Quarto Jupyter engine error when running Seqera Docker container on an Apple silicon Mac

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Quarto Jupyter error when running Seqera Docker container on an Apple silicon Mac.

Build specification: Container build report

docker run --rm --platform=linux/amd64 community.wave.seqera.io/library/jupyter_python_quarto:322a759c630b4ccb quarto check

Quarto 1.8.27
[✓] Checking environment information...
      Quarto cache location: /root/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      NOTE: Dart Sass version 1.59.1 does not strictly match 1.87.0 and strict checking is enabled. Please use 1.87.0.
      Deno version 2.3.1: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.8.27
      Path: /opt/conda/bin

[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Tex:  (not detected)

[✓] Checking Chrome Headless....................OK
      Chrome:  (not detected)

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.14.3 (Conda)
      Path: /opt/conda/bin/python
      Jupyter: 5.9.1
      Kernels: python3

(|) Checking Jupyter engine render....2026-02-17 08:03:03,645 - traitlets - ERROR - Error occurred while starting new kernel client for kernel e708196b-184f-41e3-82ab-6c3af573ac62: Kernel didn't respond in 60 seconds
(|) Checking Jupyter engine render....

Kernel didn't respond in 60 seconds
(\) Checking Jupyter engine render....WARN: Error encountered when rendering files
[✓] Checking Jupyter engine render....OK

Update: It seems to work on another Apple silicon Mac. So it is some sort of local issue.

▸ docker --version
Docker version 29.1.4, build 0e6fee6c52
▸ docker version --format '{{.Server.Platform.Name}}'
Docker Desktop 4.54.0 (212467)
▸ sw_vers
ProductName:		macOS
ProductVersion:		26.3
BuildVersion:		25D125
2

Is it just slow? Mac silicon will be running linux/amd64 via Rosetta which is slow. Maybe it just couldn’t get there in time for the 60 second timeout?

Note that if you generate a linux/arm64 image instead, it should be significantly faster I think.

3

I have tried increasing the time out `-e QUARTO_JUPYTER_TIMEOUT=300`, but that doesn’t seem to do anything. I have tried building an ARM version of the container on Seqera, but that fails straight away.

Error Log 
#1 [internal] load build definition from Containerfile
#1 DONE 0.0s

#1 [internal] load build definition from Containerfile
#1 transferring dockerfile: 560B done
#1 DONE 0.0s

#2 [internal] load metadata for docker.io/mambaorg/micromamba:1.5.10-noble
#2 DONE 1.0s

#3 [internal] load .dockerignore
#3 transferring context: 2B done
#3 DONE 0.0s

#4 [internal] load build context
#4 DONE 0.0s

#5 [1/3] FROM docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca
#5 resolve docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca 0.0s done
#5 DONE 0.0s

#6 importing cache manifest from s3:5142472200740782264
#6 DONE 0.1s

#4 [internal] load build context
#4 transferring context: 223B done
#4 DONE 0.1s

#5 [1/3] FROM docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca
#5 DONE 0.2s

#5 [1/3] FROM docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca
#5 sha256:b9afb7fce560bfbcbdc95f1ba71414d56c0ff432b8448c7d18422ccf16b8913f 345B / 345B 0.1s done
#5 sha256:a444aa1775d585edca154a7afbe0542e9fc0fe705662a1e012a99077e15b7ef7 648B / 648B 0.2s done
#5 sha256:57d1d9429ba0ed4787862d80eab63d0f7dea55b141c6f1049992f565c635acb6 0B / 687B 0.2s
#5 sha256:b8a1a9b4292438c04fc842c184ed011291b1b8dd8d771bd919240b762de9d2e2 0B / 217B 0.2s
#5 sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 0B / 32B 0.2s
#5 sha256:57d1d9429ba0ed4787862d80eab63d0f7dea55b141c6f1049992f565c635acb6 687B / 687B 0.2s done
#5 sha256:b8a1a9b4292438c04fc842c184ed011291b1b8dd8d771bd919240b762de9d2e2 217B / 217B 0.3s done
#5 sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 32B / 32B 0.2s done
#5 sha256:c0287eaf45eee1a93db5323734667500c6013941c8c3b5b95cb06f7dbf91ff46 4.08kB / 4.08kB 0.1s done
#5 sha256:ad4a1cea1cef0dc1983c645b60707022a58ecc98df79b810540a3d00939cf847 283B / 283B 0.1s done
#5 sha256:5a47b42d3e8c136ae8f5c77fa098b0944089e5b9124349d2ee725e6e8acada21 525B / 525B 0.1s done
#5 sha256:5f20d5c36a0634c47de56237687c5801eb5257c9f4ba17889a46696398f871fc 7.87MB / 7.87MB 0.2s done
#5 sha256:6e59cb05818e49ea83cbe79bd46eb80418dfe3cb3735b45570f93a23579e2cec 4.19MB / 28.89MB 0.2s
#5 sha256:6e59cb05818e49ea83cbe79bd46eb80418dfe3cb3735b45570f93a23579e2cec 28.89MB / 28.89MB 0.3s done
#5 sha256:dec6b097362e7c8d80e31302367f54d610b0e84d5c9cd5ccd300729608a54b18 126.56kB / 126.56kB 0.1s done
#5 DONE 0.8s

