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Current RStudio version does not support R 4.1.0 graphics engine #1041

Closed
fkohrt opened this issue May 21, 2021 · 12 comments · Fixed by #1104
Closed

Current RStudio version does not support R 4.1.0 graphics engine #1041

fkohrt opened this issue May 21, 2021 · 12 comments · Fixed by #1104

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@fkohrt
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fkohrt commented May 21, 2021 •
edited
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Bug description

RStudio v1.2.5001 does not support the R graphics engine v14 that comes with R v4.1.0 ("Camp Pontanezen") (see release notes).

Expected behaviour

No warning message.

Actual behaviour

Warning message:
R graphics engine version 14 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.

How to reproduce

  1. Binder (source repo)
  2. Enter R.version.string (leading R version 4.1.0 (2021-05-18))
  3. Get warning message

Your personal set up

Using mybinder.org.

Related information

See also rstudio/rstudio#8383.
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@manics
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manics commented May 24, 2021

Is it just a case of updating to the latest RStudio version? Or are there likely to be hidden problems if we do that?

@fkohrt
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fkohrt commented May 25, 2021 •
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I don't know enough about the various ways in which people use repo2docker and RStudio and how much they depend on specific versions of RStudio installed. But in general I'd say it would be best to keep the versions of R and RStudio roughly in sync (see also "Older Versions of RStudio"). So a backwards compatible way might be to install different versions of RStudio depending on the requested version of R?

@psymeg
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psymeg commented Jun 25, 2021

I have the same issue with RStudio v 1.3.1093 running on Debian Buster. A workaround is to call x11() first.

@meeseeksmachine
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This issue has been mentioned on Jupyter Community Forum. There might be relevant details there:

https://discourse.jupyter.org/t/plots-are-not-showing-in-rstudio-using-binderhub/10297/5

@choldgraf
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Just a note that upgrading RStudio might not solve the problem because it may introduce a bug. Has anybody else been able to use RStudio 4.1 on a BinderHub successfully?

I think there is a bug in the latest RStudio that I think makes it unable to work with JupyterHub:

rstudio/rstudio#8888

Unfortunately the RStudio team has put this bug on a 2022 milestone that has 1000 other issues, so I worry that this will not be fixed soon.

@fkohrt
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fkohrt commented Sep 24, 2021

Has anybody else been able to use RStudio 4.1 on a BinderHub successfully?

@choldgraf Not sure if you mean this, but see bug #1077, where RStudio runs on R 4.1

@meeseeksmachine
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This issue has been mentioned on Jupyter Community Forum. There might be relevant details there:

https://discourse.jupyter.org/t/psa-latest-rstudio-will-not-work-with-jupyterhub-or-binder-use-r-version-4-0/10957/1

Robinlovelace added a commit to geocompx/geocompr that referenced this issue Sep 24, 2021
@Robinlovelace
Update binder - #570
8fb4983 
See also jupyterhub/repo2docker#1041 and rstudio/rstudio#8888 and jupyterhub/jupyter-rsession-proxy#97
@Robinlovelace Robinlovelace mentioned this issue Sep 25, 2021
Closed
@manics manics mentioned this issue Nov 29, 2021
Closed
@yuvipanda yuvipanda mentioned this issue Jan 5, 2022
Merged
5 tasks
@yuvipanda
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Should be fixed by #1104

@fkohrt
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fkohrt commented Jan 23, 2022 •
edited
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Unfortunately, the repository does not build at all anymore: Binder

