MyBinder build failing - Githubissues

The build on MyBinder has failed repeatedly for the latest version on the master branch, apparently for a variety of reasons. Most recent failed build log attached.
Waiting for build to start...
 ---> Using cache
 ---> 8e993f039be6
Step 12/48 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 4b162157413e
Step 13/48 : RUN adduser --disabled-password     --gecos "Default user"     --uid ${NB_UID}     ${NB_USER}
 ---> Using cache
 ---> 0aa16a3915fd
Step 14/48 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> b92dcfeaccae
Step 15/48 : 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
 ---> 4233b4188718
Step 16/48 : EXPOSE 8888
 ---> Using cache
 ---> d27116d8a3cd
Step 17/48 : ENV APP_BASE /srv
 ---> Using cache
 ---> 696f6faabf07
Step 18/48 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 15b449789fbb
Step 19/48 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e980a509c6b2
Step 20/48 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 227fce8b5a2e
Step 21/48 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}
 ---> Using cache
 ---> 71110524c9f2
Step 22/48 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 076f2c80aa01
Step 23/48 : ENV PATH ${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> d04fa7e7048c
Step 24/48 : COPY conda/install-miniconda.bash /tmp/install-miniconda.bash
 ---> Using cache
 ---> 609e493c73b1
Step 25/48 : COPY conda/environment.py-3.7.frozen.yml /tmp/environment.yml
 ---> Using cache
 ---> cd53cd584901
Step 26/48 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 852ed8b9ede8
Step 27/48 : USER ${NB_USER}
 ---> Using cache
 ---> 0d7d78dc789b
Step 28/48 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 7b4f0138a3f3
Step 29/48 : USER root
 ---> Using cache
 ---> 8eedbeb1c4d6
Step 30/48 : RUN bash /tmp/install-miniconda.bash && rm /tmp/install-miniconda.bash /tmp/environment.yml
 ---> Using cache
 ---> 0684644a71fc
Step 31/48 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 3f2ebf496c08
Step 32/48 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> c32427519530
Step 33/48 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> a98cdc784c7a
Step 34/48 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 087d089990ea
Step 35/48 : USER root
 ---> Using cache
 ---> e6b8786f668f
Step 36/48 : COPY src/ ${REPO_DIR}
 ---> f02d91993436
Step 37/48 : RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Running in 67d2768a9b39
Removing intermediate container 67d2768a9b39
 ---> a6fa8246d634
Step 38/48 : RUN apt-get -qq update && apt-get install --yes --no-install-recommends texlive-latex-base texlive-latex-recommended texlive-science texlive-latex-extra texlive-fonts-recommended dvipng ghostscript graphviz && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*
 ---> Running in 0db24babc7b3
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  fonts-gfs-baskerville fonts-gfs-porson fonts-lmodern libann0
  libavahi-client3 libavahi-common-data libavahi-common3 libcdt5 libcgraph6
  libcups2 libcupsimage2 libdbus-1-3 libgd3 libgs9 libgs9-common libgts-0.7-5
  libgvc6 libgvpr2 libidn11 libijs-0.35 libjbig2dec0 libkpathsea6
  liblab-gamut1 libnspr4 libnss3 libpaper-utils libpaper1 libpathplan4
  libpoppler73 libpotrace0 libptexenc1 libsynctex1 libtexlua52 libtexluajit2
  libxaw7 libxi6 libxmu6 libxpm4 libzzip-0-13 poppler-data preview-latex-style
  t1utils tex-common texlive-base texlive-binaries texlive-lang-greek
  texlive-pictures xdg-utils
Suggested packages:
  ghostscript-x gsfonts graphviz-doc cups-common libgd-tools poppler-utils
  fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic
  | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum
  debhelper perl-tk xpdf-reader | pdf-viewer texlive-fonts-recommended-doc
  texlive-latex-base-doc python-pygments icc-profiles libfile-which-perl
  libspreadsheet-parseexcel-perl texlive-latex-extra-doc
  texlive-latex-recommended-doc texlive-pstricks dot2tex prerex ruby-tcltk
  | libtcltk-ruby texlive-pictures-doc vprerex texlive-science-doc
Recommended packages:
  gsfonts fonts-liberation libcupsfilters1 dbus fonts-droid-fallback
  libgts-bin lmodern tex-gyre tipa texlive-plain-generic ruby
  | ruby-interpreter tk libfile-mimeinfo-perl libnet-dbus-perl
  libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  dvipng fonts-gfs-baskerville fonts-gfs-porson fonts-lmodern ghostscript
  graphviz libann0 libavahi-client3 libavahi-common-data libavahi-common3
  libcdt5 libcgraph6 libcups2 libcupsimage2 libdbus-1-3 libgd3 libgs9
  libgs9-common libgts-0.7-5 libgvc6 libgvpr2 libidn11 libijs-0.35
  libjbig2dec0 libkpathsea6 liblab-gamut1 libnspr4 libnss3 libpaper-utils
  libpaper1 libpathplan4 libpoppler73 libpotrace0 libptexenc1 libsynctex1
  libtexlua52 libtexluajit2 libxaw7 libxi6 libxmu6 libxpm4 libzzip-0-13
  poppler-data preview-latex-style t1utils tex-common texlive-base
  texlive-binaries texlive-fonts-recommended texlive-lang-greek
  texlive-latex-base texlive-latex-extra texlive-latex-recommended
  texlive-pictures texlive-science xdg-utils
0 upgraded, 56 newly installed, 0 to remove and 13 not upgraded.
