying data to: /home/jovyan/content/sct/data/PAM50_normalized_metrics

Removing temporary folders...

Done!
Status:   0%|          | 0.00/18.0M [00:00<?, ?B/s]

Status:  14%|█▍        | 2.58M/18.0M [00:00<00:00, 25.8MB/s]

Status:  55%|█████▍    | 9.85M/18.0M [00:00<00:00, 53.0MB/s]

Status: 100%|██████████| 18.0M/18.0M [00:00<00:00, 68.9MB/s]
�[0;32mValidate installation...�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_check_dependencies
SYSTEM INFORMATION
SCT info:

version: git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9
path: /home/jovyan/content/sct

OS: linux (Linux-5.4.0-139-generic-x86_64-with-glibc2.27)

CPU cores: Available: 16, Used by ITK functions: 16

RAM: Total: 60286MB, Used: 3039MB, Available: 57543MB

OPTIONAL DEPENDENCIES
Check FSLeyes version...............................[  ]

(127, '/bin/sh: 1: fsleyes: not found')
MANDATORY DEPENDENCIES
Check Python executable.............................[�[92mOK�[0m]

Using bundled python 3.9.18 (main, Sep 11 2023, 13:41:44)

[GCC 11.2.0] at /home/jovyan/content/sct/python/envs/venv_sct/bin/python

Check if data are installed.........................[�[92mOK�[0m]

Check if dipy is installed..........................[�[92mOK�[0m] (1.5.0)

Check if ivadomed is installed......................[�[92mOK�[0m] (2.9.9)

Check if matplotlib is installed....................[�[92mOK�[0m] (3.8.3)

Check if monai is installed.........................[�[92mOK�[0m] (1.3.0)

Check if nibabel is installed.......................[�[92mOK�[0m] (3.2.2)

Check if nilearn is installed.......................[�[92mOK�[0m] (0.10.2)

Check if nnunetv2 is installed......................[�[92mOK�[0m]

Check if numpy is installed.........................[�[92mOK�[0m] (1.23.5)

Check if onnxruntime is installed...................[�[92mOK�[0m] (1.17.0)

Check if pandas is installed........................[�[92mOK�[0m] (1.4.4)

Check if portalocker is installed...................[�[92mOK�[0m] (2.8.2)

Check if psutil is installed........................[�[92mOK�[0m] (5.9.8)

Check if pyqt5 (5.12.3) is installed................[�[92mOK�[0m] (5.12.3)

Check if pytest is installed........................[�[92mOK�[0m] (8.0.0)

Check if pytest-cov is installed....................[�[92mOK�[0m] (4.1.0)

Check if requests is installed......................[�[92mOK�[0m] (2.31.0)

Check if requirements-parser is installed...........[�[92mOK�[0m]

Check if scipy is installed.........................[�[92mOK�[0m] (1.12.0)

Check if scikit-image is installed..................[�[92mOK�[0m] (0.22.0)

Check if scikit-learn is installed..................[�[92mOK�[0m] (1.4.0)

Check if xlwt is installed..........................[�[92mOK�[0m] (1.3.0)

Check if tqdm is installed..........................[�[92mOK�[0m] (4.66.2)

Check if transforms3d is installed..................[�[92mOK�[0m] (0.4.1)

Check if urllib3 is installed.......................[�[92mOK�[0m] (2.2.0)

Check if pytest_console_scripts is installed........[�[92mOK�[0m]

Check if pyyaml is installed........................[�[92mOK�[0m] (6.0.1)

Check if voxelmorph is installed....................[�[92mOK�[0m] (0.2)

Check if wquantiles is installed....................[�[92mOK�[0m] (0.4)

Check if xlsxwriter is installed....................[�[92mOK�[0m] (3.1.9)

Check if spinalcordtoolbox is installed.............[�[92mOK�[0m]

Check ANTs compatibility with OS ...................[�[92mOK�[0m]

Check PropSeg compatibility with OS ................[�[92mOK�[0m]

Check if figure can be opened with PyQt.............[�[91mFAIL�[0m] ($DISPLAY not set on X11-supporting system)

Check if figure can be opened with matplotlib.......[�[91mFAIL�[0m] (Using non-GUI backend 'agg')
�[0;32mOpen a new Terminal window to load environment variables, or run:

source /home/jovyan/.bashrc�[0m
�[0;32mInstallation finished successfully!�[0m
Removing intermediate container 4ed497b87397

---> 4935503ea914

Step 49/53 : ENV PYTHONUNBUFFERED=1

---> Running in 012cd8520712

Removing intermediate container 012cd8520712

---> 4afebb5c046c

Step 50/53 : COPY /python3-login /usr/local/bin/python3-login

---> ccf339ce6efd

Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint

---> 914417716b38

Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]

---> Running in a5be14cf683f

Removing intermediate container a5be14cf683f

---> e68e088d1d1d

Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]

---> Running in 821f4ba7c674

Removing intermediate container 821f4ba7c674

---> 467cd9499fd7

{"aux": {"ID": "sha256:467cd9499fd76a91ee9b82e893165a8af037a2660c731a99d7d73bc078d8fa53"}}Successfully built 467cd9499fd7

Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:3116b16edcc00fcb465831d8d8a51f98805d6374

unknown blob

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3116b16edcc00fcb465831d8d8a51f98805d6374

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

agahkarakuzu · 2024-02-15T14:26:06Z

@roboneuro build book

roboneuro · 2024-02-15T14:26:10Z

🔴 Binder build has failed 🥀

Status: Failed 7578ec35
Last updated: 2024-02-15 06:32:33 PST

ℹ️ See details

The next comment will forward the logs

roboneuro · 2024-02-15T14:32:37Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Collecting importlib-metadata>=3.6 (from pytest_console_scripts->-r requirements.txt (line 51))
  Downloading importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting neurite>=0.2 (from voxelmorph->-r requirements.txt (line 53))
  Downloading neurite-0.2-py3-none-any.whl (108 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 kB 859.1 kB/s eta 0:00:00
Collecting connected-components-3d (from acvl-utils>=0.2->nnunetv2->-r requirements.txt (line 23))
  Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (29 kB)
Collecting future (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading future-0.18.3.tar.gz (840 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 1.3 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting unittest2 (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.4/96.4 kB 139.9 kB/s eta 0:00:00
Collecting click (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting dictdiffer (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Collecting zipp>=0.5 (from importlib-metadata>=3.6->pytest_console_scripts->-r requirements.txt (line 51))
  Downloading zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)
Collecting six (from neurite>=0.2->voxelmorph->-r requirements.txt (line 53))
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pystrum>=0.2 (from neurite>=0.2->voxelmorph->-r requirements.txt (line 53))
  Downloading pystrum-0.4.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting formulaic<0.4,>=0.2.4 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading formulaic-0.3.4-py3-none-any.whl (68 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.2/68.2 kB 118.2 kB/s eta 0:00:00
Collecting sqlalchemy<1.4.0.dev0 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading SQLAlchemy-1.3.24-cp39-cp39-manylinux2010_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 2.7 MB/s eta 0:00:00
Collecting bids-validator (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading bids_validator-1.14.0-py3-none-any.whl.metadata (38 kB)
Collecting num2words (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading num2words-0.5.13-py3-none-any.whl.metadata (12 kB)
Collecting absl-py>=0.4 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting grpcio>=1.48.2 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Collecting markdown>=2.6.8 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading Markdown-3.5.2-py3-none-any.whl.metadata (7.0 kB)
Collecting tensorboard-data-server<0.8.0,>=0.7.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard_data_server-0.7.2-py3-none-any.whl.metadata (1.1 kB)
Collecting tf-keras>=2.15.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tf_keras-2.15.0-py3-none-any.whl.metadata (1.6 kB)
Collecting werkzeug>=1.0.1 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading werkzeug-3.0.1-py3-none-any.whl.metadata (4.1 kB)
Collecting filelock (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)
Collecting typing-extensions>=4.8.0 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
Collecting jinja2 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting fsspec (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading fsspec-2024.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting Deprecated (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting humanize (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading humanize-4.9.0-py3-none-any.whl.metadata (7.9 kB)
Collecting typer[all] (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading typer-0.9.0-py3-none-any.whl.metadata (14 kB)
Collecting GitPython!=3.1.29,>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading GitPython-3.1.41-py3-none-any.whl.metadata (14 kB)
Collecting sentry-sdk>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl.metadata (9.7 kB)
Collecting docker-pycreds>=0.4.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Collecting setproctitle (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.9 kB)
Collecting appdirs>=1.4.3 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 902.7 kB/s eta 0:00:00
Collecting pydicom>=2.2.0 (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB)
Collecting python-gdcm (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
Collecting mpmath>=0.19 (from sympy->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 1.1 MB/s eta 0:00:00
Collecting astor>=0.8 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting interface-meta<2.0.0,>=1.2.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading interface_meta-1.3.0-py3-none-any.whl (14 kB)
Collecting wrapt>=1.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting gitdb<5,>=4.0.1 (from GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting docopt>=0.6.2 (from num2words->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting colorama<0.5.0,>=0.4.3 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting shellingham<2.0.0,>=1.3.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting rich<14.0.0,>=10.11.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading rich-13.7.0-py3-none-any.whl.metadata (18 kB)
Collecting argparse (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
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Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt
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  Stored in directory: /home/jovyan/.cache/pip/wheels/a9/7a/70/acdee60dabd3de1dcce9e5b13c6abb0215a20e034e7e8118c7
  Building wheel for acvl-utils (setup.py): started
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  Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=9ddf72ef785639631b8d98d78c2eb33374b4cc1c6cadad133ad0158c2e1646d3
  Stored in directory: /home/jovyan/.cache/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
  Building wheel for batchgenerators (setup.py): started
  Building wheel for batchgenerators (setup.py): finished with status 'done'
  Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=5764d94cd8be74c6cfd5852e26efa3642274a44bd964fbe916b6fc708a9c8467
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  Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
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  Stored in directory: /home/jovyan/.cache/pip/wheels/4e/c0/70/740949411012a24276008fa6e920f42701ae6fa18ce6122eb5
  Building wheel for pystrum (setup.py): started
  Building wheel for pystrum (setup.py): finished with status 'done'
  Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=8c23cd65d050211f78efdec2881e6327510a81f53b54584636af75f2ef8641ab
  Stored in directory: /home/jovyan/.cache/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea
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  Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492024 sha256=5fdd8564bfae2e6c0078d185be2e1d909b9805cbeec338b28452eb2497c04461
  Stored in directory: /home/jovyan/.cache/pip/wheels/bf/5d/6a/2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b
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  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=d209651a42057b06d7575eecccea3a0ebec48a1af1ada9dcbfc3e60ac0206292
  Stored in directory: /home/jovyan/.cache/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b
Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt
Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tf-keras, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, PyQt5_sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed
Successfully installed Deprecated-1.2.14 GitPython-3.1.41 MarkupSafe-2.1.5 PyQt5_sip-12.13.0 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.48.1 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.2 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pystrum-0.4 pytest-8.0.0 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.0 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.1 tensorboard-data-server-0.7.2 tf-keras-2.15.0 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240215 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.0 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0
�[0;32mInstalling spinalcordtoolbox...�[0m
Obtaining file:///home/jovyan/content/sct