Build logs 
Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerkmdpmfyn'...
HEAD is now at f5d8582 Update to R 4.0
Building conda environment for python=3.7Using RBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/67 : FROM buildpack-deps:bionic
 ---> cb3fc72df6ea
Step 2/67 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> e8f399a11afd
Step 3/67 : 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
 ---> 5e20c71ac1f6
Step 4/67 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 41fb2019d865
Step 5/67 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 737e71e4cbb0
Step 6/67 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> fa196281cd86
Step 7/67 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> bbd0c4c7e9c6
Step 8/67 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 33e5f28f2cb0
Step 9/67 : ARG NB_USER
 ---> Using cache
 ---> 72bacbbabdbd
Step 10/67 : ARG NB_UID
 ---> Using cache
 ---> 50a4f41f21f4
Step 11/67 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 363ff1d22f0c
Step 12/67 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 406d357423cf
Step 13/67 : 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
 ---> c2ca09368c43
Step 14/67 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> a77657426295
Step 15/67 : RUN apt-get -qq update &&     apt-get -qq install --yes        libapparmor1        lsb-release        psmisc        sudo        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 0ef41d20d440
�[91mdebconf: delaying package configuration, since apt-utils is not installed
�[0mRemoving intermediate container 0ef41d20d440
 ---> 984530202b22
Step 16/67 : EXPOSE 8888
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in f64e85fb0a7e
Removing intermediate container f64e85fb0a7e
 ---> 0444dc5e6f5b
Step 17/67 : ENV APP_BASE /srv
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 05ca50b2c8ec
Removing intermediate container 05ca50b2c8ec
 ---> dff338947e08
Step 18/67 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 8c5e709501de
Removing intermediate container 8c5e709501de
 ---> 2fe862e97842
Step 19/67 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 0a39e4c6cd0f
Removing intermediate container 0a39e4c6cd0f
 ---> bd9c1765d808
Step 20/67 : ENV NPM_DIR ${APP_BASE}/npm
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 156b8ad725b1
Removing intermediate container 156b8ad725b1
 ---> 737269a90225
Step 21/67 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 019daa3ecdc4
Removing intermediate container 019daa3ecdc4
 ---> 1714a04c274d
Step 22/67 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 920d53d08876
Removing intermediate container 920d53d08876
 ---> 0a7e1dec9179
Step 23/67 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in c59ac20d7c4a
Removing intermediate container c59ac20d7c4a
 ---> 2ca02cd550d8
Step 24/67 : ENV R_LIBS_USER ${APP_BASE}/rlibs
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in c970d916a756
Removing intermediate container c970d916a756
 ---> 753a8b90f8c3
Step 25/67 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:/usr/lib/rstudio-server/bin/:${PATH}
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 8cf88dd59d3c
Removing intermediate container 8cf88dd59d3c
 ---> b74115f6dbbb
Step 26/67 : 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
 ---> bf3034943bab
Step 27/67 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
 ---> bc4596abf8c6
Step 28/67 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> 00e4175b61aa
Step 29/67 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in d37b939f410e
�[91m++ dirname /tmp/install-miniforge.bash
�[0m�[91m+ cd /tmp
�[0m�[91m+ MINIFORGE_VERSION=4.9.2-2
+ MAMBA_VERSION=0.7.4
+ SHA256SUM=7a7bfaff87680298304a97ba69bcf92f66c810995a7155a2918b99fafb8ca1dc
+ URL=https://github.com/conda-forge/miniforge/releases/download/4.9.2-2/Mambaforge-4.9.2-2-Linux-x86_64.sh
+ INSTALLER_PATH=/tmp/miniforge-installer.sh
�[0m�[91m+ unset HOME
+ wget --quiet https://github.com/conda-forge/miniforge/releases/download/4.9.2-2/Mambaforge-4.9.2-2-Linux-x86_64.sh -O /tmp/miniforge-installer.sh
�[0m�[91mtime: 3.393
+ chmod +x /tmp/miniforge-installer.sh
�[0m�[91m+ echo '7a7bfaff87680298304a97ba69bcf92f66c810995a7155a2918b99fafb8ca1dc  /tmp/miniforge-installer.sh'
�[0m�[91m+ sha256sum --quiet -c -
�[0m�[91m+ bash /tmp/miniforge-installer.sh -b -p /srv/conda
�[0mPREFIX=/srv/conda
Unpacking payload ...
�[91m
  0%|          | 0/57 [00:00<?, ?it/s]�[0m�[91m
Extracting : _libgcc_mutex-0.1-conda_forge.tar.bz2:   0%|          | 0/57 [00:00<?, ?it/s]�[0m�[91m
Extracting : conda-4.9.2-py38h578d9bd_0.tar.bz2:   2%|â–�         | 1/57 [00:00<00:40,  1.38it/s]�[0m�[91m
Extracting : conda-4.9.2-py38h578d9bd_0.tar.bz2:   4%|â–Ž         | 2/57 [00:00<00:19,  2.77it/s]�[0m�[91m
Extracting : icu-67.1-he1b5a44_0.tar.bz2:   4%|â–Ž         | 2/57 [00:02<00:19,  2.77it/s]       �[0m�[91m
Extracting : icu-67.1-he1b5a44_0.tar.bz2:   5%|▌         | 3/57 [00:02<00:40,  1.32it/s]�[0m�[91m
Extracting : wheel-0.36.1-pyhd3deb0d_0.tar.bz2:   5%|▌         | 3/57 [00:02<00:40,  1.32it/s]�[0m�[91m
Extracting : brotlipy-0.7.0-py38h8df0ef7_1001.tar.bz2:   7%|â–‹         | 4/57 [00:02<00:40,  1.32it/s]�[0m�[91m
Extracting : libstdcxx-ng-9.3.0-h2ae2ef3_17.tar.bz2:   9%|â–‰         | 5/57 [00:02<00:39,  1.32it/s]  �[0m�[91m
Extracting : readline-8.0-he28a2e2_2.tar.bz2:  11%|â–ˆ         | 6/57 [00:02<00:38,  1.32it/s]       �[0m�[91m
Extracting : libnghttp2-1.41.0-h8cfc5f6_2.tar.bz2:  12%|█�        | 7/57 [00:02<00:37,  1.32it/s]
Extracting : tk-8.6.10-hed695b0_1.tar.bz2:  14%|█�        | 8/57 [00:02<00:37,  1.32it/s]        
Extracting : libgomp-9.3.0-h5dbcf3e_17.tar.bz2:  16%|█▌        | 9/57 [00:02<00:36,  1.32it/s]
Extracting : bzip2-1.0.8-h7f98852_4.tar.bz2:  18%|█▊        | 10/57 [00:02<00:35,  1.32it/s]  
Extracting : c-ares-1.17.1-h36c2ea0_0.tar.bz2:  19%|█▉        | 11/57 [00:02<00:34,  1.32it/s]
Extracting : ca-certificates-2020.12.5-ha878542_0.tar.bz2:  21%|██        | 12/57 [00:02<00:34,  1.32it/s]
Extracting : reproc-cpp-14.2.1-h58526e2_0.tar.bz2:  23%|██▎       | 13/57 [00:02<00:33,  1.32it/s]        
Extracting : idna-2.10-pyh9f0ad1d_0.tar.bz2:  25%|██�       | 14/57 [00:02<00:32,  1.32it/s]      
Extracting : chardet-3.0.4-py38h924ce5b_1008.tar.bz2:  26%|██▋       | 15/57 [00:02<00:31,  1.32it/s]
Extracting : zstd-1.4.5-h6597ccf_2.tar.bz2:  28%|██▊       | 16/57 [00:02<00:31,  1.32it/s]          
Extracting : lz4-c-1.9.2-he1b5a44_3.tar.bz2:  30%|██▉       | 17/57 [00:02<00:30,  1.32it/s]
Extracting : setuptools-49.6.0-py38h924ce5b_2.tar.bz2:  32%|███�      | 18/57 [00:02<00:29,  1.32it/s]
Extracting : conda-package-handling-1.7.2-py38h8df0ef7_0.tar.bz2:  33%|███▎      | 19/57 [00:02<00:28,  1.32it/s]
Extracting : libffi-3.3-h58526e2_1.tar.bz2:  35%|███▌      | 20/57 [00:02<00:28,  1.32it/s]                      
Extracting : libedit-3.1.20191231-he28a2e2_2.tar.bz2:  37%|███▋      | 21/57 [00:02<00:27,  1.32it/s]�[0m�[91m
Extracting : yaml-0.2.5-h516909a_0.tar.bz2:  39%|███▊      | 22/57 [00:02<00:26,  1.32it/s]          �[0m�[91m
Extracting : libarchive-3.3.3-hddc7a2b_1008.tar.bz2:  40%|████      | 23/57 [00:02<00:25,  1.32it/s]�[0m�[91m
Extracting : pip-20.3.1-pyhd8ed1ab_0.tar.bz2:  42%|████�     | 24/57 [00:02<00:25,  1.32it/s]       �[0m�[91m
Extracting : libgcc-ng-9.3.0-h5dbcf3e_17.tar.bz2:  44%|████�     | 25/57 [00:02<00:24,  1.32it/s]�[0m�[91m
Extracting : libgcc-ng-9.3.0-h5dbcf3e_17.tar.bz2:  46%|████▌     | 26/57 [00:02<00:16,  1.86it/s]�[0m�[91m
Extracting : mamba-0.7.4-py38h4c9354d_0.tar.bz2:  46%|████▌     | 26/57 [00:02<00:16,  1.86it/s] �[0m�[91m
Extracting : python_abi-3.8-1_cp38.tar.bz2:  47%|████▋     | 27/57 [00:02<00:16,  1.86it/s]     �[0m�[91m
Extracting : xz-5.2.5-h516909a_1.tar.bz2:  49%|████▉     | 28/57 [00:02<00:15,  1.86it/s]  �[0m�[91m
Extracting : zlib-1.2.11-h516909a_1010.tar.bz2:  51%|█████     | 29/57 [00:02<00:15,  1.86it/s]�[0m�[91m
Extracting : cffi-1.14.4-py38ha65f79e_1.tar.bz2:  53%|█████▎    | 30/57 [00:02<00:14,  1.86it/s]�[0m�[91m
Extracting : pyopenssl-20.0.0-pyhd8ed1ab_0.tar.bz2:  54%|█████�    | 31/57 [00:02<00:13,  1.86it/s]�[0m�[91m
Extracting : urllib3-1.25.11-py_0.tar.bz2:  56%|█████▌    | 32/57 [00:02<00:13,  1.86it/s]         �[0m�[91m
Extracting : six-1.15.0-pyh9f0ad1d_0.tar.bz2:  58%|█████▊    | 33/57 [00:02<00:12,  1.86it/s]�[0m�[91m
Extracting : python-3.8.6-hffdb5ce_1_cpython.tar.bz2:  60%|█████▉    | 34/57 [00:06<00:12,  1.86it/s]
Extracting : python-3.8.6-hffdb5ce_1_cpython.tar.bz2:  61%|██████�   | 35/57 [00:06<00:10,  2.06it/s]�[0m�[91m
Extracting : ld_impl_linux-64-2.35.1-hed1e6ac_0.tar.bz2:  61%|██████�   | 35/57 [00:06<00:10,  2.06it/s]�[0m�[91m
Extracting : libssh2-1.9.0-hab1572f_5.tar.bz2:  63%|██████▎   | 36/57 [00:06<00:10,  2.06it/s]          �[0m�[91m
Extracting : ncurses-6.2-h58526e2_4.tar.bz2:  65%|██████�   | 37/57 [00:06<00:09,  2.06it/s]  �[0m�[91m
Extracting : libcurl-7.71.1-hcdd3856_8.tar.bz2:  67%|██████▋   | 38/57 [00:06<00:09,  2.06it/s]�[0m�[91m
Extracting : libev-4.33-h516909a_1.tar.bz2:  68%|██████▊   | 39/57 [00:06<00:08,  2.06it/s]    �[0m�[91m
Extracting : pycparser-2.20-pyh9f0ad1d_2.tar.bz2:  70%|███████   | 40/57 [00:06<00:08,  2.06it/s]�[0m�[91m
Extracting : certifi-2020.12.5-py38h578d9bd_0.tar.bz2:  72%|███████�  | 41/57 [00:06<00:07,  2.06it/s]�[0m�[91m
Extracting : krb5-1.17.2-h926e7f8_0.tar.bz2:  74%|███████▎  | 42/57 [00:06<00:07,  2.06it/s]          �[0m�[91m
Extracting : requests-2.25.0-pyhd3deb0d_0.tar.bz2:  75%|███████▌  | 43/57 [00:06<00:06,  2.06it/s]
Extracting : pysocks-1.7.1-py38h924ce5b_2.tar.bz2:  77%|███████▋  | 44/57 [00:06<00:06,  2.06it/s]
Extracting : ruamel_yaml-0.15.80-py38h8df0ef7_1003.tar.bz2:  79%|███████▉  | 45/57 [00:06<00:05,  2.06it/s]
Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2:  81%|████████  | 46/57 [00:06<00:05,  2.06it/s]              
Extracting : sqlite-3.34.0-h74cdb3f_0.tar.bz2:  82%|████████� | 47/57 [00:06<00:04,  2.06it/s]
Extracting : pycosat-0.6.3-py38h8df0ef7_1005.tar.bz2:  84%|████████� | 48/57 [00:06<00:04,  2.06it/s]
Extracting : tqdm-4.54.1-pyhd8ed1ab_0.tar.bz2:  86%|████████▌ | 49/57 [00:06<00:03,  2.06it/s]       
Extracting : libxml2-2.9.10-h68273f3_2.tar.bz2:  88%|████████▊ | 50/57 [00:06<00:03,  2.06it/s]
Extracting : libsolv-0.7.16-h8b12597_0.tar.bz2:  89%|████████▉ | 51/57 [00:06<00:02,  2.06it/s]�[0m�[91m
Extracting : openssl-1.1.1h-h516909a_0.tar.bz2:  91%|█████████ | 52/57 [00:06<00:02,  2.06it/s]�[0m�[91m
Extracting : reproc-14.2.1-h36c2ea0_0.tar.bz2:  93%|█████████▎| 53/57 [00:06<00:01,  2.06it/s] �[0m�[91m
Extracting : libiconv-1.16-h516909a_0.tar.bz2:  95%|█████████�| 54/57 [00:06<00:01,  2.06it/s]�[0m�[91m
Extracting : lzo-2.10-h516909a_1000.tar.bz2:  96%|█████████▋| 55/57 [00:06<00:00,  2.06it/s]  
Extracting : cryptography-3.2.1-py38h7699a38_0.tar.bz2:  98%|█████████▊| 56/57 [00:06<00:00,  2.06it/s]
                                                                                                       �[0m�[91m
�[0mCollecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /srv/conda