Need to get 161 MB of archives.
After this operation, 399 MB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 poppler-data all 0.4.8-2 [1,479 kB]
Get:2 http://archive.ubuntu.com/ubuntu bionic/main amd64 tex-common all 6.09 [33.0 kB]
Get:3 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdbus-1-3 amd64 1.12.2-1ubuntu1 [175 kB]
Get:4 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libidn11 amd64 1.33-2.1ubuntu1.1 [45.9 kB]
Get:5 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxpm4 amd64 1:3.5.12-1 [34.0 kB]
Get:6 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgd3 amd64 2.2.5-4ubuntu0.3 [119 kB]
Get:7 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libkpathsea6 amd64 2017.20170613.44572-8ubuntu0.1 [54.9 kB]
Get:8 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libptexenc1 amd64 2017.20170613.44572-8ubuntu0.1 [34.5 kB]
Get:9 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libsynctex1 amd64 2017.20170613.44572-8ubuntu0.1 [41.4 kB]
Get:10 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libtexlua52 amd64 2017.20170613.44572-8ubuntu0.1 [91.2 kB]
Get:11 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libtexluajit2 amd64 2017.20170613.44572-8ubuntu0.1 [230 kB]
Get:12 http://archive.ubuntu.com/ubuntu bionic/main amd64 t1utils amd64 1.41-2 [56.0 kB]
Get:13 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libavahi-common-data amd64 0.7-3.1ubuntu1.2 [22.1 kB]
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Get:16 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libcups2 amd64 2.2.7-1ubuntu2.4 [211 kB]
Get:17 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libcupsimage2 amd64 2.2.7-1ubuntu2.4 [18.6 kB]
Get:18 http://archive.ubuntu.com/ubuntu bionic/main amd64 libijs-0.35 amd64 0.35-13 [15.5 kB]
Get:19 http://archive.ubuntu.com/ubuntu bionic/main amd64 libjbig2dec0 amd64 0.13-6 [55.9 kB]
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Get:21 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgs9-common all 9.26~dfsg+0-0ubuntu0.18.04.8 [5,092 kB]
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Get:25 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpoppler73 amd64 0.62.0-2ubuntu2.8 [799 kB]
Get:26 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpotrace0 amd64 1.14-2 [17.4 kB]
Get:27 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB]
Get:28 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxaw7 amd64 2:1.0.13-1 [173 kB]
Get:29 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxi6 amd64 2:1.7.9-1 [29.2 kB]
Get:30 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libzzip-0-13 amd64 0.13.62-3.1ubuntu0.18.04.1 [26.0 kB]
Get:31 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 texlive-binaries amd64 2017.20170613.44572-8ubuntu0.1 [8,179 kB]
Get:32 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 ghostscript amd64 9.26~dfsg+0-0ubuntu0.18.04.8 [51.2 kB]
Get:33 http://archive.ubuntu.com/ubuntu bionic/universe amd64 dvipng amd64 1.15-1 [78.2 kB]
Get:34 http://archive.ubuntu.com/ubuntu bionic/universe amd64 fonts-gfs-baskerville all 1.1-5 [43.4 kB]
Get:35 http://archive.ubuntu.com/ubuntu bionic/universe amd64 fonts-gfs-porson all 1.1-6 [33.7 kB]
Get:36 http://archive.ubuntu.com/ubuntu bionic/main amd64 fonts-lmodern all 2.004.5-3 [4,551 kB]