Preparing metadata (setup.py): started

Preparing metadata (setup.py): finished with status 'done'

Installing collected packages: spinalcordtoolbox

Running setup.py develop for spinalcordtoolbox

Successfully installed spinalcordtoolbox-6.2.dev0
�[0;32mCreating launchers for Python scripts...�[0m
�[0;32mInstalling binaries...�[0m
�[0;34msct_download_data -d binaries_linux -k�[0m
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Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d binaries_linux -k
Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz

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Creating temporary folder (/tmp/sct_2024-02-15_14-29-04_install-data_mm7ligjj)

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Copying data to: /home/jovyan/content/sct/bin

Removing temporary folders...

Done!
�[0;32mAll requirements installed!�[0m
�[0;32mInstalling data...�[0m
�[0;34mmkdir -p /home/jovyan/content/sct/data�[0m
�[0;34msct_download_data -d PAM50�[0m
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Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d PAM50
Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20231024/PAM50-r20231024.zip

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�[0;34msct_download_data -d deepseg_sc_models�[0m
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Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_sc_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip

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Done!
�[0;34msct_download_data -d deepseg_gm_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_gm_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip

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Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_lesion_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepseg_lesion_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip

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Done!
�[0;34msct_download_data -d deepreg_models�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d deepreg_models
Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip

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Removing temporary folders...

Done!
�[0;34msct_download_data -d PAM50_normalized_metrics�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_download_data -d PAM50_normalized_metrics
Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20230222.zip

Downloading: PAM50-normalized-metrics-r20230222.zip
Status:   0%|          | 0.00/1.00 [00:00<?, ?B/s]

Status: 47.3kB [00:00, 349kB/s]

Status: 209kB [00:00, 822kB/s]

Status: 887kB [00:00, 2.63MB/s]

Status: 3.15MB [00:00, 8.93MB/s]

Status: 4.94MB [00:00, 11.6MB/s]

Status: 6.25MB [00:00, 9.97MB/s]

Status: 6.92MB [00:00, 7.82MB/s]

Creating temporary folder (/tmp/sct_2024-02-15_14-29-18_install-data_k6rpa12l)

Unzip data to: /tmp/sct_2024-02-15_14-29-18_install-data_k6rpa12l

Copying data to: /home/jovyan/content/sct/data/PAM50_normalized_metrics

Removing temporary folders...

Done!
Status:   0%|          | 0.00/18.0M [00:00<?, ?B/s]

Status:  16%|█▌        | 2.85M/18.0M [00:00<00:00, 28.4MB/s]

Status:  61%|██████    | 11.0M/18.0M [00:00<00:00, 59.4MB/s]

Status: 100%|██████████| 18.0M/18.0M [00:00<00:00, 71.9MB/s]
�[0;32mValidate installation...�[0m
--

Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)
sct_check_dependencies
SYSTEM INFORMATION
SCT info:

version: git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9
path: /home/jovyan/content/sct

OS: linux (Linux-5.4.0-139-generic-x86_64-with-glibc2.27)

CPU cores: Available: 16, Used by ITK functions: 16

RAM: Total: 60286MB, Used: 3047MB, Available: 57536MB

OPTIONAL DEPENDENCIES
Check FSLeyes version...............................[  ]

(127, '/bin/sh: 1: fsleyes: not found')
MANDATORY DEPENDENCIES
Check Python executable.............................[�[92mOK�[0m]

Using bundled python 3.9.18 (main, Sep 11 2023, 13:41:44)

[GCC 11.2.0] at /home/jovyan/content/sct/python/envs/venv_sct/bin/python

Check if data are installed.........................[�[92mOK�[0m]

Check if dipy is installed..........................[�[92mOK�[0m] (1.5.0)

Check if ivadomed is installed......................[�[92mOK�[0m] (2.9.9)

Check if matplotlib is installed....................[�[92mOK�[0m] (3.8.3)

Check if monai is installed.........................[�[92mOK�[0m] (1.3.0)

Check if nibabel is installed.......................[�[92mOK�[0m] (3.2.2)

Check if nilearn is installed.......................[�[92mOK�[0m] (0.10.2)

Check if nnunetv2 is installed......................[�[92mOK�[0m]

Check if numpy is installed.........................[�[92mOK�[0m] (1.23.5)

Check if onnxruntime is installed...................[�[92mOK�[0m] (1.17.0)

Check if pandas is installed........................[�[92mOK�[0m] (1.4.4)

Check if portalocker is installed...................[�[92mOK�[0m] (2.8.2)

Check if psutil is installed........................[�[92mOK�[0m] (5.9.8)

Check if pyqt5 (5.12.3) is installed................[�[92mOK�[0m] (5.12.3)

Check if pytest is installed........................[�[92mOK�[0m] (8.0.0)

Check if pytest-cov is installed....................[�[92mOK�[0m] (4.1.0)

Check if requests is installed......................[�[92mOK�[0m] (2.31.0)

Check if requirements-parser is installed...........[�[92mOK�[0m]

Check if scipy is installed.........................[�[92mOK�[0m] (1.12.0)

Check if scikit-image is installed..................[�[92mOK�[0m] (0.22.0)

Check if scikit-learn is installed..................[�[92mOK�[0m] (1.4.0)

Check if xlwt is installed..........................[�[92mOK�[0m] (1.3.0)

Check if tqdm is installed..........................[�[92mOK�[0m] (4.66.2)

Check if transforms3d is installed..................[�[92mOK�[0m] (0.4.1)

Check if urllib3 is installed.......................[�[92mOK�[0m] (2.2.0)

Check if pytest_console_scripts is installed........[�[92mOK�[0m]

Check if pyyaml is installed........................[�[92mOK�[0m] (6.0.1)

Check if voxelmorph is installed....................[�[92mOK�[0m] (0.2)

Check if wquantiles is installed....................[�[92mOK�[0m] (0.4)

Check if xlsxwriter is installed....................[�[92mOK�[0m] (3.1.9)

Check if spinalcordtoolbox is installed.............[�[92mOK�[0m]

Check ANTs compatibility with OS ...................[�[92mOK�[0m]

Check PropSeg compatibility with OS ................[�[92mOK�[0m]

Check if figure can be opened with PyQt.............[�[91mFAIL�[0m] ($DISPLAY not set on X11-supporting system)

Check if figure can be opened with matplotlib.......[�[91mFAIL�[0m] (Using non-GUI backend 'agg')
�[0;32mOpen a new Terminal window to load environment variables, or run:

source /home/jovyan/.bashrc�[0m
�[0;32mInstallation finished successfully!�[0m
Removing intermediate container ab95b2dfce03

---> 295ab521f30b

Step 49/53 : ENV PYTHONUNBUFFERED=1

---> Running in bde6afaee674

Removing intermediate container bde6afaee674

---> ba175ccd1c3c

Step 50/53 : COPY /python3-login /usr/local/bin/python3-login

---> 6f7b32adac39

Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint

---> a183e7b3ca73

Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]

---> Running in 1f167b924790

Removing intermediate container 1f167b924790

---> b5fc6e143d60

Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]

---> Running in f88e44addbfe

Removing intermediate container f88e44addbfe

---> 1e6e06b9d60a

{"aux": {"ID": "sha256:1e6e06b9d60ab617371c38f6d0fe5afb409be67e9de0de5f3980f5574c00de1c"}}Successfully built 1e6e06b9d60a

Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:3116b16edcc00fcb465831d8d8a51f98805d6374

unknown blob

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3116b16edcc00fcb465831d8d8a51f98805d6374