  added / updated specs:
    - _libgcc_mutex==0.1=conda_forge
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py38h8df0ef7_1001
    - bzip2==1.0.8=h7f98852_4
    - c-ares==1.17.1=h36c2ea0_0
    - ca-certificates==2020.12.5=ha878542_0
    - certifi==2020.12.5=py38h578d9bd_0
    - cffi==1.14.4=py38ha65f79e_1
    - chardet==3.0.4=py38h924ce5b_1008
    - conda-package-handling==1.7.2=py38h8df0ef7_0
    - conda==4.9.2=py38h578d9bd_0
    - cryptography==3.2.1=py38h7699a38_0
    - icu==67.1=he1b5a44_0
    - idna==2.10=pyh9f0ad1d_0
    - krb5==1.17.2=h926e7f8_0
    - ld_impl_linux-64==2.35.1=hed1e6ac_0
    - libarchive==3.3.3=hddc7a2b_1008
    - libcurl==7.71.1=hcdd3856_8
    - libedit==3.1.20191231=he28a2e2_2
    - libev==4.33=h516909a_1
    - libffi==3.3=h58526e2_1
    - libgcc-ng==9.3.0=h5dbcf3e_17
    - libgomp==9.3.0=h5dbcf3e_17
    - libiconv==1.16=h516909a_0
    - libnghttp2==1.41.0=h8cfc5f6_2
    - libsolv==0.7.16=h8b12597_0
    - libssh2==1.9.0=hab1572f_5
    - libstdcxx-ng==9.3.0=h2ae2ef3_17
    - libxml2==2.9.10=h68273f3_2
    - lz4-c==1.9.2=he1b5a44_3
    - lzo==2.10=h516909a_1000
    - mamba==0.7.4=py38h4c9354d_0
    - ncurses==6.2=h58526e2_4
    - openssl==1.1.1h=h516909a_0
    - pip==20.3.1=pyhd8ed1ab_0
    - pycosat==0.6.3=py38h8df0ef7_1005
    - pycparser==2.20=pyh9f0ad1d_2
    - pyopenssl==20.0.0=pyhd8ed1ab_0
    - pysocks==1.7.1=py38h924ce5b_2
    - python==3.8.6=hffdb5ce_1_cpython
    - python_abi==3.8=1_cp38
    - readline==8.0=he28a2e2_2
    - reproc-cpp==14.2.1=h58526e2_0
    - reproc==14.2.1=h36c2ea0_0
    - requests==2.25.0=pyhd3deb0d_0
    - ruamel_yaml==0.15.80=py38h8df0ef7_1003
    - setuptools==49.6.0=py38h924ce5b_2
    - six==1.15.0=pyh9f0ad1d_0
    - sqlite==3.34.0=h74cdb3f_0
    - tk==8.6.10=hed695b0_1
    - tqdm==4.54.1=pyhd8ed1ab_0
    - urllib3==1.25.11=py_0
    - wheel==0.36.1=pyhd3deb0d_0
    - xz==5.2.5=h516909a_1
    - yaml==0.2.5=h516909a_0
    - zlib==1.2.11=h516909a_1010
    - zstd==1.4.5=h6597ccf_2


