FAIRplus / the-fair-cookbook

The FAIR cookbook, containing recipes to make your data more FAIR. Find the rendered version on:
https://faircookbook.elixir-europe.org/
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Dockebuild failure #421

Closed ronna closed 2 years ago

ronna commented 2 years ago

docker build --progress plain -t fcb . && docker run --name asdf fcb && docker cp asdf:/out.tar . && docker rm asdf && tar -xf out.tar && rm out.tar Sending build context to Docker daemon 173.8MB Step 1/35 : FROM python:3.7.8-slim-buster AS jupyterbookbuilder-base-image ---> 6bd913dd0ca1 Step 2/35 : RUN pip install alabaster==0.7.12 anyio==2.2.0 argon2-cffi==20.1.0 async-generator==1.10 attrs==20.3.0 Babel==2.9.0 backcall==0.2.0 beautifulsoup4==4.9.3 bleach==3.3.0 certifi==2020.12.5 cffi==1.14.5 chardet==4.0.0 click==7.1.2 colorama==0.4.4 decorator==5.0.7 defusedxml==0.7.1 deprecation==2.1.0 docutils==0.16 entrypoints==0.3 gitdb==4.0.7 GitPython==3.1.14 idna==2.10 imagesize==1.2.0 importlib-metadata==4.0.1 ipykernel==5.5.3 ipython==7.31.1 ipython-genutils==0.2.0 ipywidgets==7.6.3 jedi==0.18.0 Jinja2==2.11.3 jsonschema==3.2.0 jupyter-book==0.10.2 jupyter-cache==0.4.2 jupyter-client==6.1.12 jupyter-core==4.7.1 jupyter-packaging==0.9.2 jupyter-server==1.6.4 jupyter-server-mathjax==0.2.2 jupyter-sphinx==0.3.1 jupyterbook-latex==0.2.0 jupyterlab-widgets==1.0.0 jupytext==1.10.3 latexcodec==2.0.1 linkify-it-py==1.0.1 markdown-it-py==0.6.2 MarkupSafe==1.1.1 mdit-py-plugins==0.2.6 mistune==0.8.4 myst-nb==0.12.0 myst-parser==0.13.6 nbclient==0.5.3 nbconvert==5.6.1 nbdime==3.1.1 nbformat==5.1.3 nest-asyncio==1.5.1 nested-lookup==0.2.22 notebook>=6.4.1 packaging==20.9 pandocfilters==1.4.3 parso==0.8.2 pexpect==4.8.0 pickleshare==0.7.5 prometheus-client==0.10.1 prompt-toolkit==3.0.18 ptyprocess==0.7.0 pybtex==0.24.0 pybtex-docutils==1.0.0 pycparser==2.20 pydata-sphinx-theme==0.4.3 Pygments==2.8.1 pyparsing==2.4.7 pyrsistent==0.17.3 python-dateutil==2.8.1 pytz==2021.1 PyYAML==5.4.1 pyzmq==22.0.3 requests==2.25.1 Send2Trash==1.5.0 six==1.15.0 smmap==4.0.0 sniffio==1.2.0 snowballstemmer==2.1.0 soupsieve==2.2.1 Sphinx==3.5.4 sphinx-book-theme==0.0.42 sphinx-comments==0.0.3 sphinx-copybutton==0.3.1 sphinx-panels==0.5.2 sphinx-thebe==0.0.8 sphinx-togglebutton==0.2.3 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-bibtex==2.1.0 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==1.0.3 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.4 sphinx-sitemap==2.2.0 SQLAlchemy==1.3.24 terminado==0.9.4 testpath==0.4.4 toml==0.10.2 tomlkit==0.7.0 tornado==6.1 traitlets==5.0.5 uc-micro-py==1.0.1 urllib3==1.26.4 wcwidth==0.2.5 webencodings==0.5.1 widgetsnbextension==3.5.1 zipp==3.4.1 pygments-csv-lexer==0.1.3 ---> Using cache ---> f1a8bd327589 Step 3/35 : RUN pip freeze > /pip_freeze_actual.txt ---> Using cache ---> 1681271c3079 Step 4/35 : RUN cat /pip_freeze_actual.txt ---> Using cache ---> 906ad7776307 Step 5/35 : FROM alpine as orchestrator ---> 0ac33e5f5afa Step 6/35 : COPY ./ ./ ---> Using cache ---> 647074a3a829 Step 7/35 : RUN find . -iname "*.mmd" > list_of_all_mermaid_files.txt ---> Using cache ---> d1418e52b9bc Step 8/35 : RUN tar c -f all_mermaid_files.tar -T list_of_all_mermaid_files.txt ---> Using cache ---> 6e71ccd20b2e Step 9/35 : RUN ls -lh all_mermaid_files.tar ---> Using cache ---> 98fdc0c59844 Step 10/35 : FROM minlag/mermaid-cli:8.13.4 as imageconverter ---> 5cf7fc075b74 Step 11/35 : WORKDIR /home/mermaidcli ---> Using cache ---> cde9fb17751e Step 12/35 : RUN echo "{\"args\": [ \"--no-sandbox\" ] }" > puppeteer-config.json ---> Using cache ---> 38fd6f806d31 Step 13/35 : COPY --from=orchestrator all_mermaid_files.tar list_of_all_mermaid_files.txt . When using COPY with more than one source file, the destination must be a directory and end with a /

ghost commented 2 years ago

should be fixed in bc5147bf , could you give it another try @ronna ?