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

agahkarakuzu · 2024-02-15T14:39:04Z

@roboneuro build book

roboneuro · 2024-02-15T14:39:08Z

🔴 Binder build has failed 🥀

Status: Failed 52a7d825
Last updated: 2024-02-15 06:45:35 PST

ℹ️ See details

The next comment will forward the logs

roboneuro · 2024-02-15T14:45:39Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockervoqc6kqv'...
HEAD is now at 3116b16 Update data to release in this repo instead of depricated repo
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> c686d3b638a4
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 78d0bdd256b4
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> e38b8fcb0fbd
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 35dbdf6176db
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 77ef363567fb
Step 31/53 : USER root
 ---> Using cache
 ---> 9848a0cccf77
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 4e3241167052
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> fee82a54343b
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4fb91435c67e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> be3e63cb11d8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 4f20431eee2a
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 40e55985010d
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 5971166c5297
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 17d6eea84084
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> f7275c32720b
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> d1ac2e317c84
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 5503202ada55
Step 43/53 : LABEL repo2docker.ref="3116b16edcc00fcb465831d8d8a51f98805d6374"
 ---> Running in aca4a2631536
Removing intermediate container aca4a2631536
 ---> f52e1187b517
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in 0206851ad9c0
Removing intermediate container 0206851ad9c0
 ---> 1846414b0a3b
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 51ea4a3376e4
Removing intermediate container 51ea4a3376e4
 ---> 5004dcf29919
Step 46/53 : USER ${NB_USER}
 ---> Running in 0355fceed8a2
Removing intermediate container 0355fceed8a2
 ---> 5a3bd7ca88fe
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in ef05d4bf4531
Removing intermediate container ef05d4bf4531
 ---> 1be0fd512824
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 858b9b6ec130
---- repo2data starting ----
/srv/conda/envs/notebook/lib/python3.8/site-packages/repo2data
Config from file :
../binder/data_requirement.json
Destination:
../data/rf-shimming-7t
File downloaded to: ../data/rf-shimming-7t/ds004906.zip

patool: Extracting ../data/rf-shimming-7t/ds004906.zip ...

patool: ... ../data/rf-shimming-7t/ds004906.zip extracted to `../data/rf-shimming-7t'.

Info : ds004906.zip Decompressed

�[91mCloning into '/home/jovyan/content/sct'...

�[0m

�[0;32m


Welcome to SCT installation *


�[0m
�[0;32mChecking OS type and version...�[0m
Linux 858b9b6ec130 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
�[0;32mChecking requirements...�[0m
�[0;32mOK!�[0m
SCT version ......... 6.2.dev0

Installation type ... in-place

Operating system .... linux (unknown)

Shell config ........ /home/jovyan/.bashrc
�[0;32mSCT will be installed here: [/home/jovyan/content/sct]�[0m
�[0;92m

Do you agree? [y]es/[n]o: �[0m

�[0;32mSkipping copy of source files (source and destination folders are the same)�[0m
�[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: �[0m

�[0;32mDownloading Miniconda...�[0m
�[0;34mwget -nv -O /tmp/tmp.R5RFeZvt3B/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh�[0m
2024-02-15 14:41:40 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.R5RFeZvt3B/miniconda.sh" [1]
�[0;32mInstalling Miniconda...�[0m
�[0;34mbash /tmp/tmp.R5RFeZvt3B/miniconda.sh -p /home/jovyan/content/sct/python -b -f�[0m
PREFIX=/home/jovyan/content/sct/python

Unpacking payload ...
0%|          | 0/73 [00:00<?, ?it/s]

Extracting : tqdm-4.65.0-py311h92b7b1e_0.conda:   0%|          | 0/73 [00:00<?, ?it/s]

Extracting : tk-8.6.12-h1ccaba5_0.conda:   1%|▏         | 1/73 [00:00<00:25,  2.85it/s]

Extracting : tk-8.6.12-h1ccaba5_0.conda:   3%|▎         | 2/73 [00:00<00:12,  5.69it/s]

Extracting : reproc-cpp-14.2.4-h295c915_1.conda:   3%|▎         | 2/73 [00:00<00:12,  5.69it/s]

Extracting : zlib-1.2.13-h5eee18b_0.conda:   4%|▍         | 3/73 [00:00<00:12,  5.69it/s]

Extracting : conda-content-trust-0.2.0-py311h06a4308_0.conda:   5%|▌         | 4/73 [00:00<00:12,  5.69it/s]

Extracting : icu-73.1-h6a678d5_0.conda:   7%|▋         | 5/73 [00:00<00:11,  5.69it/s]

Extracting : icu-73.1-h6a678d5_0.conda:   8%|▊         | 6/73 [00:00<00:06, 10.07it/s]

Extracting : archspec-0.2.1-pyhd3eb1b0_0.conda:   8%|▊         | 6/73 [00:00<00:06, 10.07it/s]

Extracting : pyopenssl-23.2.0-py311h06a4308_0.conda:  10%|▉         | 7/73 [00:00<00:06, 10.07it/s]

Extracting : libstdcxx-ng-11.2.0-h1234567_1.conda:  11%|█         | 8/73 [00:00<00:06, 10.07it/s]

Extracting : platformdirs-3.10.0-py311h06a4308_0.conda:  12%|█▏        | 9/73 [00:00<00:06, 10.07it/s]

Extracting : boltons-23.0.0-py311h06a4308_0.conda:  14%|█▎        | 10/73 [00:00<00:06, 10.07it/s]

Extracting : lz4-c-1.9.4-h6a678d5_0.conda:  15%|█▌        | 11/73 [00:00<00:06, 10.07it/s]

Extracting : python-3.11.5-h955ad1f_0.conda:  16%|█▋        | 12/73 [00:01<00:06, 10.07it/s]

Extracting : python-3.11.5-h955ad1f_0.conda:  18%|█▊        | 13/73 [00:01<00:08,  6.86it/s]

Extracting : openssl-3.0.12-h7f8727e_0.conda:  18%|█▊        | 13/73 [00:01<00:08,  6.86it/s]

Extracting : cryptography-41.0.7-py311hdda0065_0.conda:  19%|█▉        | 14/73 [00:01<00:08,  6.86it/s]

Extracting : xz-5.4.5-h5eee18b_0.conda:  21%|██        | 15/73 [00:01<00:08,  6.86it/s]

Extracting : packaging-23.1-py311h06a4308_0.conda:  22%|██▏       | 16/73 [00:01<00:08,  6.86it/s]

Extracting : fmt-9.1.0-hdb19cb5_0.conda:  23%|██▎       | 17/73 [00:01<00:08,  6.86it/s]

Extracting : bzip2-1.0.8-h7b6447c_0.conda:  25%|██▍       | 18/73 [00:01<00:08,  6.86it/s]

Extracting : conda-package-streaming-0.9.0-py311h06a4308_0.conda:  26%|██▌       | 19/73 [00:01<00:07,  6.86it/s]

Extracting : libssh2-1.10.0-hdbd6064_2.conda:  27%|██▋       | 20/73 [00:01<00:07,  6.86it/s]

Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda:  29%|██▉       | 21/73 [00:01<00:07,  6.86it/s]

Extracting : wheel-0.41.2-py311h06a4308_0.conda:  30%|███       | 22/73 [00:01<00:07,  6.86it/s]

Extracting : tzdata-2023c-h04d1e81_0.conda:  32%|███▏      | 23/73 [00:01<00:07,  6.86it/s]

Extracting : jsonpatch-1.32-pyhd3eb1b0_0.conda:  33%|███▎      | 24/73 [00:01<00:07,  6.86it/s]

Extracting : libffi-3.4.4-h6a678d5_0.conda:  34%|███▍      | 25/73 [00:01<00:06,  6.86it/s]

Extracting : libcurl-8.4.0-h251f7ec_1.conda:  36%|███▌      | 26/73 [00:01<00:06,  6.86it/s]

Extracting : zstd-1.5.5-hc292b87_0.conda:  37%|███▋      | 27/73 [00:01<00:06,  6.86it/s]

Extracting : pluggy-1.0.0-py311h06a4308_1.conda:  38%|███▊      | 28/73 [00:01<00:06,  6.86it/s]

Extracting : menuinst-2.0.1-py311h06a4308_1.conda:  40%|███▉      | 29/73 [00:01<00:06,  6.86it/s]

Extracting : ncurses-6.4-h6a678d5_0.conda:  41%|████      | 30/73 [00:02<00:06,  6.86it/s]

Extracting : ncurses-6.4-h6a678d5_0.conda:  42%|████▏     | 31/73 [00:02<00:02, 18.21it/s]

Extracting : readline-8.2-h5eee18b_0.conda:  42%|████▏     | 31/73 [00:02<00:02, 18.21it/s]

Extracting : yaml-cpp-0.8.0-h6a678d5_0.conda:  44%|████▍     | 32/73 [00:02<00:02, 18.21it/s]

Extracting : zstandard-0.19.0-py311h5eee18b_0.conda:  45%|████▌     | 33/73 [00:02<00:02, 18.21it/s]

Extracting : pycosat-0.6.6-py311h5eee18b_0.conda:  47%|████▋     | 34/73 [00:02<00:02, 18.21it/s]

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Installing base environment...
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installation finished.
�[0;32mCreating conda environment...�[0m
Channels:

defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

Package Plan
environment location: /home/jovyan/content/sct/python/envs/venv_sct
added / updated specs:

- python=3.9
The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
openssl-3.0.13             |       h7f8727e_0         5.2 MB
pip-23.3.1                 |   py39h06a4308_0         2.6 MB
python-3.9.18              |       h955ad1f_0        25.1 MB
setuptools-68.2.2          |   py39h06a4308_0         948 KB
tzdata-2023d               |       h04d1e81_0         117 KB
wheel-0.41.2               |   py39h06a4308_0         108 KB
------------------------------------------------------------
                                       Total:        34.0 MB

The following NEW packages will be INSTALLED:
_libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main

_openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu

ca-certificates    pkgs/main/linux-64::ca-certificates-2023.12.12-h06a4308_0

ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1

libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0

libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1

libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1

libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1

ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0

openssl            pkgs/main/linux-64::openssl-3.0.13-h7f8727e_0

pip                pkgs/main/linux-64::pip-23.3.1-py39h06a4308_0

python             pkgs/main/linux-64::python-3.9.18-h955ad1f_0

readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0

setuptools         pkgs/main/linux-64::setuptools-68.2.2-py39h06a4308_0

sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0

tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0

tzdata             pkgs/main/noarch::tzdata-2023d-h04d1e81_0

wheel              pkgs/main/linux-64::wheel-0.41.2-py39h06a4308_0

xz                 pkgs/main/linux-64::xz-5.4.5-h5eee18b_0

zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0
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Verifying transaction: ...working... done

Executing transaction: ...working... done

To activate this environment, use

$ conda activate /home/jovyan/content/sct/python/envs/venv_sct

To deactivate an active environment, use

$ conda deactivate
Channels:

conda-forge
defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

Package Plan
environment location: /home/jovyan/content/sct/python/envs/venv_sct
added / updated specs:

- libstdcxx-ng
The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
_libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
_openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
ca-certificates-2024.2.2   |       hbcca054_0         152 KB  conda-forge
libgcc-ng-13.2.0           |       h807b86a_5         752 KB  conda-forge
libgomp-13.2.0             |       h807b86a_5         410 KB  conda-forge
libstdcxx-ng-13.2.0        |       h7e041cc_5         3.7 MB  conda-forge
openssl-3.2.1              |       hd590300_0         2.7 MB  conda-forge
------------------------------------------------------------
                                       Total:         7.7 MB

The following packages will be UPDATED:
ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-hbcca054_0

libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5

libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5

libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5

openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0
The following packages will be SUPERSEDED by a higher-priority channel:
_libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge

_openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu
Downloading and Extracting Packages: ...working... done

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Channels:

conda-forge
defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

All requested packages already installed.
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)

Collecting pip!=21.2.*

Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)

Downloading pip-24.0-py3-none-any.whl (2.1 MB)

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Installing collected packages: pip

Attempting uninstall: pip

Found existing installation: pip 23.3.1

Uninstalling pip-23.3.1:

Successfully uninstalled pip-23.3.1

Successfully installed pip-24.0
�[0;32mInstalling Python dependencies...�[0m
�[0;32mUsing requirements.txt (git installation)�[0m
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu

Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment

Collecting certifi

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Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)

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Installing build dependencies: started

Installing build dependencies: finished with status 'done'

Getting requirements to build wheel: started

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Installing backend dependencies: started

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Preparing metadata (pyproject.toml): started

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Collecting numpy<1.24 (from -r requirements.txt (line 27))

Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)

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Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))

Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)

Collecting pandas (from -r requirements.txt (line 32))

Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)

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Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)

Collecting psutil (from -r requirements.txt (line 34))

Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)

Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39))

Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (62.4 MB)

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Collecting pytest (from -r requirements.txt (line 40))

Downloading pytest-8.0.0-py3-none-any.whl.metadata (7.8 kB)

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Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)

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Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)

Collecting requirements-parser (from -r requirements.txt (line 43))

Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB)

Collecting scipy (from -r requirements.txt (line 44))

Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)

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Collecting scikit-image (from -r requirements.txt (line 45))

Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)

Collecting scikit-learn (from -r requirements.txt (line 46))

Downloading scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)

Collecting xlwt (from -r requirements.txt (line 47))

Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)

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Collecting tqdm (from -r requirements.txt (line 48))

Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)

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Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB)

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Downloading urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB)

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Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB)

Collecting pyyaml (from -r requirements.txt (line 52))

Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)

Collecting voxelmorph (from -r requirements.txt (line 53))

Downloading voxelmorph-0.2-py3-none-any.whl (54 kB)

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Collecting wquantiles (from -r requirements.txt (line 54))

Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)

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Downloading XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB)

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Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB)

Collecting PyQt5_sip<13,>=4.19.14 (from pyqt5==5.12.3->-r requirements.txt (line 39))

Downloading PyQt5_sip-12.13.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (504 bytes)

Collecting h5py>=2.8.0 (from dipy!=1.6.,!=1.7.,!=1.8.*->-r requirements.txt (line 7))

Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)

Collecting pyparsing<3,>=2.0.2 (from ivadomed->-r requirements.txt (line 11))

Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)

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Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 11))

Downloading csv_diff-1.1-py3-none-any.whl (12 kB)

Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 11))

Downloading loguru-0.7.2-py3-none-any.whl.metadata (23 kB)

Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 11))

Downloading imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB)

Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 11))

Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)

Collecting nibabel (from -r requirements.txt (line 21))

Downloading nibabel-3.2.2-py3-none-any.whl (3.3 MB)

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Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (15 kB)

Collecting pandas (from -r requirements.txt (line 32))

Downloading pandas-1.4.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)

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Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 11))

Downloading pybids-0.15.5-py3-none-any.whl (14.9 MB)

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Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 11))

Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)

Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 11))

Downloading tensorboard-2.16.1-py3-none-any.whl.metadata (1.6 kB)

Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 11))

Downloading torchio-0.19.5-py2.py3-none-any.whl.metadata (48 kB)

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Collecting torch>=1.8.1 (from ivadomed->-r requirements.txt (line 11))

Downloading https://download.pytorch.org/whl/cpu/torch-2.2.0%2Bcpu-cp39-cp39-linux_x86_64.whl (186.8 MB)

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ERROR: Exception:

Traceback (most recent call last):

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 438, in _error_catcher

yield

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 561, in read

data = self._fp_read(amt) if not fp_closed else b""

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 527, in _fp_read

return self._fp.read(amt) if amt is not None else self._fp.read()

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 98, in read

data: bytes = self.__fp.read(amt)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/http/client.py", line 463, in read

n = self.readinto(b)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/http/client.py", line 507, in readinto

n = self.fp.readinto(b)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/socket.py", line 704, in readinto

return self._sock.recv_into(b)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/ssl.py", line 1275, in recv_into

return self.read(nbytes, buffer)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/ssl.py", line 1133, in read

return self._sslobj.read(len, buffer)

socket.timeout: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper

status = run_func(*args)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper

return func(self, options, args)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 377, in run

requirement_set = resolver.resolve(

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 95, in resolve

result = self._result = resolver.resolve(

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve

state = resolution.resolve(requirements, max_rounds=max_rounds)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 427, in resolve

failure_causes = self._attempt_to_pin_criterion(name)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 239, in _attempt_to_pin_criterion

criteria = self._get_updated_criteria(candidate)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 230, in _get_updated_criteria

self._add_to_criteria(criteria, requirement, parent=candidate)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria

if not criterion.candidates:

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/structs.py", line 156, in bool

return bool(self._sequence)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in bool

return any(self)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in 

return (c for c in iterator if id(c) not in self._incompatible_ids)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built

candidate = func()

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 182, in _make_candidate_from_link

base: Optional[BaseCandidate] = self._make_base_candidate_from_link(

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link

self._link_candidate_cache[link] = LinkCandidate(

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in init

super().init(

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in init

self.dist = self._prepare()

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare

dist = self._prepare_distribution()

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution

return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement

return self._prepare_linked_requirement(req, parallel_builds)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 596, in _prepare_linked_requirement

local_file = unpack_url(

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 168, in unpack_url

file = get_http_url(

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 109, in get_http_url

from_path, content_type = download(link, temp_dir.path)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/network/download.py", line 147, in call

for chunk in chunks:

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/cli/progress_bars.py", line 53, in _rich_progress_bar

for chunk in iterable:

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/network/utils.py", line 63, in response_chunks

for chunk in response.raw.stream(

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 622, in stream

data = self.read(amt=amt, decode_content=decode_content)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 587, in read

raise IncompleteRead(self._fp_bytes_read, self.length_remaining)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/contextlib.py", line 137, in exit

self.gen.throw(typ, value, traceback)

File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 443, in _error_catcher

raise ReadTimeoutError(self._pool, None, "Read timed out.")

pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='download.pytorch.org', port=443): Read timed out.
�[0;31mFailed running pip install: 2�[0m
�[0;31mInstallation failed!
Please find the file "/home/jovyan/content/sct/install_sct_log.txt",

then upload it as a .txt attachment in a new topic on SCT's forum:

--> http://forum.spinalcordmri.org/c/sct�[0m
Removing intermediate container 858b9b6ec130

The command '/bin/sh -c ./binder/postBuild' returned a non-zero code: 1Built image, launching...

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3116b16edcc00fcb465831d8d8a51f98805d6374

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

agahkarakuzu · 2024-02-16T10:33:55Z

@roboneuro build book

roboneuro · 2024-02-16T10:33:59Z

🔴 Binder build has failed 🥀

Status: Failed b1e599a4
Last updated: 2024-02-16 02:49:14 PST

ℹ️ See details

The next comment will forward the logs

roboneuro · 2024-02-16T10:49:17Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerb8tq14y2'...
HEAD is now at 47f08c4 Comment out repo2data in postBuild
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> c686d3b638a4
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 78d0bdd256b4
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> e38b8fcb0fbd
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 35dbdf6176db
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 77ef363567fb
Step 31/53 : USER root
 ---> Using cache
 ---> 9848a0cccf77
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 4e3241167052
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> fee82a54343b
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4fb91435c67e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> be3e63cb11d8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 4f20431eee2a
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 40e55985010d
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 5971166c5297
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 17d6eea84084
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> f7275c32720b
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> d1ac2e317c84
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> a793bb39bb75
Step 43/53 : LABEL repo2docker.ref="47f08c4a054636c29aacb31a1bd1d33972874b82"
 ---> Running in ef161d654a16
Removing intermediate container ef161d654a16
 ---> 056f9ee24c61
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in 5b1f4ccceaa9
Removing intermediate container 5b1f4ccceaa9
 ---> a088cf3db8b0
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 8f81015e3e8e
Removing intermediate container 8f81015e3e8e
 ---> 0eb3f830cd1b
Step 46/53 : USER ${NB_USER}
 ---> Running in efcfdbd420fd
Removing intermediate container efcfdbd420fd
 ---> 797cf904a455
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 6f5c90a5784b
Removing intermediate container 6f5c90a5784b
 ---> 2bf71939ad8e
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 54c3a4382265
�[91mCloning into '/home/jovyan/content/sct'...
�[0m
�[0;32m
*******************************
* Welcome to SCT installation *
*******************************
�[0m
�[0;32mChecking OS type and version...�[0m
Linux 54c3a4382265 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
�[0;32mChecking requirements...�[0m
�[0;32mOK!�[0m
SCT version ......... 6.3.dev0