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  brotlipy           conda-forge/linux-64::brotlipy-0.7.0-py38h8df0ef7_1001
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.17.1-h36c2ea0_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
  certifi            conda-forge/linux-64::certifi-2020.12.5-py38h578d9bd_0
  cffi               conda-forge/linux-64::cffi-1.14.4-py38ha65f79e_1
  chardet            conda-forge/linux-64::chardet-3.0.4-py38h924ce5b_1008
  conda              conda-forge/linux-64::conda-4.9.2-py38h578d9bd_0
  conda-package-han~ conda-forge/linux-64::conda-package-handling-1.7.2-py38h8df0ef7_0
  cryptography       conda-forge/linux-64::cryptography-3.2.1-py38h7699a38_0
  icu                conda-forge/linux-64::icu-67.1-he1b5a44_0
  idna               conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
  krb5               conda-forge/linux-64::krb5-1.17.2-h926e7f8_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35.1-hed1e6ac_0
  libarchive         conda-forge/linux-64::libarchive-3.3.3-hddc7a2b_1008
  libcurl            conda-forge/linux-64::libcurl-7.71.1-hcdd3856_8
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_1
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h5dbcf3e_17
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h5dbcf3e_17
  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
  libnghttp2         conda-forge/linux-64::libnghttp2-1.41.0-h8cfc5f6_2
  libsolv            conda-forge/linux-64::libsolv-0.7.16-h8b12597_0
  libssh2            conda-forge/linux-64::libssh2-1.9.0-hab1572f_5
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h2ae2ef3_17
  libxml2            conda-forge/linux-64::libxml2-2.9.10-h68273f3_2
  lz4-c              conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_3
  lzo                conda-forge/linux-64::lzo-2.10-h516909a_1000
  mamba              conda-forge/linux-64::mamba-0.7.4-py38h4c9354d_0
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  openssl            conda-forge/linux-64::openssl-1.1.1h-h516909a_0
  pip                conda-forge/noarch::pip-20.3.1-pyhd8ed1ab_0
  pycosat            conda-forge/linux-64::pycosat-0.6.3-py38h8df0ef7_1005
  pycparser          conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
  pyopenssl          conda-forge/noarch::pyopenssl-20.0.0-pyhd8ed1ab_0
  pysocks            conda-forge/linux-64::pysocks-1.7.1-py38h924ce5b_2
  python             conda-forge/linux-64::python-3.8.6-hffdb5ce_1_cpython
  python_abi         conda-forge/linux-64::python_abi-3.8-1_cp38
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  reproc             conda-forge/linux-64::reproc-14.2.1-h36c2ea0_0
  reproc-cpp         conda-forge/linux-64::reproc-cpp-14.2.1-h58526e2_0
  requests           conda-forge/noarch::requests-2.25.0-pyhd3deb0d_0
  ruamel_yaml        conda-forge/linux-64::ruamel_yaml-0.15.80-py38h8df0ef7_1003
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py38h924ce5b_2
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  sqlite             conda-forge/linux-64::sqlite-3.34.0-h74cdb3f_0
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_1
  tqdm               conda-forge/noarch::tqdm-4.54.1-pyhd8ed1ab_0
  urllib3            conda-forge/noarch::urllib3-1.25.11-py_0
  wheel              conda-forge/noarch::wheel-0.36.1-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  yaml               conda-forge/linux-64::yaml-0.2.5-h516909a_0
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010
  zstd               conda-forge/linux-64::zstd-1.4.5-h6597ccf_2


Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
�[91mtime: 12.328
�[0m�[91m+ export PATH=/srv/conda/bin:/srv/conda/envs/notebook/bin:/srv/conda/bin:/srv/npm/bin:/usr/lib/rstudio-server/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ PATH=/srv/conda/bin:/srv/conda/envs/notebook/bin:/srv/conda/bin:/srv/npm/bin:/usr/lib/rstudio-server/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ conda config --system --append channels defaults
�[0m�[91m+ conda config --system --set auto_update_conda false
�[0m�[91m+ conda config --system --set show_channel_urls true
�[0m�[91m+ echo 'update_dependencies: false'
+ conda config --system --set channel_priority flexible
�[0m�[91m+ mamba install -y mamba==0.7.4
�[0mpkgs/main/noarch          
pkgs/r/linux-64           
pkgs/r/noarch             
pkgs/main/linux-64        
conda-forge/noarch        
conda-forge/linux-64      
Transaction

  Prefix: /srv/conda

  Updating specs:

   - mamba==0.7.4



                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔��██╗████╗ ████║██╔��██╗██╔��██╗
        ██╔████╔██║███████║██╔████╔██║██████╔�███████║
        ██║╚██╔�██║██╔��██║██║╚██╔�██║██╔��██╗██╔��██║
        ██║ ╚�� ██║██║  ██║██║ ╚�� ██║██████╔�██║  ██║
        ╚��     ╚��╚��  ╚��╚��     ╚��╚������ ╚��  ╚��

        mamba (0.7.4) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['mamba==0.7.4']

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
  Package             Version  Build           Channel                    Size
────────────────────────────────────────────────────────────────────────────────
  Upgrade:
────────────────────────────────────────────────────────────────────────────────

  ca-certificates   2020.12.5  ha878542_0      installed                      
  ca-certificates  2021.10.26  h06a4308_2      pkgs/main/linux-64       115 KB
  certifi           2020.12.5  py38h578d9bd_0  installed                      
  certifi           2021.10.8  py38h578d9bd_1  conda-forge/linux-64     145 KB
  openssl              1.1.1h  h516909a_0      installed                      
  openssl              1.1.1m  h7f8727e_0      pkgs/main/linux-64         3 MB

  Summary:

  Upgrade: 3 packages

  Total download: 3 MB

────────────────────────────────────────────────────────────────────────────────

ca-certificates           Finished ca-certificates                      (00m:00s)             115 KB    440 KB/s
certifi                   Finished certifi                              (00m:00s)             145 KB    550 KB/s
openssl                   Finished openssl                              (00m:00s)               3 MB      8 MB/s
�[91mtime: 15.713
+ echo 'installing notebook env:'
+ cat /tmp/env/environment.lock
�[0minstalling notebook env:
# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
# Frozen on 2021-12-23 13:53:23 UTC
# Generated by conda-lock.
# platform: linux-64
# input_hash: 9e31218e2091d124575e4f0e9b6f8dd8ad5df70cbdd1c0763e318d8932286afe
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2021.10.8-ha878542_0.tar.bz2#575611b8a84f45960e87722eeb51fa26
https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2#bd4f2e711b39af170e7ff15163fe87ee
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-11.2.0-he4da1e4_11.tar.bz2#0bf83958e788f1e75ba26154cb702afe
https://conda.anaconda.org/conda-forge/linux-64/pandoc-2.16.2-h7f98852_0.tar.bz2#a33b21929f07f2d64f41a0e8593f16f0
https://conda.anaconda.org/conda-forge/linux-64/libgomp-11.2.0-h1d223b6_11.tar.bz2#1d16527c76842bf9c41e9399d39d8097
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-1_gnu.tar.bz2#561e277319a41d4f24f5c05a9ef63c04
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-11.2.0-h1d223b6_11.tar.bz2#e3495f4f93cfd6b68021cbe2b5844cd5
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2#f26ef8098fab1f719c91eb760d63381a
https://conda.anaconda.org/conda-forge/linux-64/icu-68.2-h9c3ff4c_0.tar.bz2#6618c9b191638993f2a818c6529e1b49
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.18-h36c2ea0_1.tar.bz2#c3788462a6fbddafdb413a9f9053e58d
https://conda.anaconda.org/conda-forge/linux-64/libuv-1.42.0-h7f98852_0.tar.bz2#5b3e8d9da3e6a68a0e945c37eef6b472
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.11-h36c2ea0_1013.tar.bz2#dcddf696ff5dfcab567100d691678e18
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.2-h58526e2_4.tar.bz2#509f2a21c4a09214cd737a480dfd80c9
https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1l-h7f98852_0.tar.bz2#de7b38a1542dbe6f41653a8ae71adc53
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.5-h516909a_1.tar.bz2#33f601066901f3e1a85af3522a8113f9
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
https://conda.anaconda.org/conda-forge/linux-64/readline-8.1-h46c0cb4_0.tar.bz2#5788de3c8d7a7d64ac56c784c4ef48e6
https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.11-h36c2ea0_1013.tar.bz2#cf7190238072a41e9579e4476a6a60b8
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.43.0-h812cca2_1.tar.bz2#d0a7846b7b3b8fb0d8b36904a53b8155
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-ha56f1ee_2.tar.bz2#6ab4eaa11ff01801cffca0a27489dc04
https://conda.anaconda.org/conda-forge/linux-64/nodejs-14.17.4-h92b4a50_0.tar.bz2#e6e81754fbab03fcc3cde8aff8545467
https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.37.0-h9cd32fc_0.tar.bz2#eb66fc098824d25518a79e83d12a81d6
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.11-h27826a3_1.tar.bz2#84e76fb280e735fec1efd2d21fd9cb27
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.19.2-hcc1bbae_3.tar.bz2#e29650992ae593bc05fc93722483e5c3
https://conda.anaconda.org/conda-forge/linux-64/python-3.7.12-hb7a2778_100_cpython.tar.bz2#2d94b3e6a9fdaf83f6955d008c8011a7
https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12
https://conda.anaconda.org/conda-forge/noarch/attrs-21.2.0-pyhd8ed1ab_0.tar.bz2#d2e1c7f388ac403df7079b411c37cc50
https://conda.anaconda.org/conda-forge/noarch/backcall-0.2.0-pyh9f0ad1d_0.tar.bz2#6006a6d08a3fa99268a2681c7fb55213
https://conda.anaconda.org/conda-forge/noarch/backports-1.0-py_2.tar.bz2#0da16b293affa6ac31812376f8eb79dd
https://conda.anaconda.org/conda-forge/noarch/blinker-1.4-py_1.tar.bz2#fa509a09190583f869ae442bf4d17f5f
https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-2.0.9-pyhd8ed1ab_0.tar.bz2#a57a3f6f2b0a7400e340f850c405df19
https://conda.anaconda.org/conda-forge/noarch/decorator-5.1.0-pyhd8ed1ab_0.tar.bz2#71b13ba2e0efcff45646f05d619534b0
https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2#961b3a227b437d82ad7054484cfa71b2
https://conda.anaconda.org/conda-forge/noarch/entrypoints-0.3-pyhd8ed1ab_1003.tar.bz2#bbf9a201f6ce99a506f4955374d9a9f4
https://conda.anaconda.org/conda-forge/noarch/idna-3.1-pyhd3deb0d_0.tar.bz2#9c9aea4b8391264477df484f798562d0
https://conda.anaconda.org/conda-forge/noarch/ipython_genutils-0.2.0-py_1.tar.bz2#5071c982548b3a20caf70462f04f5287
https://conda.anaconda.org/conda-forge/noarch/json5-0.9.5-pyh9f0ad1d_0.tar.bz2#10759827a94e6b14996e81fb002c0bda
https://conda.anaconda.org/conda-forge/noarch/jupyterlab_widgets-1.0.2-pyhd8ed1ab_0.tar.bz2#eaff56fe28d1236076aa3bb13c35b434
https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.80.0-h2574ce0_0.tar.bz2#5d0784b790350f7939bb5d3f2c32e700
https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.5.4-pyhd8ed1ab_0.tar.bz2#0d86e4e6ac78912f3f47e0453b124aca
https://conda.anaconda.org/conda-forge/noarch/pamela-1.0.0-py_0.tar.bz2#36f6f18d2f3ae0c93d77a9dbedad08c3
https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.tar.bz2#457c2c8c08e54905d6954e79cb5b5db9
https://conda.anaconda.org/conda-forge/noarch/parso-0.8.3-pyhd8ed1ab_0.tar.bz2#17a565a0c3899244e938cdf417e7b094
https://conda.anaconda.org/conda-forge/noarch/pickleshare-0.7.5-py_1003.tar.bz2#415f0ebb6198cc2801c73438a9fb5761
https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.12.0-pyhd8ed1ab_0.tar.bz2#d7b366cccdf2c1e8ebdddbfff7c2ba00
https://conda.anaconda.org/conda-forge/noarch/ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2#359eeb6536da0e687af562ed265ec263
https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2#076becd9e05608f8dc72757d5f3a91ff
https://conda.anaconda.org/conda-forge/noarch/pyjwt-2.3.0-pyhd8ed1ab_1.tar.bz2#b7bc0de380f114658af5fe57cebdcd9e
https://conda.anaconda.org/conda-forge/noarch/pyparsing-3.0.6-pyhd8ed1ab_0.tar.bz2#3087df8c636c5a00e694605c39ce4982
https://conda.anaconda.org/conda-forge/noarch/python-json-logger-2.0.1-pyh9f0ad1d_0.tar.bz2#aed452f2f9f8bc8b2b0c412975051b5b
https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.7-2_cp37m.tar.bz2#afff88bf9a7048da740c70aeb8cdbb82
https://conda.anaconda.org/conda-forge/noarch/pytz-2021.3-pyhd8ed1ab_0.tar.bz2#7e4f811bff46a5a6a7e0094921389395
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�[91m+ mamba create -p /srv/conda/envs/notebook --file /tmp/env/environment.lock
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wheel-0.37.1         |            |   0% 
wheel-0.37.1         | ########## | 100% 