Get:37 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libann0 amd64 1.1.2+doc-6 [24.8 kB]
Get:38 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libcdt5 amd64 2.40.1-2 [19.6 kB]
Get:39 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libcgraph6 amd64 2.40.1-2 [40.8 kB]
Get:40 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4 [150 kB]
Get:41 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libpathplan4 amd64 2.40.1-2 [22.6 kB]
Get:42 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libgvc6 amd64 2.40.1-2 [601 kB]
Get:43 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libgvpr2 amd64 2.40.1-2 [169 kB]
Get:44 http://archive.ubuntu.com/ubuntu bionic/universe amd64 liblab-gamut1 amd64 2.40.1-2 [178 kB]
Get:45 http://archive.ubuntu.com/ubuntu bionic/universe amd64 graphviz amd64 2.40.1-2 [601 kB]
Get:46 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpaper-utils amd64 1.1.24+nmu5ubuntu1 [8,170 B]
Get:47 http://archive.ubuntu.com/ubuntu bionic/main amd64 preview-latex-style all 11.91-1ubuntu1 [185 kB]
Get:48 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 xdg-utils all 1.1.2-1ubuntu2.3 [60.7 kB]
Get:49 http://archive.ubuntu.com/ubuntu bionic/main amd64 texlive-base all 2017.20180305-1 [18.7 MB]
Get:50 http://archive.ubuntu.com/ubuntu bionic/universe amd64 texlive-fonts-recommended all 2017.20180305-1 [5,262 kB]
Get:51 http://archive.ubuntu.com/ubuntu bionic/universe amd64 texlive-lang-greek all 2017.20180305-1 [76.3 MB]
Get:52 http://archive.ubuntu.com/ubuntu bionic/main amd64 texlive-latex-base all 2017.20180305-1 [951 kB]
Get:53 http://archive.ubuntu.com/ubuntu bionic/main amd64 texlive-latex-recommended all 2017.20180305-1 [14.9 MB]
Get:54 http://archive.ubuntu.com/ubuntu bionic/universe amd64 texlive-pictures all 2017.20180305-1 [4,026 kB]
Get:55 http://archive.ubuntu.com/ubuntu bionic/universe amd64 texlive-latex-extra all 2017.20180305-2 [10.6 MB]
Get:56 http://archive.ubuntu.com/ubuntu bionic/universe amd64 texlive-science all 2017.20180305-2 [3,077 kB]
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Setting up libgs9-common (9.26~dfsg+0-0ubuntu0.18.04.8) ...
Setting up libxi6:amd64 (2:1.7.9-1) ...
Setting up libkpathsea6:amd64 (2017.20170613.44572-8ubuntu0.1) ...
Setting up libpaper1:amd64 (1.1.24+nmu5ubuntu1) ...

Creating config file /etc/papersize with new version
Setting up libtexlua52:amd64 (2017.20170613.44572-8ubuntu0.1) ...
Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-4) ...
Setting up libpathplan4 (2.40.1-2) ...
Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ...
Setting up liblab-gamut1 (2.40.1-2) ...
Setting up libsynctex1:amd64 (2017.20170613.44572-8ubuntu0.1) ...
Setting up libptexenc1:amd64 (2017.20170613.44572-8ubuntu0.1) ...
Setting up tex-common (6.09) ...
update-language: texlive-base not installed and configured, doing nothing!
Processing triggers for mime-support (3.60ubuntu1) ...
Setting up poppler-data (0.4.8-2) ...
Setting up fonts-gfs-porson (1.1-6) ...
Setting up preview-latex-style (11.91-1ubuntu1) ...
Setting up libnspr4:amd64 (2:4.18-1ubuntu1) ...
Setting up libxmu6:amd64 (2:1.1.2-2) ...
Setting up libjbig2dec0:amd64 (0.13-6) ...
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Setting up fonts-gfs-baskerville (1.1-5) ...
Setting up t1utils (1.41-2) ...