Installation type ... in-place

Operating system .... linux (unknown)

Shell config ........ /home/jovyan/.bashrc
�[0;32mSCT will be installed here: [/home/jovyan/content/sct]�[0m
�[0;92m

Do you agree? [y]es/[n]o: �[0m

�[0;32mSkipping copy of source files (source and destination folders are the same)�[0m
�[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: �[0m

�[0;32mDownloading Miniconda...�[0m
�[0;34mwget -nv -O /tmp/tmp.s8hYF9AA16/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh�[0m
2024-02-16 10:34:54 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.s8hYF9AA16/miniconda.sh" [1]
�[0;32mInstalling Miniconda...�[0m
�[0;34mbash /tmp/tmp.s8hYF9AA16/miniconda.sh -p /home/jovyan/content/sct/python -b -f�[0m
PREFIX=/home/jovyan/content/sct/python

Unpacking payload ...
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Extracting : tqdm-4.65.0-py311h92b7b1e_0.conda:   0%|          | 0/73 [00:00<?, ?it/s]

Extracting : tk-8.6.12-h1ccaba5_0.conda:   1%|▏         | 1/73 [00:00<00:23,  3.04it/s]

Extracting : tk-8.6.12-h1ccaba5_0.conda:   3%|▎         | 2/73 [00:00<00:11,  6.09it/s]

Extracting : reproc-cpp-14.2.4-h295c915_1.conda:   3%|▎         | 2/73 [00:00<00:11,  6.09it/s]

Extracting : zlib-1.2.13-h5eee18b_0.conda:   4%|▍         | 3/73 [00:00<00:11,  6.09it/s]

Extracting : conda-content-trust-0.2.0-py311h06a4308_0.conda:   5%|▌         | 4/73 [00:00<00:11,  6.09it/s]

Extracting : icu-73.1-h6a678d5_0.conda:   7%|▋         | 5/73 [00:00<00:11,  6.09it/s]

Extracting : icu-73.1-h6a678d5_0.conda:   8%|▊         | 6/73 [00:00<00:06,  9.96it/s]

Extracting : archspec-0.2.1-pyhd3eb1b0_0.conda:   8%|▊         | 6/73 [00:00<00:06,  9.96it/s]

Extracting : pyopenssl-23.2.0-py311h06a4308_0.conda:  10%|▉         | 7/73 [00:00<00:06,  9.96it/s]

Extracting : libstdcxx-ng-11.2.0-h1234567_1.conda:  11%|█         | 8/73 [00:00<00:06,  9.96it/s]

Extracting : platformdirs-3.10.0-py311h06a4308_0.conda:  12%|█▏        | 9/73 [00:00<00:06,  9.96it/s]

Extracting : boltons-23.0.0-py311h06a4308_0.conda:  14%|█▎        | 10/73 [00:00<00:06,  9.96it/s]

Extracting : lz4-c-1.9.4-h6a678d5_0.conda:  15%|█▌        | 11/73 [00:00<00:06,  9.96it/s]

Extracting : python-3.11.5-h955ad1f_0.conda:  16%|█▋        | 12/73 [00:01<00:06,  9.96it/s]

Extracting : python-3.11.5-h955ad1f_0.conda:  18%|█▊        | 13/73 [00:01<00:09,  6.26it/s]

Extracting : openssl-3.0.12-h7f8727e_0.conda:  18%|█▊        | 13/73 [00:01<00:09,  6.26it/s]

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Extracting : urllib3-1.26.18-py311h06a4308_0.conda:  59%|█████▉    | 43/73 [00:02<00:01, 21.81it/s]

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Extracting : libedit-3.1.20230828-h5eee18b_0.conda:  78%|███████▊  | 57/73 [00:02<00:00, 24.84it/s]

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Extracting : brotli-python-1.0.9-py311h6a678d5_7.conda:  90%|█████████ | 66/73 [00:02<00:00, 24.84it/s]

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Installing base environment...
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Executing transaction: ...working... done

installation finished.
�[0;32mCreating conda environment...�[0m
Channels:

defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

Package Plan
environment location: /home/jovyan/content/sct/python/envs/venv_sct
added / updated specs:

- python=3.9
The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
openssl-3.0.13             |       h7f8727e_0         5.2 MB
pip-23.3.1                 |   py39h06a4308_0         2.6 MB
python-3.9.18              |       h955ad1f_0        25.1 MB
setuptools-68.2.2          |   py39h06a4308_0         948 KB
tzdata-2023d               |       h04d1e81_0         117 KB
wheel-0.41.2               |   py39h06a4308_0         108 KB
------------------------------------------------------------
                                       Total:        34.0 MB

The following NEW packages will be INSTALLED:
_libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main

_openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu

ca-certificates    pkgs/main/linux-64::ca-certificates-2023.12.12-h06a4308_0

ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1

libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0

libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1

libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1

libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1

ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0

openssl            pkgs/main/linux-64::openssl-3.0.13-h7f8727e_0

pip                pkgs/main/linux-64::pip-23.3.1-py39h06a4308_0

python             pkgs/main/linux-64::python-3.9.18-h955ad1f_0

readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0

setuptools         pkgs/main/linux-64::setuptools-68.2.2-py39h06a4308_0

sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0

tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0

tzdata             pkgs/main/noarch::tzdata-2023d-h04d1e81_0

wheel              pkgs/main/linux-64::wheel-0.41.2-py39h06a4308_0

xz                 pkgs/main/linux-64::xz-5.4.5-h5eee18b_0

zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0
Downloading and Extracting Packages: ...working... done

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

To activate this environment, use

$ conda activate /home/jovyan/content/sct/python/envs/venv_sct

To deactivate an active environment, use

$ conda deactivate
Channels:

conda-forge
defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

Package Plan
environment location: /home/jovyan/content/sct/python/envs/venv_sct
added / updated specs:

- libstdcxx-ng
The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
_libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
_openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
ca-certificates-2024.2.2   |       hbcca054_0         152 KB  conda-forge
libgcc-ng-13.2.0           |       h807b86a_5         752 KB  conda-forge
libgomp-13.2.0             |       h807b86a_5         410 KB  conda-forge
libstdcxx-ng-13.2.0        |       h7e041cc_5         3.7 MB  conda-forge
openssl-3.2.1              |       hd590300_0         2.7 MB  conda-forge
------------------------------------------------------------
                                       Total:         7.7 MB

The following packages will be UPDATED:
ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-hbcca054_0

libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5

libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5

libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5

openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0
The following packages will be SUPERSEDED by a higher-priority channel:
_libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge

_openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu
Downloading and Extracting Packages: ...working... done

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Channels:

conda-forge
defaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

All requested packages already installed.
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)

Collecting pip!=21.2.*

Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)

Downloading pip-24.0-py3-none-any.whl (2.1 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 7.1 MB/s eta 0:00:00

Installing collected packages: pip

Attempting uninstall: pip

Found existing installation: pip 23.3.1

Uninstalling pip-23.3.1:

Successfully uninstalled pip-23.3.1

Successfully installed pip-24.0
�[0;32mInstalling Python dependencies...�[0m
�[0;32mUsing requirements.txt (git installation)�[0m
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu

Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment

Collecting certifi

Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)

Collecting dipy!=1.6.,!=1.7.,!=1.8.* (from -r requirements.txt (line 7))

Downloading dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB)

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Collecting ivadomed (from -r requirements.txt (line 11))

Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)

Collecting matplotlib (from -r requirements.txt (line 12))

Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)

Collecting nibabel (from -r requirements.txt (line 21))

Downloading nibabel-5.2.0-py3-none-any.whl.metadata (8.8 kB)

Collecting nilearn (from -r requirements.txt (line 22))

Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB)

Collecting nnunetv2 (from -r requirements.txt (line 23))

Downloading nnunetv2-2.2.1.tar.gz (178 kB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.6/178.6 kB 332.5 kB/s eta 0:00:00

Installing build dependencies: started

Installing build dependencies: finished with status 'done'

Getting requirements to build wheel: started

Getting requirements to build wheel: finished with status 'done'

Installing backend dependencies: started

Installing backend dependencies: finished with status 'done'

Preparing metadata (pyproject.toml): started

Preparing metadata (pyproject.toml): finished with status 'done'

Collecting numpy<1.24 (from -r requirements.txt (line 27))

Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 24.1 MB/s eta 0:00:00

Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))

Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)

Collecting pandas (from -r requirements.txt (line 32))

Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)

Collecting portalocker (from -r requirements.txt (line 33))

Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)

Collecting psutil (from -r requirements.txt (line 34))

Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)

Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39))

Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (62.4 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.4/62.4 MB 10.9 MB/s eta 0:00:00

Collecting pyqt5-sip<12.13.0 (from -r requirements.txt (line 41))

Downloading PyQt5_sip-12.12.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (504 bytes)

Collecting pytest (from -r requirements.txt (line 42))

Downloading pytest-8.0.0-py3-none-any.whl.metadata (7.8 kB)

Collecting pytest-cov (from -r requirements.txt (line 43))

Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)

Collecting requests (from -r requirements.txt (line 44))

Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)

Collecting requirements-parser (from -r requirements.txt (line 45))

Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB)

Collecting scipy (from -r requirements.txt (line 46))

Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 1.6 MB/s eta 0:00:00

Collecting scikit-image (from -r requirements.txt (line 47))

Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)

Collecting scikit-learn (from -r requirements.txt (line 48))

Downloading scikit_learn-1.4.1.post1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)

Collecting xlwt (from -r requirements.txt (line 49))

Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 580.6 kB/s eta 0:00:00

Collecting tqdm (from -r requirements.txt (line 50))

Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 186.3 kB/s eta 0:00:00

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Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt

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Building wheel for acvl-utils (setup.py): started

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Stored in directory: /home/jovyan/.cache/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7

Building wheel for batchgenerators (setup.py): started

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Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=cf97138ab5e4ffe8324353f8dd47d8ae7aa4d8f05c94bc41b093846af6ca59a7

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Building wheel for dynamic-network-architectures (setup.py): started

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Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.2-py3-none-any.whl size=27245 sha256=2c0f07517695fdd192ad06b9b6aaf6ffb1e3a8fe4fba419f8aa03f483065cc12

Stored in directory: /home/jovyan/.cache/pip/wheels/4e/c0/70/740949411012a24276008fa6e920f42701ae6fa18ce6122eb5

Building wheel for pystrum (setup.py): started

Building wheel for pystrum (setup.py): finished with status 'done'

Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=cc2aa73bc876f544b97515ec0daf71c95d5b2c150d137d2f995c5f9bff752a92

Stored in directory: /home/jovyan/.cache/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea

Building wheel for future (setup.py): started

Building wheel for future (setup.py): finished with status 'done'

Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492024 sha256=bd984687474811870e347bd06ee25445a6fe6f69d7f833da3fd1414b245a9a36

Stored in directory: /home/jovyan/.cache/pip/wheels/bf/5d/6a/2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b

Building wheel for docopt (setup.py): started

Building wheel for docopt (setup.py): finished with status 'done'

Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=0558a834ddf304d308827da2933dba8f40deb3665898103703025e2bb4b73584

Stored in directory: /home/jovyan/.cache/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b

Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt

Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tf-keras, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, pyqt5-sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed

Successfully installed Deprecated-1.2.14 GitPython-3.1.42 MarkupSafe-2.1.5 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.49.0 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.3 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pyqt5-sip-12.12.2 pystrum-0.4 pytest-8.0.0 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.1.post1 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.1 tensorboard-data-server-0.7.2 tf-keras-2.15.0 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240215 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.0 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0
�[0;32mInstalling spinalcordtoolbox...�[0m
Obtaining file:///home/jovyan/content/sct

Preparing metadata (setup.py): started

Preparing metadata (setup.py): finished with status 'done'

Installing collected packages: spinalcordtoolbox

Running setup.py develop for spinalcordtoolbox

Successfully installed spinalcordtoolbox-6.3.dev0
�[0;32mCreating launchers for Python scripts...�[0m
�[0;32mInstalling binaries...�[0m
�[0;34msct_download_data -d binaries_linux -k�[0m
--

Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)
sct_download_data -d binaries_linux -k
Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz

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Creating temporary folder (/tmp/sct_2024-02-16_10-41-29_install-data_qzmb911l)

Unzip data to: /tmp/sct_2024-02-16_10-41-29_install-data_qzmb911l

Copying data to: /home/jovyan/content/sct/bin

Removing temporary folders...

Done!
�[0;32mAll requirements installed!�[0m
�[0;32mInstalling data...�[0m
�[0;34mmkdir -p /home/jovyan/content/sct/data�[0m
�[0;34msct_download_data -d PAM50�[0m
--

Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)
sct_download_data -d PAM50
Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20240215/PAM50-r20240215.zip

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Creating temporary folder (/tmp/sct_2024-02-16_10-41-34_install-data_c6yrtu66)

Unzip data to: /tmp/sct_2024-02-16_10-41-34_install-data_c6yrtu66

Copying data to: /home/jovyan/content/sct/data/PAM50

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_sc_models�[0m
--

Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)
sct_download_data -d deepseg_sc_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip

Downloading: 20220325_deepseg_sc_models_onnx.zip
Status:   0%|          | 0.00/19.5M [00:00<?, ?B/s]

Status:  59%|█████▉    | 11.6M/19.5M [00:00<00:00, 116MB/s]

Status: 100%|██████████| 19.5M/19.5M [00:00<00:00, 128MB/s]

Creating temporary folder (/tmp/sct_2024-02-16_10-41-35_install-data_ofqaiqs7)

Unzip data to: /tmp/sct_2024-02-16_10-41-35_install-data_ofqaiqs7

Copying data to: /home/jovyan/content/sct/data/deepseg_sc_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_gm_models�[0m
--

Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)
sct_download_data -d deepseg_gm_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip

Downloading: 20220325_deepseg_gm_models_onnx.zip
Status:   0%|          | 0.00/2.24M [00:00<?, ?B/s]

Status: 100%|██████████| 2.24M/2.24M [00:00<00:00, 71.7MB/s]

Creating temporary folder (/tmp/sct_2024-02-16_10-41-36_install-data_nvg34x_g)

Unzip data to: /tmp/sct_2024-02-16_10-41-36_install-data_nvg34x_g

Copying data to: /home/jovyan/content/sct/data/deepseg_gm_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepseg_lesion_models�[0m
--

Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)
sct_download_data -d deepseg_lesion_models
Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip

Downloading: 20220325_deepseg_lesion_models_onnx.zip
Status:   0%|          | 0.00/5.35M [00:00<?, ?B/s]

Status: 100%|██████████| 5.35M/5.35M [00:00<00:00, 98.4MB/s]

Creating temporary folder (/tmp/sct_2024-02-16_10-41-37_install-data_hj2xj3i0)

Unzip data to: /tmp/sct_2024-02-16_10-41-37_install-data_hj2xj3i0

Copying data to: /home/jovyan/content/sct/data/deepseg_lesion_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d deepreg_models�[0m
--

Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)
sct_download_data -d deepreg_models
Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip

Downloading: models.zip
Status:   0%|          | 0.00/158M [00:00<?, ?B/s]

Status:   2%|▏         | 2.69M/158M [00:00<00:05, 26.6MB/s]

Status:   6%|▌         | 9.57M/158M [00:00<00:02, 51.3MB/s]

Status:  15%|█▍        | 23.6M/158M [00:00<00:01, 92.0MB/s]

Status:  24%|██▍       | 38.5M/158M [00:00<00:01, 114MB/s]

Status:  34%|███▍      | 53.5M/158M [00:00<00:00, 127MB/s]

Status:  43%|████▎     | 67.4M/158M [00:00<00:00, 131MB/s]

Status:  52%|█████▏    | 82.0M/158M [00:00<00:00, 136MB/s]

Status:  61%|██████    | 96.1M/158M [00:00<00:00, 138MB/s]

Status:  70%|██████▉   | 110M/158M [00:00<00:00, 138MB/s]

Status:  79%|███████▊  | 124M/158M [00:01<00:00, 139MB/s]

Status:  87%|████████▋ | 138M/158M [00:01<00:00, 140MB/s]

Status:  96%|█████████▋| 153M/158M [00:01<00:00, 140MB/s]

Status: 100%|██████████| 158M/158M [00:01<00:00, 127MB/s]

Creating temporary folder (/tmp/sct_2024-02-16_10-41-39_install-data_e72qt981)

Unzip data to: /tmp/sct_2024-02-16_10-41-39_install-data_e72qt981

Copying data to: /home/jovyan/content/sct/data/deepreg_models

Removing temporary folders...

Done!
�[0;34msct_download_data -d PAM50_normalized_metrics�[0m
--

Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)
sct_download_data -d PAM50_normalized_metrics
Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20230222.zip

Downloading: PAM50-normalized-metrics-r20230222.zip
Status:   0%|          | 0.00/1.00 [00:00<?, ?B/s]

Status: 47.3kB [00:00, 350kB/s]

Status: 214kB [00:00, 823kB/s]

Status: 827kB [00:00, 2.41MB/s]

Status: 2.51MB [00:00, 6.93MB/s]

Status: 4.77MB [00:00, 11.4MB/s]

Status: 6.02MB [00:00, 9.92MB/s]

Status: 6.92MB [00:00, 7.65MB/s]

Creating temporary folder (/tmp/sct_2024-02-16_10-41-43_install-data_2sqo5kgd)

Unzip data to: /tmp/sct_2024-02-16_10-41-43_install-data_2sqo5kgd

Copying data to: /home/jovyan/content/sct/data/PAM50_normalized_metrics

Removing temporary folders...