zipp-3.6.0           |            |   0% 
zipp-3.6.0           | ########## | 100% 

babel-2.9.1          |            |   0% 
babel-2.9.1          | #########4 |  95% 
babel-2.9.1          | ########## | 100% 

certifi-2021.10.8    |            |   0% 
certifi-2021.10.8    | ########## | 100% 

cffi-1.15.0          |            |   0% 
cffi-1.15.0          | ########## | 100% 

debugpy-1.5.1        |            |   0% 
debugpy-1.5.1        | ########## | 100% 
debugpy-1.5.1        | ########## | 100% 

greenlet-1.1.2       |            |   0% 
greenlet-1.1.2       | ########## | 100% 

importlib-metadata-4 |            |   0% 
importlib-metadata-4 | ########## | 100% 

importlib_resources- |            |   0% 
importlib_resources- | ########## | 100% 

jedi-0.18.1          |            |   0% 
jedi-0.18.1          | ########## | 100% 
jedi-0.18.1          | ########## | 100% 

jupyter_core-4.9.1   |            |   0% 
jupyter_core-4.9.1   | ########## | 100% 

markupsafe-2.0.1     |            |   0% 
markupsafe-2.0.1     | ########## | 100% 

matplotlib-inline-0. |            |   0% 
matplotlib-inline-0. | ########## | 100% 

mistune-0.8.4        |            |   0% 
mistune-0.8.4        | ########## | 100% 

packaging-21.3       |            |   0% 
packaging-21.3       | ########## | 100% 

pexpect-4.8.0        |            |   0% 
pexpect-4.8.0        | ########## | 100% 

psutil-5.8.0         |            |   0% 
psutil-5.8.0         | ########## | 100% 

pycurl-7.44.1        |            |   0% 
pycurl-7.44.1        | ##2        |  23% 
pycurl-7.44.1        | ########## | 100% 

pyrsistent-0.18.0    |            |   0% 
pyrsistent-0.18.0    | ########## | 100% 

pysocks-1.7.1        |            |   0% 
pysocks-1.7.1        | ########## | 100% 

python-dateutil-2.8. |            |   0% 
python-dateutil-2.8. | ########## | 100% 

pyzmq-22.3.0         |            |   0% 
pyzmq-22.3.0         | ########## | 100% 
pyzmq-22.3.0         | ########## | 100% 

ruamel.yaml.clib-0.2 |            |   0% 
ruamel.yaml.clib-0.2 | ########## | 100% 

setuptools-60.0.4    |            |   0% 
setuptools-60.0.4    | ########## | 100% 
setuptools-60.0.4    | ########## | 100% 

sniffio-1.2.0        |            |   0% 
sniffio-1.2.0        | ########## | 100% 

tornado-6.1          |            |   0% 
tornado-6.1          | ########## | 100% 
tornado-6.1          | ########## | 100% 

anyio-3.4.0          |            |   0% 
anyio-3.4.0          | ########## | 100% 

argon2-cffi-21.1.0   |            |   0% 
argon2-cffi-21.1.0   | ########## | 100% 

backports.functools_ |            |   0% 
backports.functools_ | ########## | 100% 

bleach-4.1.0         |            |   0% 
bleach-4.1.0         | ########## | 100% 

brotlipy-0.7.0       |            |   0% 
brotlipy-0.7.0       | ########## | 100% 

cryptography-36.0.1  |            |   0% 
cryptography-36.0.1  | ########## | 100% 
cryptography-36.0.1  | ########## | 100% 

importlib_metadata-4 |            |   0% 
importlib_metadata-4 | ########## | 100% 

jinja2-3.0.3         |            |   0% 
jinja2-3.0.3         | ########## | 100% 

jsonschema-4.3.2     |            |   0% 
jsonschema-4.3.2     | ########## | 100% 

jupyter_client-7.1.0 |            |   0% 
jupyter_client-7.1.0 | ########## | 100% 

mako-1.1.6           |            |   0% 
mako-1.1.6           | ########## | 100% 

pip-21.3.1           |            |   0% 
pip-21.3.1           | ########## | 100% 
pip-21.3.1           | ########## | 100% 

pygments-2.10.0      |            |   0% 
pygments-2.10.0      | ########## | 100% 
pygments-2.10.0      | ########## | 100% 

ruamel.yaml-0.17.17  |            |   0% 
ruamel.yaml-0.17.17  | ########## | 100% 

sqlalchemy-1.4.29    |            |   0% 
sqlalchemy-1.4.29    | ########## | 100% 
sqlalchemy-1.4.29    | ########## | 100% 

terminado-0.12.1     |            |   0% 
terminado-0.12.1     | ########## | 100% 

alembic-1.7.5        |            |   0% 
alembic-1.7.5        | ########## | 100% 

argcomplete-1.12.3   |            |   0% 
argcomplete-1.12.3   | ########## | 100% 

jupyter_telemetry-0. |            |   0% 
jupyter_telemetry-0. | ########## | 100% 

jupyterlab_pygments- |            |   0% 
jupyterlab_pygments- | ########## | 100% 

nbformat-5.1.3       |            |   0% 
nbformat-5.1.3       | ########## | 100% 

oauthlib-3.1.1       |            |   0% 
oauthlib-3.1.1       | ########## | 100% 

pyopenssl-21.0.0     |            |   0% 
pyopenssl-21.0.0     | ########## | 100% 

wcwidth-0.2.5        |            |   0% 
wcwidth-0.2.5        | ########## | 100% 

certipy-0.1.3        |            |   0% 
certipy-0.1.3        | ########## | 100% 

nbclient-0.5.9       |            |   0% 
nbclient-0.5.9       | ########## | 100% 

prompt-toolkit-3.0.2 |            |   0% 
prompt-toolkit-3.0.2 | ########## | 100% 
prompt-toolkit-3.0.2 | ########## | 100% 

urllib3-1.26.7       |            |   0% 
urllib3-1.26.7       | ########## | 100% 

ipython-7.30.1       |            |   0% 
ipython-7.30.1       | ########## | 100% 
ipython-7.30.1       | ########## | 100% 