Setting up libijs-0.35:amd64 (0.35-13) ...
Setting up libann0 (1.1.2+doc-6) ...
Setting up libxpm4:amd64 (1:3.5.12-1) ...
Setting up libpotrace0 (1.14-2) ...
Setting up libzzip-0-13:amd64 (0.13.62-3.1ubuntu0.18.04.1) ...
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Setting up libavahi-common-data:amd64 (0.7-3.1ubuntu1.2) ...
Setting up libcgraph6 (2.40.1-2) ...
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Setting up libgvpr2 (2.40.1-2) ...
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Setting up libnss3:amd64 (2:3.35-2ubuntu2.2) ...
Setting up libpoppler73:amd64 (0.62.0-2ubuntu2.8) ...
Setting up libavahi-common3:amd64 (0.7-3.1ubuntu1.2) ...
Setting up libgvc6 (2.40.1-2) ...
Setting up libavahi-client3:amd64 (0.7-3.1ubuntu1.2) ...
Setting up libcups2:amd64 (2.2.7-1ubuntu2.4) ...
Setting up graphviz (2.40.1-2) ...
Setting up libcupsimage2:amd64 (2.2.7-1ubuntu2.4) ...
Setting up libgs9:amd64 (9.26~dfsg+0-0ubuntu0.18.04.8) ...
Setting up ghostscript (9.26~dfsg+0-0ubuntu0.18.04.8) ...
Setting up texlive-binaries (2017.20170613.44572-8ubuntu0.1) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/bibtex.1.gz because associated file /usr/share/man/man1/bibtex.original.1.gz (of link group bibtex) doesn't exist
Setting up texlive-base (2017.20180305-1) ...
tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex
tl-paper: setting paper size for dvipdfmx to letter: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for dvips to letter: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for pdftex to letter: /var/lib/texmf/tex/generic/config/pdftexconfig.tex
tl-paper: setting paper size for xdvi to letter: /var/lib/texmf/xdvi/XDvi-paper
Setting up texlive-fonts-recommended (2017.20180305-1) ...
Setting up texlive-latex-base (2017.20180305-1) ...
Setting up texlive-latex-recommended (2017.20180305-1) ...
Setting up texlive-lang-greek (2017.20180305-1) ...
Setting up texlive-science (2017.20180305-2) ...
Setting up texlive-pictures (2017.20180305-1) ...
Setting up dvipng (1.15-1) ...
Setting up texlive-latex-extra (2017.20180305-2) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...
Processing triggers for tex-common (6.09) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
        This may take some time... done.
Removing intermediate container 0db24babc7b3
 ---> faf1373800b2
Step 39/48 : USER ${NB_USER}
 ---> Running in 7f25251d520b
Removing intermediate container 7f25251d520b
 ---> a5c58d0a1a79
Step 40/48 : RUN pip install "pip<19" && ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"
 ---> Running in 56c95d21c1ef
Collecting pip<19
  Downloading https://files.pythonhosted.org/packages/c2/d7/90f34cb0d83a6c5631cf71dfe64cc1054598c843a92b400e55675cc2ac37/pip-18.1-py2.py3-none-any.whl (1.3MB)
Installing collected packages: pip
  Found existing installation: pip 19.0.3
    Uninstalling pip-19.0.3:
      Successfully uninstalled pip-19.0.3
Successfully installed pip-18.1
Processing /home/jovyan
Collecting antlr4-python3-runtime==4.5.3 (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/6d/a7/13e7b9e14d405974fcdbd4c1eb64864e0c48c98c2d3013f46cff79c370fa/antlr4-python3-runtime-4.5.3.tar.gz (109kB)
Collecting graphviz (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/1f/e2/ef2581b5b86625657afd32030f90cf2717456c1d2b711ba074bf007c0f1a/graphviz-0.10.1-py2.py3-none-any.whl
Collecting ipykernel<4.7 (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/18/c3/76775a650cae2e3d9c033b26153583e61282692d9a3af12a3022d8f0cefa/ipykernel-4.6.1-py3-none-any.whl(104kB)
Requirement already satisfied: ipython in /srv/conda/lib/python3.7/site-packages (from mumot===1.0.0-release->-r requirements.txt (line 1)) (7.4.0)
Requirement already satisfied: ipywidgets in /srv/conda/lib/python3.7/site-packages (from mumot===1.0.0-release->-r requirements.txt (line 1)) (7.4.2)
Collecting matplotlib<3.0 (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/98/06/3236cd45dcdc236b38c4c3d94534af918d1e9321ba9fad34d5cfe321ee11/matplotlib-2.2.4-cp37-cp37m-manylinux1_x86_64.whl (12.8MB)