Done!
Status:   0%|          | 0.00/18.0M [00:00<?, ?B/s]

Status:  67%|██████▋   | 12.0M/18.0M [00:00<00:00, 120MB/s]

Status: 100%|██████████| 18.0M/18.0M [00:00<00:00, 122MB/s]
�[0;32mValidate installation...�[0m
--

Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)
sct_check_dependencies
SYSTEM INFORMATION
SCT info:

version: git-master-6962e03b5906ab3466e6e330438dbea58d949407
path: /home/jovyan/content/sct

OS: linux (Linux-5.4.0-139-generic-x86_64-with-glibc2.27)

CPU cores: Available: 16, Used by ITK functions: 16

RAM: Total: 60286MB, Used: 3003MB, Available: 57581MB

OPTIONAL DEPENDENCIES
Check FSLeyes version...............................[  ]

(127, '/bin/sh: 1: fsleyes: not found')
MANDATORY DEPENDENCIES
Check Python executable.............................[�[92mOK�[0m]

Using bundled python 3.9.18 (main, Sep 11 2023, 13:41:44)

[GCC 11.2.0] at /home/jovyan/content/sct/python/envs/venv_sct/bin/python

Check if data are installed.........................[�[92mOK�[0m]

Check if dipy is installed..........................[�[92mOK�[0m] (1.5.0)

Check if ivadomed is installed......................[�[92mOK�[0m] (2.9.9)

Check if matplotlib is installed....................[�[92mOK�[0m] (3.8.3)

Check if monai is installed.........................[�[92mOK�[0m] (1.3.0)

Check if nibabel is installed.......................[�[92mOK�[0m] (3.2.2)

Check if nilearn is installed.......................[�[92mOK�[0m] (0.10.2)

Check if nnunetv2 is installed......................[�[92mOK�[0m]

Check if numpy is installed.........................[�[92mOK�[0m] (1.23.5)

Check if onnxruntime is installed...................[�[92mOK�[0m] (1.17.0)

Check if pandas is installed........................[�[92mOK�[0m] (1.4.4)

Check if portalocker is installed...................[�[92mOK�[0m] (2.8.2)

Check if psutil is installed........................[�[92mOK�[0m] (5.9.8)

Check if pyqt5 (5.12.3) is installed................[�[92mOK�[0m] (5.12.3)

Check if pyqt5-sip is installed.....................[�[92mOK�[0m]

Check if pytest is installed........................[�[92mOK�[0m] (8.0.0)

Check if pytest-cov is installed....................[�[92mOK�[0m] (4.1.0)

Check if requests is installed......................[�[92mOK�[0m] (2.31.0)

Check if requirements-parser is installed...........[�[92mOK�[0m]

Check if scipy is installed.........................[�[92mOK�[0m] (1.12.0)

Check if scikit-image is installed..................[�[92mOK�[0m] (0.22.0)

Check if scikit-learn is installed..................[�[92mOK�[0m] (1.4.1.post1)

Check if xlwt is installed..........................[�[92mOK�[0m] (1.3.0)

Check if tqdm is installed..........................[�[92mOK�[0m] (4.66.2)

Check if transforms3d is installed..................[�[92mOK�[0m] (0.4.1)

Check if urllib3 is installed.......................[�[92mOK�[0m] (2.2.0)

Check if pytest_console_scripts is installed........[�[92mOK�[0m]

Check if pyyaml is installed........................[�[92mOK�[0m] (6.0.1)

Check if voxelmorph is installed....................[�[92mOK�[0m] (0.2)

Check if wquantiles is installed....................[�[92mOK�[0m] (0.4)

Check if xlsxwriter is installed....................[�[92mOK�[0m] (3.1.9)

Check if spinalcordtoolbox is installed.............[�[92mOK�[0m]

Check ANTs compatibility with OS ...................[�[92mOK�[0m]

Check PropSeg compatibility with OS ................[�[92mOK�[0m]

Check if figure can be opened with PyQt.............[�[91mFAIL�[0m] ($DISPLAY not set on X11-supporting system)

Check if figure can be opened with matplotlib.......[�[91mFAIL�[0m] (Using non-GUI backend 'agg')
�[0;32mOpen a new Terminal window to load environment variables, or run:

source /home/jovyan/.bashrc�[0m
�[0;32mInstallation finished successfully!�[0m
Removing intermediate container 54c3a4382265

---> 63a0cc0007f3

Step 49/53 : ENV PYTHONUNBUFFERED=1

---> Running in 033bc7cb7cf6

Removing intermediate container 033bc7cb7cf6

---> 8870f7401a0a

Step 50/53 : COPY /python3-login /usr/local/bin/python3-login

---> 5c04ab56e187

Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint

---> eefcf7517471

Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]

---> Running in f344ae8fa9bb

Removing intermediate container f344ae8fa9bb

---> d1110a253aef

Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]

---> Running in 0de95c662fa1

Removing intermediate container 0de95c662fa1

---> 112b28e19ac8

{"aux": {"ID": "sha256:112b28e19ac8b32a5eab3d53c936fb3d2fc22bb0f0b4a0aa06c32cc1210dcc1d"}}Successfully built 112b28e19ac8

Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:47f08c4a054636c29aacb31a1bd1d33972874b82

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received unexpected HTTP status: 500 Internal Server Error

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for shimming-toolbox/rf-shimming-7t at 47f08c4a054636c29aacb31a1bd1d33972874b82

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

agahkarakuzu · 2024-02-16T11:08:54Z

The issue is caused by large image size, the docker image with data included is ~9GB and w/o about 7.23GB.

I'll remove the size limit altogether and see if it works.

agahkarakuzu · 2024-04-04T20:11:46Z

@roboneuro zenodo publish

roboneuro · 2024-04-04T20:11:49Z

🟣 Publish Reproducibility Assets

Status: Already exists 2e6c5dc0
Last updated: 2024-04-04 13:11:57 PDT

Looks like the reproducibility assets have already been published! So...

GPT is AFK, keep hanging out with roboneuro.

roboneuro · 2024-04-04T20:12:00Z

@roboneuro set 10.5281/zenodo.10844538 as book archive

roboneuro · 2024-04-04T20:12:02Z

@roboneuro set 10.5281/zenodo.10844540 as repository archive

roboneuro · 2024-04-04T20:12:05Z

@roboneuro set 10.5281/zenodo.10844542 as data archive

roboneuro · 2024-04-04T20:12:07Z

@roboneuro set 10.5281/zenodo.10844544 as docker archive

agahkarakuzu · 2024-04-04T20:12:33Z

@roboneuro set 10.5281/zenodo.10844538 as book archive

roboneuro · 2024-04-04T20:12:35Z

Done, book archive is now 10.5281/zenodo.10844538

agahkarakuzu · 2024-04-04T20:12:43Z

@roboneuro set 10.5281/zenodo.10844540 as repository archive

roboneuro · 2024-04-04T20:12:45Z

Done, repository archive is now 10.5281/zenodo.10844540

agahkarakuzu · 2024-04-04T20:12:50Z

@roboneuro set 10.5281/zenodo.10844542 as data archive

roboneuro · 2024-04-04T20:12:52Z

Done, data archive is now 10.5281/zenodo.10844542

agahkarakuzu · 2024-04-04T20:13:12Z

@roboneuro set 10.5281/zenodo.10844544 as docker archive

roboneuro · 2024-04-04T20:13:14Z

Done, docker archive is now 10.5281/zenodo.10844544

agahkarakuzu · 2024-04-04T20:13:59Z

@roboneuro recommend-accept

roboneuro · 2024-04-04T20:14:02Z

Attempting dry run of processing paper acceptance...

roboneuro · 2024-04-04T20:14:04Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/mrm.29528 is OK
- 10.1016/j.neuroimage.2016.10.009 is OK
- 10.1038/nrneurol.2015.80 is OK
- 10.1038/s41582-019-0270-5 is OK
- 10.1016/S0730-725X(01)00300-9 is OK
- 10.1002/jmri.20245 is OK
- 10.1118/1.595995 is OK
- 10.1002/mrm.10137 is OK
- 10.1016/j.neuroimage.2017.10.041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

roboneuro · 2024-04-04T20:15:14Z

👋 @neurolibre/executable-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in neurolibre/preprints#78, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

agahkarakuzu · 2024-04-04T20:18:10Z

@roboneuro commands

roboneuro · 2024-04-04T20:18:15Z

Hello @agahkarakuzu, here are the things you can ask me to do:


# List all available commands
@roboneuro commands

# Add to this issue's reviewers list
@roboneuro add @username as reviewer

# Remove from this issue's reviewers list
@roboneuro remove @username from reviewers

# Get a list of all editors's GitHub handles
@roboneuro list editors

# Assign a user as the editor of this submission
@roboneuro assign @username as editor

# Remove the editor assigned to this submission
@roboneuro remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@roboneuro remind @reviewer in 2 weeks

# Check the references of the PDF for missing DOIs
@roboneuro check references

# Perform checks on the repository
@roboneuro check repository

# Adds a checklist for the reviewer using this command
@roboneuro generate my checklist

# Set a value for version
@roboneuro set v1.0.0 as version

# Set a value for branch
@roboneuro set neurolibre-paper as branch

# Set a value for repository
@roboneuro set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@roboneuro set set 10.5281/zenodo.6861996 as archive

# Set a value for the (data/book/repository/docker) archive DOI.
@roboneuro set 10.5281/zenodo.6861996 as data archive

# Set executable book URI for the preprint.
@roboneuro set book uri

# Mention the EiCs for the correct track
@roboneuro ping track-eic

# Reject paper
@roboneuro reject

# Withdraw paper
@roboneuro withdraw

# Invite an editor to edit a submission (sending them an email)
@roboneuro invite @(.*) as editor

# Generates the pdf paper
@roboneuro generate pdf

# Recommends the submission for acceptance
@roboneuro recommend-accept

# Accept and publish the paper
@roboneuro accept

# Update data on an accepted/published paper
@roboneuro reaccept

# Generates a LaTeX preprint file
@roboneuro generate preprint

# Flag submission with questionable scope
@roboneuro query scope

# Get a link to the complete list of reviewers
@roboneuro list reviewers

# Creates a post-review checklist with editor and authors tasks
@roboneuro create post-review checklist

# Open the review issue
@roboneuro start review

# Check the status of the NeuroLibre preview server.
@roboneuro preview server status

# Check the status of the NeuroLibre preprint (production) server.
@roboneuro preprint server status

# Build a NeuroLibre reproducible preprint for technical screening.
@roboneuro build book

# After screening, build book from the forked reository.
@roboneuro production build book

# Transfer data from preview to the preprint (production) server.
@roboneuro production sync data

# Transfer the final preprint (forked repo) to the preprint (production) server (DOI URL).
@roboneuro production sync book