nbconvert-6.0.7      |            |   0% 
nbconvert-6.0.7      | ########## | 100% 
nbconvert-6.0.7      | ########## | 100% 

requests-2.26.0      |            |   0% 
requests-2.26.0      | ########## | 100% 

ipykernel-6.6.0      |            |   0% 
ipykernel-6.6.0      | ########## | 100% 

jupyter_server-1.13. |            |   0% 
jupyter_server-1.13. | ########## | 100% 
jupyter_server-1.13. | ########## | 100% 

jupyterhub-base-1.4. |            |   0% 
jupyterhub-base-1.4. | ########## | 100% 
jupyterhub-base-1.4. | ########## | 100% 

jupyter-resource-usa |            |   0% 
jupyter-resource-usa | ########## | 100% 

jupyterlab_server-2. |            |   0% 
jupyterlab_server-2. | ########## | 100% 

notebook-6.3.0       |            |   0% 
notebook-6.3.0       | #######8   |  79% 
notebook-6.3.0       | ########## | 100% 

jupyter-offlinenoteb |            |   0% 
jupyter-offlinenoteb | ########## | 100% 
jupyter-offlinenoteb | ########## | 100% 

jupyterhub-singleuse |            |   0% 
jupyterhub-singleuse | ########## | 100% 

nbclassic-0.3.4      |            |   0% 
nbclassic-0.3.4      | ########## | 100% 

nteract_on_jupyter-2 |            |   0% 
nteract_on_jupyter-2 | ##5        |  25% 
nteract_on_jupyter-2 | ####7      |  47% 
nteract_on_jupyter-2 | #########2 |  92% 
nteract_on_jupyter-2 | ########## | 100% 

widgetsnbextension-3 |            |   0% 
widgetsnbextension-3 | #####9     |  60% 
widgetsnbextension-3 | ########## | 100% 
widgetsnbextension-3 | ########## | 100% 

ipywidgets-7.6.3     |            |   0% 
ipywidgets-7.6.3     | ########## | 100% 

jupyterlab-3.2.5     |            |   0% 
jupyterlab-3.2.5     | ###5       |  36% 
jupyterlab-3.2.5     | ########## | 100% 
jupyterlab-3.2.5     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: �[32mOK�[0m

done
�[91mtime: 50.002
+ [[ ! -z '' ]]
�[0m�[91m+ echo ''
�[0m�[91m+ [[ ! -z '' ]]
+ mamba clean --all -f -y
�[0m
                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔��██╗████╗ ████║██╔��██╗██╔��██╗
        ██╔████╔██║███████║██╔████╔██║██████╔�███████║
        ██║╚██╔�██║██╔��██║██║╚██╔�██║██╔��██╗██╔��██║
        ██║ ╚�� ██║██║  ██║██║ ╚�� ██║██████╔�██║  ██║
        ╚��     ╚��╚��  ╚��╚��     ╚��╚������ ╚��  ╚��

        mamba (0.7.4) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Remove all contents from the following package caches?
  - /srv/conda/pkgs
�[91mtime: 1.056
+ rm /tmp/miniforge-installer.sh
�[0m�[91m+ rm -rf /root/.cache
�[0m�[91m+ chown -R jovyan:jovyan /srv/conda
�[0m�[91m+ mamba list -n root
�[0m
                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔��██╗████╗ ████║██╔��██╗██╔��██╗
        ██╔████╔██║███████║██╔████╔██║██████╔�███████║
        ██║╚██╔�██║██╔��██║██║╚██╔�██║██╔��██╗██╔��██║
        ██║ ╚�� ██║██║  ██║██║ ╚�� ██║██████╔�██║  ██║
        ╚��     ╚��╚��  ╚��╚��     ╚��╚������ ╚��  ╚��

        mamba (0.7.4) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

# packages in environment at /srv/conda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
brotlipy                  0.7.0           py38h8df0ef7_1001    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h36c2ea0_0    conda-forge
ca-certificates           2021.10.26           h06a4308_2    defaults
certifi                   2021.10.8        py38h578d9bd_1    conda-forge
cffi                      1.14.4           py38ha65f79e_1    conda-forge
chardet                   3.0.4           py38h924ce5b_1008    conda-forge
conda                     4.9.2            py38h578d9bd_0    conda-forge
conda-package-handling    1.7.2            py38h8df0ef7_0    conda-forge
cryptography              3.2.1            py38h7699a38_0    conda-forge
icu                       67.1                 he1b5a44_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
krb5                      1.17.2               h926e7f8_0    conda-forge
ld_impl_linux-64          2.35.1               hed1e6ac_0    conda-forge
libarchive                3.3.3             hddc7a2b_1008    conda-forge
libcurl                   7.71.1               hcdd3856_8    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  h58526e2_1    conda-forge
libgcc-ng                 9.3.0               h5dbcf3e_17    conda-forge
libgomp                   9.3.0               h5dbcf3e_17    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libnghttp2                1.41.0               h8cfc5f6_2    conda-forge
libsolv                   0.7.16               h8b12597_0    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.3.0               h2ae2ef3_17    conda-forge
libxml2                   2.9.10               h68273f3_2    conda-forge
lz4-c                     1.9.2                he1b5a44_3    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     0.7.4            py38h4c9354d_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openssl                   1.1.1m               h7f8727e_0    defaults
pip                       20.3.1             pyhd8ed1ab_0    conda-forge
pycosat                   0.6.3           py38h8df0ef7_1005    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyopenssl                 20.0.0             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py38h924ce5b_2    conda-forge
python                    3.8.6           hffdb5ce_1_cpython    conda-forge
python_abi                3.8                      1_cp38    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
reproc                    14.2.1               h36c2ea0_0    conda-forge
reproc-cpp                14.2.1               h58526e2_0    conda-forge
requests                  2.25.0             pyhd3deb0d_0    conda-forge
ruamel_yaml               0.15.80         py38h8df0ef7_1003    conda-forge
setuptools                49.6.0           py38h924ce5b_2    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlite                    3.34.0               h74cdb3f_0    conda-forge
tk                        8.6.10               hed695b0_1    conda-forge
tqdm                      4.54.1             pyhd8ed1ab_0    conda-forge
urllib3                   1.25.11                    py_0    conda-forge
wheel                     0.36.1             pyhd3deb0d_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.5                h6597ccf_2    conda-forge
�[91m+ mamba list -p /srv/conda/envs/notebook
�[0m
                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔��██╗████╗ ████║██╔��██╗██╔��██╗
        ██╔████╔██║███████║██╔████╔██║██████╔�███████║
        ██║╚██╔�██║██╔��██║██║╚██╔�██║██╔��██╗██╔��██║
        ██║ ╚�� ██║██║  ██║██║ ╚�� ██║██████╔�██║  ██║
        ╚��     ╚��╚��  ╚��╚��     ╚��╚������ ╚��  ╚��

        mamba (0.7.4) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

# packages in environment at /srv/conda/envs/notebook:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
alembic                   1.7.5              pyhd8ed1ab_0    conda-forge
anyio                     3.4.0            py37h89c1867_0    conda-forge
argcomplete               1.12.3             pyhd8ed1ab_2    conda-forge
argon2-cffi               21.1.0           py37h5e8e339_2    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
blinker                   1.4                        py_1    conda-forge
brotlipy                  0.7.0           py37h5e8e339_1003    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
certifi                   2021.10.8        py37h89c1867_1    conda-forge
certipy                   0.1.3                      py_0    conda-forge
cffi                      1.15.0           py37h036bc23_0    conda-forge
charset-normalizer        2.0.9              pyhd8ed1ab_0    conda-forge
cryptography              36.0.1           py37hf1a17b8_0    conda-forge
debugpy                   1.5.1            py37hcd2ae1e_0    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.3             pyhd8ed1ab_1003    conda-forge
greenlet                  1.1.2            py37hcd2ae1e_1    conda-forge
icu                       68.2                 h9c3ff4c_0    conda-forge
idna                      3.1                pyhd3deb0d_0    conda-forge
importlib-metadata        4.10.0           py37h89c1867_0    conda-forge
importlib_metadata        4.10.0               hd8ed1ab_0    conda-forge
importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.6.0            py37h6531663_0    conda-forge
ipython                   7.30.1           py37h89c1867_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.3              pyhd3deb0d_0    conda-forge
jedi                      0.18.1           py37h89c1867_0    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.3.2              pyhd8ed1ab_0    conda-forge
jupyter-offlinenotebook   0.2.1              pyhd8ed1ab_0    conda-forge
jupyter-resource-usage    0.6.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.1.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.1            py37h89c1867_1    conda-forge
jupyter_server            1.13.1             pyhd8ed1ab_0    conda-forge
jupyter_telemetry         0.1.0              pyhd8ed1ab_1    conda-forge
jupyterhub-base           1.4.2            py37h89c1867_0    conda-forge
jupyterhub-singleuser     1.4.2            py37h89c1867_0    conda-forge
jupyterlab                3.2.5              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_server         2.10.1             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
krb5                      1.19.2               hcc1bbae_3    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libcurl                   7.80.0               h2574ce0_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 11.2.0              h1d223b6_11    conda-forge
libgomp                   11.2.0              h1d223b6_11    conda-forge
libnghttp2                1.43.0               h812cca2_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libuv                     1.42.0               h7f98852_0    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
mako                      1.1.6              pyhd8ed1ab_0    conda-forge
markupsafe                2.0.1            py37h5e8e339_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mistune                   0.8.4           py37h5e8e339_1005    conda-forge
nbclassic                 0.3.4              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.9              pyhd8ed1ab_0    conda-forge
nbconvert                 6.0.7            py37h89c1867_3    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge
nodejs                    14.17.4              h92b4a50_0    conda-forge
notebook                  6.3.0              pyha770c72_1    conda-forge
nteract_on_jupyter        2.1.3                      py_0    conda-forge
oauthlib                  3.1.1              pyhd8ed1ab_0    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandoc                    2.16.2               h7f98852_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
prometheus_client         0.12.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.24             pyha770c72_0    conda-forge
psutil                    5.8.0            py37h5e8e339_2    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pycurl                    7.44.1           py37h88a64d2_1    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.3.0              pyhd8ed1ab_1    conda-forge
pyopenssl                 21.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.6              pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.0           py37h5e8e339_0    conda-forge
pysocks                   1.7.1            py37h89c1867_4    conda-forge
python                    3.7.12          hb7a2778_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.1              pyh9f0ad1d_0    conda-forge
python_abi                3.7                     2_cp37m    conda-forge
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
pyzmq                     22.3.0           py37h336d617_1    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_1    conda-forge
ruamel.yaml               0.17.17          py37h5e8e339_1    conda-forge
ruamel.yaml.clib          0.2.6            py37h5e8e339_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                60.0.4           py37h89c1867_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.2.0            py37h89c1867_2    conda-forge
sqlalchemy                1.4.29           py37h5e8e339_0    conda-forge
sqlite                    3.37.0               h9cd32fc_0    conda-forge
terminado                 0.12.1           py37h89c1867_1    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tornado                   6.1              py37h5e8e339_2    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typing_extensions         4.0.1              pyha770c72_0    conda-forge
urllib3                   1.26.7             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.2.3              pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.5.2            py37h89c1867_1    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.6.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
�[91m+ /srv/conda/envs/notebook/bin/npm config --global set prefix /srv/npm
�[0m�[91mtime: 90.827
�[0mRemoving intermediate container d37b939f410e
 ---> 13235cb3bb56
Step 30/67 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in b2354f64d1e8
Removing intermediate container b2354f64d1e8
 ---> 451d1704e07e
Step 31/67 : RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/" > /etc/apt/sources.list.d/r-ubuntu.list
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 1732ade2282a
Removing intermediate container 1732ade2282a
 ---> 77554c45e7d5
Step 32/67 : RUN wget --quiet -O - 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xe298a3a825c0d65dfd57cbb651716619e084dab9' | apt-key add -
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 66165d89813f
�[91mWarning: apt-key output should not be parsed (stdout is not a terminal)
�[0mOK
Removing intermediate container 66165d89813f
 ---> b6296b37fe86
Step 33/67 : RUN apt-get update > /dev/null && apt-get install --yes r-base=4.0.5-1.1804.0 r-base-core=4.0.5-1.1804.0         r-base-dev=4.0.5-1.1804.0         r-recommended=4.0.5-1.1804.0         libclang-dev         libzmq3-dev > /dev/null && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*
 ---> [Warning] Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
 ---> Running in 9ede65c4848d
�[91mE: Unable to correct problems, you have held broken packages.
�[0mRemoving intermediate container 9ede65c4848d
The command '/bin/sh -c apt-get update > /dev/null && apt-get install --yes r-base=4.0.5-1.1804.0 r-base-core=4.0.5-1.1804.0         r-base-dev=4.0.5-1.1804.0         r-recommended=4.0.5-1.1804.0         libclang-dev         libzmq3-dev > /dev/null && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*' returned a non-zero code: 100Built image, launching...
Failed to connect to event stream

Maybe related: #1116

@yuvipanda
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@fkohrt that issue is unrelated, but is fixed now! Should be deployed on mybinder.org soon.

@fkohrt
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fkohrt commented Jan 25, 2022

@yuvipanda And now it works, so it may have been solved by #1114. Whatever, just happy it builds!

@yuvipanda yuvipanda mentioned this issue Mar 23, 2022
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Get binary R packages from packagemanager.rstudio.com yuvipanda/repo2docker
6 participants
@yuvipanda @psymeg @manics @choldgraf @fkohrt @meeseeksmachine