Collecting networkx (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/f3/f4/7e20ef40b118478191cec0b58c3192f822cace858c19505c7670961b76b2/networkx-2.2.zip (1.7MB)
Collecting notebook<5.5 (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/96/1f/e113875e6b8c8ee0e8c5748bf6fc942a109874adc9ca25248e95cf069803/notebook-5.4.1-py2.py3-none-any.whl (8.0MB)
Collecting pydstool (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/c8/5d/9618268c502d6b38d7cfe9be7e9ee967e77c0416c1660c8dbb0368c8ce29/PyDSTool-0.90.2.tar.gz (957kB)
Collecting pyzmq<17 (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/52/ab/aad6fda6fb247893613629920472770da19bf94af5617852fd49d3047c4b/pyzmq-16.0.4.tar.gz (1.1MB)
Collecting scipy<1.0.0 (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/52/67/d9ef9b5058d4a9e3f0ae641ec151790622cbeb37f157de5773358e2bf3da/scipy-0.19.1.tar.gz (14.1MB)
Collecting sympy<1.3,>=1.1.1 (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/b0/47/54f3a752f3b88b9487f38e5e6b7bb96e0b60286b50fd818999f1ffead0cc/sympy-1.2.tar.gz (5.4MB)
Collecting tornado<5 (from mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/e3/7b/e29ab3d51c8df66922fea216e2bddfcb6430fb29620e5165b16a216e0d3c/tornado-4.5.3.tar.gz (484kB)
Requirement already satisfied: traitlets>=4.1.0 in /srv/conda/lib/python3.7/site-packages (from ipykernel<4.7->mumot===1.0.0-release->-r requirements.txt(line 1)) (4.3.2)
Requirement already satisfied: jupyter-client in /srv/conda/lib/python3.7/site-packages (from ipykernel<4.7->mumot===1.0.0-release->-r requirements.txt (line 1)) (5.2.4)
Requirement already satisfied: setuptools>=18.5 in /srv/conda/lib/python3.7/site-packages (from ipython->mumot===1.0.0-release->-r requirements.txt (line1)) (40.8.0)
Requirement already satisfied: jedi>=0.10 in /srv/conda/lib/python3.7/site-packages (from ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.13.3)
Requirement already satisfied: decorator in /srv/conda/lib/python3.7/site-packages (from ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (4.4.0)
Requirement already satisfied: pickleshare in /srv/conda/lib/python3.7/site-packages (from ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.7.5)
Requirement already satisfied: prompt_toolkit<2.1.0,>=2.0.0 in /srv/conda/lib/python3.7/site-packages (from ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (2.0.9)
Requirement already satisfied: pygments in /srv/conda/lib/python3.7/site-packages (from ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (2.3.1)
Requirement already satisfied: backcall in /srv/conda/lib/python3.7/site-packages (from ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.1.0)
Requirement already satisfied: pexpect in /srv/conda/lib/python3.7/site-packages (from ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (4.6.0)
Requirement already satisfied: widgetsnbextension~=3.4.0 in /srv/conda/lib/python3.7/site-packages (from ipywidgets->mumot===1.0.0-release->-r requirements.txt (line 1)) (3.4.2)
Requirement already satisfied: nbformat>=4.2.0 in /srv/conda/lib/python3.7/site-packages (from ipywidgets->mumot===1.0.0-release->-r requirements.txt (line 1)) (4.4.0)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib<3.0->mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl (61kB)
Collecting numpy>=1.7.1 (from matplotlib<3.0->mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/91/e7/6c780e612d245cca62bc3ba8e263038f7c144a96a54f877f3714a0e8427e/numpy-1.16.2-cp37-cp37m-manylinux1_x86_64.whl (17.3MB)
Collecting kiwisolver>=1.0.1 (from matplotlib<3.0->mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/5c/7e/d6cae2f241ba474a2665f24b480bf4e247036d63939dda2bbc4d2ee5069d/kiwisolver-1.0.1-cp37-cp37m-manylinux1_x86_64.whl (89kB)
Requirement already satisfied: python-dateutil>=2.1 in /srv/conda/lib/python3.7/site-packages (from matplotlib<3.0->mumot===1.0.0-release->-r requirements.txt (line 1)) (2.8.0)