# Start the production process by forking repository and configuring it.
@roboneuro production start

# Creates Zenodo deposits (a.k.a buckets) for archiving reproducibility assets.
@roboneuro zenodo create buckets

# Status check for the archival of the reproducibility assets.
@roboneuro zenodo status

# Copy summary PDF from the preprints repository to the NeuroLibre production server.
@roboneuro production sync pdf

# Upload the latest Jupyter Book to Zenodo for archival.
@roboneuro zenodo upload book

# Upload the latest version of the book repository to Zenodo for archival.
@roboneuro zenodo upload repository

# Upload the latest version of the docker image to Zenodo for archival.
@roboneuro zenodo upload docker

# Upload the submission data to Zenodo for archival. Will not take effect if the data is already archived.
@roboneuro zenodo upload data

# DESTRUCTIVE ACTION: Deletes zenodo records and all the data that has been uploaded. Cannot perform after zenodo publish.
@roboneuro zenodo flush

# Publish reproducibility assets on Zenodo. Sets DOIs if successful.
@roboneuro zenodo publish

# Build an extended PDF for the target repository.
@roboneuro build extended pdf

# Download the submission data.
@roboneuro cache data

agahkarakuzu · 2024-04-04T20:18:32Z

@roboneuro production sync pdf

roboneuro · 2024-04-04T20:18:35Z

🌱♻️📄 Synced the summary PDF from the source, should be now available at https://preprint.neurolibre.org/10.55458/neurolibre.00025.pdf?no-cache

agahkarakuzu · 2024-04-04T20:19:03Z

@roboneuro accept

roboneuro · 2024-04-04T20:19:05Z

Doing it live! Attempting automated processing of paper acceptance...

roboneuro · 2024-04-04T20:21:54Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Papp
  given-names: Daniel
  orcid: "https://orcid.org/0000-0003-1481-1413"
- family-names: Gilbert
  given-names: Kyle M.
  orcid: "https://orcid.org/0000-0003-3026-5686"
- family-names: Cereza
  given-names: Gaspard
- family-names: D'Astous
  given-names: Alexandre
  orcid: "https://orcid.org/0000-0003-0381-7334"
- family-names: Lopez-Rios
  given-names: Nibardo
  orcid: "https://orcid.org/0000-0002-4791-8260"
- family-names: Boudreau
  given-names: Mathieu
  orcid: "https://orcid.org/0000-0002-7726-4456"
- family-names: Couch
  given-names: Marcus
  orcid: "https://orcid.org/0000-0002-2732-8941"
- family-names: Yazdanbakhsh
  given-names: Pedram
  orcid: "https://orcid.org/0000-0003-4456-5997"
- family-names: Barry
  given-names: Robert L.
- family-names: Ortiz
  given-names: Eva Alonso
  orcid: "https://orcid.org/0000-0001-6590-7234"
- family-names: Cohen-Adad
  given-names: Julien
  orcid: "https://orcid.org/0000-0003-3662-9532"
doi: 10.55458
message: To reference this work, please cite our reproducible preprint
  in NeuroLibre.
preferred-citation:
  authors:
  - family-names: Papp
    given-names: Daniel
    orcid: "https://orcid.org/0000-0003-1481-1413"
  - family-names: Gilbert
    given-names: Kyle M.
    orcid: "https://orcid.org/0000-0003-3026-5686"
  - family-names: Cereza
    given-names: Gaspard
  - family-names: D'Astous
    given-names: Alexandre
    orcid: "https://orcid.org/0000-0003-0381-7334"
  - family-names: Lopez-Rios
    given-names: Nibardo
    orcid: "https://orcid.org/0000-0002-4791-8260"
  - family-names: Boudreau
    given-names: Mathieu
    orcid: "https://orcid.org/0000-0002-7726-4456"
  - family-names: Couch
    given-names: Marcus
    orcid: "https://orcid.org/0000-0002-2732-8941"
  - family-names: Yazdanbakhsh
    given-names: Pedram
    orcid: "https://orcid.org/0000-0003-4456-5997"
  - family-names: Barry
    given-names: Robert L.
  - family-names: Ortiz
    given-names: Eva Alonso
    orcid: "https://orcid.org/0000-0001-6590-7234"
  - family-names: Cohen-Adad
    given-names: Julien
    orcid: "https://orcid.org/0000-0003-3662-9532"
  date-published: 2024-04-04
  doi: 10.55458/neurolibre.00025
  journal: NeuroLibre Reproducible Preprints
  publisher:
    name: NeuroLibre
  start: 25
  title: Analysis code for the paper "RF shimming in the cervical spinal
    cord at 7T"
  type: preprint
  url: "https://neurolibre.org/papers/10.55458/neurolibre.00025"
title: Analysis code for the paper "RF shimming in the cervical spinal
  cord at 7T"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

roboneuro · 2024-04-04T20:21:55Z

🌰🌱🌺 THIS IS NOT A DRILL, YOU HAVE JUST PUBLISHED A NEUROLIBRE REPRODUCIBLE PREPRINT! 🌺🌸🍀

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.55458.neurolibre.00025 preprints#79
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.55458/neurolibre.00025
If everything looks good, then close this review issue.
Party like you just published more than a PDF! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

agahkarakuzu · 2024-04-04T20:24:52Z

@jcohenadad @mathieuboudreau congrats, this is now published! Sorry took a while as I was travelling.

https://doi.org/10.55458/neurolibre.00025

Feel free to add CITATION.cff above to the repository (or substitute entries with MRM DOIs :) ).

jcohenadad · 2024-04-04T20:33:52Z

amazing! thank you so much @agahkarakuzu and @mathieuboudreau

now we are doing the review of the submitted MRM paper, so the manuscript and the code and figure will have to change 😅

roboneuro added review Track: 1 (executable) labels Feb 15, 2024

roboneuro assigned pbellec Feb 15, 2024

roboneuro mentioned this issue Feb 15, 2024

[PRE REVIEW]: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T" #24

Closed

roboneuro added CSS Jupyter Notebook Shell labels Feb 15, 2024

mathieuboudreau mentioned this issue Feb 15, 2024

Steps towards a NeuroLibre pre-print publication shimming-toolbox/rf-shimming-7t#42

Open

roboneuro added accepted published labels Apr 4, 2024

[REVIEW]: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T" #25

[REVIEW]: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T" #25

Comments

roboneuro commented Feb 15, 2024 • edited

Status

Reviewer instructions & questions

Checklists

roboneuro commented Feb 15, 2024

roboneuro commented Feb 15, 2024

roboneuro commented Feb 15, 2024

roboneuro commented Feb 15, 2024

agahkarakuzu commented Feb 15, 2024

roboneuro commented Feb 15, 2024 • edited

🔴 Binder build has failed 🥀

roboneuro commented Feb 15, 2024

roboneuro commented Feb 15, 2024

Package Plan

To activate this environment, use

$ conda activate /home/jovyan/content/sct/python/envs/venv_sct

To deactivate an active environment, use

$ conda deactivate

Package Plan

All requested packages already installed.

sct_download_data -d binaries_linux -k

sct_download_data -d PAM50

sct_download_data -d deepseg_sc_models

sct_download_data -d deepseg_gm_models

sct_download_data -d deepseg_lesion_models

sct_download_data -d deepreg_models

sct_download_data -d PAM50_normalized_metrics

sct_check_dependencies

SYSTEM INFORMATION

OPTIONAL DEPENDENCIES

MANDATORY DEPENDENCIES

agahkarakuzu commented Feb 15, 2024 • edited

agahkarakuzu commented Feb 15, 2024

roboneuro commented Feb 15, 2024 • edited

🔴 Binder build has failed 🥀

roboneuro commented Feb 15, 2024

Package Plan

To activate this environment, use

$ conda activate /home/jovyan/content/sct/python/envs/venv_sct

To deactivate an active environment, use

$ conda deactivate

Package Plan

All requested packages already installed.

sct_download_data -d binaries_linux -k

sct_download_data -d PAM50

sct_download_data -d deepseg_sc_models

sct_download_data -d deepseg_gm_models

sct_download_data -d deepseg_lesion_models

sct_download_data -d deepreg_models

sct_download_data -d PAM50_normalized_metrics

sct_check_dependencies

SYSTEM INFORMATION

OPTIONAL DEPENDENCIES

MANDATORY DEPENDENCIES

agahkarakuzu commented Feb 15, 2024

roboneuro commented Feb 15, 2024 • edited

🔴 Binder build has failed 🥀

roboneuro commented Feb 15, 2024

sct_download_data -d binaries_linux -k

sct_download_data -d PAM50

sct_download_data -d deepseg_sc_models

sct_download_data -d deepseg_gm_models

sct_download_data -d deepseg_lesion_models

sct_download_data -d deepreg_models

sct_download_data -d PAM50_normalized_metrics

sct_check_dependencies

SYSTEM INFORMATION

OPTIONAL DEPENDENCIES

MANDATORY DEPENDENCIES

agahkarakuzu commented Feb 15, 2024

roboneuro commented Feb 15, 2024 • edited

🔴 Binder build has failed 🥀

roboneuro commented Feb 15, 2024

Package Plan

To activate this environment, use

$ conda activate /home/jovyan/content/sct/python/envs/venv_sct

To deactivate an active environment, use

roboneuro commented Feb 15, 2024 •

edited

roboneuro commented Feb 15, 2024 •

edited

agahkarakuzu commented Feb 15, 2024 •

edited

roboneuro commented Feb 15, 2024 •

edited

roboneuro commented Feb 15, 2024 •

edited

roboneuro commented Feb 15, 2024 •

edited

roboneuro commented Feb 16, 2024 •

edited

roboneuro commented Apr 4, 2024 •

edited