#5 [1/3] FROM docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca
#5 extracting sha256:6e59cb05818e49ea83cbe79bd46eb80418dfe3cb3735b45570f93a23579e2cec
#5 extracting sha256:6e59cb05818e49ea83cbe79bd46eb80418dfe3cb3735b45570f93a23579e2cec 0.7s done
#5 DONE 1.5s

#5 [1/3] FROM docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca
#5 extracting sha256:dec6b097362e7c8d80e31302367f54d610b0e84d5c9cd5ccd300729608a54b18
#5 extracting sha256:dec6b097362e7c8d80e31302367f54d610b0e84d5c9cd5ccd300729608a54b18 0.2s done
#5 DONE 1.7s

#5 [1/3] FROM docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca
#5 extracting sha256:5f20d5c36a0634c47de56237687c5801eb5257c9f4ba17889a46696398f871fc 0.1s done
#5 DONE 1.8s

#5 [1/3] FROM docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca
#5 extracting sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 0.0s done
#5 extracting sha256:5a47b42d3e8c136ae8f5c77fa098b0944089e5b9124349d2ee725e6e8acada21 0.0s done
#5 extracting sha256:ad4a1cea1cef0dc1983c645b60707022a58ecc98df79b810540a3d00939cf847 0.0s done
#5 extracting sha256:c0287eaf45eee1a93db5323734667500c6013941c8c3b5b95cb06f7dbf91ff46 0.0s done
#5 extracting sha256:b8a1a9b4292438c04fc842c184ed011291b1b8dd8d771bd919240b762de9d2e2 0.0s done
#5 DONE 1.9s

#5 [1/3] FROM docker.io/mambaorg/micromamba:1.5.10-noble@sha256:a0a4da2d5315f0d5b9d98196f2e9ecf50152c750bed4023bb127baade7e8faca
#5 extracting sha256:57d1d9429ba0ed4787862d80eab63d0f7dea55b141c6f1049992f565c635acb6 0.0s done
#5 extracting sha256:a444aa1775d585edca154a7afbe0542e9fc0fe705662a1e012a99077e15b7ef7 0.0s done
#5 extracting sha256:b9afb7fce560bfbcbdc95f1ba71414d56c0ff432b8448c7d18422ccf16b8913f 0.0s done
#5 DONE 2.0s

#7 [2/3] COPY --chown=mambauser:mambauser conda.yml /tmp/conda.yml
#7 DONE 0.0s

#8 [3/3] RUN micromamba install -y -n base -f /tmp/conda.yml     && micromamba install -y -n base conda-forge::procps-ng     && micromamba env export --name base --explicit > environment.lock     && echo ">> CONDA_LOCK_START"     && cat environment.lock     && echo "<< CONDA_LOCK_END"     && micromamba clean -a -y
#8 17.76 error    libmamba Could not solve for environment specs
#8 17.76     The following package could not be installed
#8 17.76     └─ quarto 1.8.27*  does not exist (perhaps a typo or a missing channel).
#8 17.78 critical libmamba Could not solve for environment specs
#8 ERROR: process "/usr/local/bin/_dockerfile_shell.sh micromamba install -y -n base -f /tmp/conda.yml     && micromamba install -y -n base conda-forge::procps-ng     && micromamba env export --name base --explicit > environment.lock     && echo \">> CONDA_LOCK_START\"     && cat environment.lock     && echo \"<< CONDA_LOCK_END\"     && micromamba clean -a -y" did not complete successfully: exit code: 1
------
 > [3/3] RUN micromamba install -y -n base -f /tmp/conda.yml     && micromamba install -y -n base conda-forge::procps-ng     && micromamba env export --name base --explicit > environment.lock     && echo ">> CONDA_LOCK_START"     && cat environment.lock     && echo "<< CONDA_LOCK_END"     && micromamba clean -a -y:
17.76 error    libmamba Could not solve for environment specs
17.76     The following package could not be installed
17.76     └─ quarto 1.8.27*  does not exist (perhaps a typo or a missing channel).
17.78 critical libmamba Could not solve for environment specs
------
Containerfile:3
--------------------
   2 |     COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
   3 | >>> RUN micromamba install -y -n base -f /tmp/conda.yml \
   4 | >>>     && micromamba install -y -n base conda-forge::procps-ng \
   5 | >>>     && micromamba env export --name base --explicit > environment.lock \
   6 | >>>     && echo ">> CONDA_LOCK_START" \
   7 | >>>     && cat environment.lock \
   8 | >>>     && echo "<< CONDA_LOCK_END" \
   9 | >>>     && micromamba clean -a -y
  10 |     USER root
--------------------
error: failed to solve: process "/usr/local/bin/_dockerfile_shell.sh micromamba install -y -n base -f /tmp/conda.yml     && micromamba install -y -n base conda-forge::procps-ng     && micromamba env export --name base --explicit > environment.lock     && echo \">> CONDA_LOCK_START\"     && cat environment.lock     && echo \"<< CONDA_LOCK_END\"     && micromamba clean -a -y" did not complete successfully: exit code: 1

I previously mentioned that it worked on another Apple silicon Mac, I compared the versions.

Failed:
MacOS Tahoe 26.3
Docker version 29.1.4, build 0e6fee6c52
Docker Desktop 4.54.0 (212467)

Worked:
MacOS Sequoia 15.7.3
Docker version 27.5.1, build 9f9e405
Docker Desktop 4.38.0 (181591)