Collecting pytz (from matplotlib<3.0->mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl(510kB)
Collecting cycler>=0.10 (from matplotlib<3.0->mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.10 in /srv/conda/lib/python3.7/site-packages (from matplotlib<3.0->mumot===1.0.0-release->-r requirements.txt (line1)) (1.12.0)
Requirement already satisfied: jupyter-core>=4.4.0 in /srv/conda/lib/python3.7/site-packages (from notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (4.4.0)
Requirement already satisfied: Send2Trash in /srv/conda/lib/python3.7/site-packages (from notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (1.5.0)
Requirement already satisfied: ipython-genutils in /srv/conda/lib/python3.7/site-packages (from notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.2.0)
Requirement already satisfied: nbconvert in /srv/conda/lib/python3.7/site-packages (from notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (5.4.1)
Requirement already satisfied: terminado>=0.8.1 in /srv/conda/lib/python3.7/site-packages (from notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.8.1)
Requirement already satisfied: jinja2 in /srv/conda/lib/python3.7/site-packages (from notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (2.10)
Collecting mpmath>=0.19 (from sympy<1.3,>=1.1.1->mumot===1.0.0-release->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/ca/63/3384ebb3b51af9610086b23ea976e6d27d6d97bf140a76a365bd77a3eb32/mpmath-1.1.0.tar.gz (512kB)
Requirement already satisfied: parso>=0.3.0 in /srv/conda/lib/python3.7/site-packages (from jedi>=0.10->ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.3.4)
Requirement already satisfied: wcwidth in /srv/conda/lib/python3.7/site-packages (from prompt_toolkit<2.1.0,>=2.0.0->ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.1.7)
Requirement already satisfied: ptyprocess>=0.5 in /srv/conda/lib/python3.7/site-packages (from pexpect->ipython->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.6.0)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /srv/conda/lib/python3.7/site-packages (from nbformat>=4.2.0->ipywidgets->mumot===1.0.0-release->-r requirements.txt (line 1)) (3.0.1)
Requirement already satisfied: mistune>=0.8.1 in /srv/conda/lib/python3.7/site-packages (from nbconvert->notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.8.4)
Requirement already satisfied: entrypoints>=0.2.2 in /srv/conda/lib/python3.7/site-packages (from nbconvert->notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.3)
Requirement already satisfied: bleach in /srv/conda/lib/python3.7/site-packages (from nbconvert->notebook<5.5->mumot===1.0.0-release->-r requirements.txt(line 1)) (3.1.0)
Requirement already satisfied: pandocfilters>=1.4.1 in /srv/conda/lib/python3.7/site-packages (from nbconvert->notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (1.4.2)
Requirement already satisfied: testpath in /srv/conda/lib/python3.7/site-packages (from nbconvert->notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.4.2)
Requirement already satisfied: defusedxml in /srv/conda/lib/python3.7/site-packages (from nbconvert->notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.5.0)
Requirement already satisfied: MarkupSafe>=0.23 in /srv/conda/lib/python3.7/site-packages (from jinja2->notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (1.1.1)
Requirement already satisfied: attrs>=17.4.0 in /srv/conda/lib/python3.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->mumot===1.0.0-release->-r requirements.txt (line 1)) (19.1.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /srv/conda/lib/python3.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.14.11)
Requirement already satisfied: webencodings in /srv/conda/lib/python3.7/site-packages (from bleach->nbconvert->notebook<5.5->mumot===1.0.0-release->-r requirements.txt (line 1)) (0.5.1)
jupyterhub 0.9.4 has requirement tornado>=5.0, but you'll have tornado 4.5.3 which is incompatible.
Installing collected packages: antlr4-python3-runtime, graphviz, tornado, ipykernel, pyparsing, numpy, kiwisolver, pytz, cycler, matplotlib, networkx, notebook, scipy, pydstool, pyzmq, mpmath, sympy, mumot
  Running setup.py install for antlr4-python3-runtime: started
    Running setup.py install for antlr4-python3-runtime: finished with status 'done'
  Found existing installation: tornado 6.0.1
    Uninstalling tornado-6.0.1:
      Successfully uninstalled tornado-6.0.1
  Running setup.py install for tornado: started
    Running setup.py install for tornado: finished with status 'done'
  Found existing installation: ipykernel 5.1.0
    Uninstalling ipykernel-5.1.0:
      Successfully uninstalled ipykernel-5.1.0
  Running setup.py install for networkx: started
    Running setup.py install for networkx: finished with status 'done'
  Found existing installation: notebook 5.7.6
    Uninstalling notebook-5.7.6:
      Successfully uninstalled notebook-5.7.6
  Running setup.py install for scipy: started
    Running setup.py install for scipy: finished with status 'error'
    Complete output from command /srv/conda/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-8yecypf1/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-mar73u9i/install-record.txt --single-version-externally-managed --compile:

    Note: if you need reliable uninstall behavior, then install
    with pip instead of using `setup.py install`:

      - `pip install .`       (from a git repo or downloaded source
                               release)
      - `pip install scipy`   (last SciPy release on PyPI)

    lapack_opt_info:
    lapack_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/srv/conda/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    openblas_lapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas not found in ['/srv/conda/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    openblas_clapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas,lapack not found in ['/srv/conda/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries lapack_atlas not found in /srv/conda/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /srv/conda/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE

    atlas_3_10_info:
    customize UnixCCompiler
      libraries lapack_atlas not found in /srv/conda/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /srv/conda/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries lapack_atlas not found in /srv/conda/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /srv/conda/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
    customize UnixCCompiler
      libraries lapack_atlas not found in /srv/conda/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /srv/conda/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    accelerate_info:
      NOT AVAILABLE

    /srv/conda/lib/python3.7/site-packages/numpy/distutils/system_info.py:638: UserWarning:
        Atlas (http://math-atlas.sourceforge.net/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [atlas]) or by setting
        the ATLAS environment variable.
      self.calc_info()
    lapack_info:
    customize UnixCCompiler
      libraries lapack not found in ['/srv/conda/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    /srv/conda/lib/python3.7/site-packages/numpy/distutils/system_info.py:638: UserWarning:
        Lapack (http://www.netlib.org/lapack/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [lapack]) or by setting
        the LAPACK environment variable.
      self.calc_info()
    lapack_src_info:
      NOT AVAILABLE

    /srv/conda/lib/python3.7/site-packages/numpy/distutils/system_info.py:638: UserWarning:
        Lapack (http://www.netlib.org/lapack/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [lapack_src]) or by setting
        the LAPACK_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE

    Running from scipy source directory.
    non-existing path in 'scipy/integrate': 'quadpack.h'
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-8yecypf1/scipy/setup.py", line 416, in <module>
        setup_package()
      File "/tmp/pip-install-8yecypf1/scipy/setup.py", line 412, in setup_package
        setup(**metadata)
      File "/srv/conda/lib/python3.7/site-packages/numpy/distutils/core.py", line 137, in setup
        config = configuration()
      File "/tmp/pip-install-8yecypf1/scipy/setup.py", line 336, in configuration
        config.add_subpackage('scipy')
      File "/srv/conda/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 1036, in add_subpackage
        caller_level = 2)
      File "/srv/conda/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 1005, in get_subpackage
        caller_level = caller_level + 1)
      File "/srv/conda/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 942, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/setup.py", line 15, in configuration
        config.add_subpackage('linalg')
      File "/srv/conda/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 1036, in add_subpackage
        caller_level = 2)
      File "/srv/conda/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 1005, in get_subpackage
        caller_level = caller_level + 1)
      File "/srv/conda/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 942, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/linalg/setup.py", line 20, in configuration
        raise NotFoundError('no lapack/blas resources found')
    numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

    ----------------------------------------
Command "/srv/conda/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-8yecypf1/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-mar73u9i/install-record.txt--single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-8yecypf1/scipy/
You are using pip version 18.1, however version 19.0.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Removing intermediate container 56c95d21c1ef
The command '/bin/sh -c pip install "pip<19" && ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"' returned a non-zero code: 1
DiODeProject / MuMoT

MyBinder build failing #313
