Read the Docs build information Build id: 3194043 Project: um-advanced-computing-acs-docs Version: latest Commit: 5e75862a434b470fc42fd8957401a0abb13fe061 Date: 2025-07-14T17:37:26.896077Z State: finished Success: True [rtd-command-info] start-time: 2025-07-14T17:37:27.895256Z, end-time: 2025-07-14T17:37:29.183734Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/um-acs/acs_docs.git . Cloning into '.'... [rtd-command-info] start-time: 2025-07-14T17:37:29.323673Z, end-time: 2025-07-14T17:37:29.756527Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/master:refs/remotes/origin/master [rtd-command-info] start-time: 2025-07-14T17:37:30.460316Z, end-time: 2025-07-14T17:37:30.635305Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: switching to 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 5e75862 Update RStudio.rst [rtd-command-info] start-time: 2025-07-14T17:37:30.723939Z, end-time: 2025-07-14T17:37:30.759139Z, duration: 0, exit-code: 0 cat .readthedocs.yaml # Read the Docs configuration file for Sphinx projects # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the OS, Python version and other tools you might need build: os: ubuntu-22.04 tools: python: "3.11" # You can also specify other tool versions: # nodejs: "20" # rust: "1.70" # golang: "1.20" # Build documentation in the "docs/" directory with Sphinx sphinx: configuration: docs/conf.py # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs # builder: "dirhtml" # Fail on all warnings to avoid broken references # fail_on_warning: true # Optionally build your docs in additional formats such as PDF and ePub # formats: # - pdf # - epub # Optional but recommended, declare the Python requirements required # to build your documentation # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html python: install: - requirements: docs/requirements.txt [rtd-command-info] start-time: 2025-07-14T17:37:34.813928Z, end-time: 2025-07-14T17:37:34.864130Z, duration: 0, exit-code: 0 asdf global python 3.11.12 [rtd-command-info] start-time: 2025-07-14T17:37:35.185958Z, end-time: 2025-07-14T17:37:35.961843Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.12.final.0-64 in 492ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2025-07-14T17:37:36.058929Z, end-time: 2025-07-14T17:37:42.118801Z, duration: 6, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/envs/latest/lib/python3.11/site-packages (23.1) Collecting pip Downloading pip-25.1.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 14.0 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/envs/latest/lib/python3.11/site-packages (67.6.1) Collecting setuptools Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB) 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idna-3.10-py3-none-any.whl.metadata (10 kB) Collecting urllib3<3,>=1.21.1 (from requests>=2.30.0->sphinx) Downloading urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB) Collecting certifi>=2017.4.17 (from requests>=2.30.0->sphinx) Downloading certifi-2025.7.14-py3-none-any.whl.metadata (2.4 kB) Downloading sphinx-8.2.3-py3-none-any.whl (3.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 150.4 MB/s eta 0:00:00 Downloading docutils-0.21.2-py3-none-any.whl (587 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.4/587.4 kB 1.1 GB/s eta 0:00:00 Downloading alabaster-1.0.0-py3-none-any.whl (13 kB) Downloading babel-2.17.0-py3-none-any.whl (10.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.2/10.2 MB 462.1 MB/s eta 0:00:00 Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Downloading jinja2-3.1.6-py3-none-any.whl (134 kB) Downloading MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB) Downloading packaging-25.0-py3-none-any.whl (66 kB) 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urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, roman-numerals-py, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset_normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.7.14 charset_normalizer-3.4.2 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-25.0 requests-2.32.4 roman-numerals-py-3.1.0 snowballstemmer-3.0.1 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.5.0 [rtd-command-info] start-time: 2025-07-14T17:37:45.909259Z, end-time: 2025-07-14T17:37:46.691563Z, duration: 0, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt 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/home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/envs/latest/lib/python3.11/site-packages (from requests>=2.30.0->sphinx<9,>=6->sphinx-rtd-theme->-r docs/requirements.txt (line 8)) (2025.7.14) Downloading sphinx_rtd_theme-3.0.2-py2.py3-none-any.whl (7.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.7/7.7 MB 162.2 MB/s eta 0:00:00 Downloading sphinxcontrib_jquery-4.1-py2.py3-none-any.whl (121 kB) Installing collected packages: sphinxcontrib-jquery, sphinx-rtd-theme Successfully installed sphinx-rtd-theme-3.0.2 sphinxcontrib-jquery-4.1 [rtd-command-info] start-time: 2025-07-14T17:37:46.866304Z, end-time: 2025-07-14T17:37:46.904148Z, duration: 0, exit-code: 0 cat docs/conf.py # Configuration file for the Sphinx documentation builder. # # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # # import os # import sys # sys.path.insert(0, os.path.abspath('.')) # -- Project information ----------------------------------------------------- project = "acs_docs" copyright = "2024, UM IDSC ACS" author = "IDSC Advanced Computing Services" # -- General configuration --------------------------------------------------- # -- General configuration extensions = [ "sphinx.ext.duration", "sphinx.ext.doctest", "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.intersphinx", "sphinx.ext.autosectionlabel" ] intersphinx_mapping = { "rtd": ("https://docs.readthedocs.io/en/stable/", None), "python": ("https://docs.python.org/3/", None), "sphinx": ("https://www.sphinx-doc.org/en/master/", None), } intersphinx_disabled_domains = ["std"] templates_path = ["_templates"] # -- Options for EPUB output epub_show_urls = "footnote" # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = "sphinx_rtd_theme" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ["_static"] [rtd-command-info] start-time: 2025-07-14T17:37:46.990524Z, end-time: 2025-07-14T17:37:50.003983Z, duration: 3, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.2.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist [autosummary] generating autosummary for: index.rst, linux/1-nav.rst, linux/2-files.rst, linux/3-rwx.rst, linux/4-acl.rst, linux/README.rst, pegasus/README.rst, pegasus/Singularity/Singularityinfo.rst, pegasus/Singularity/apptainerinfo.rst, pegasus/centos7test.rst, ..., triton/2-sw/jh.rst, triton/2-sw/modules.rst, triton/2-sw/wmlce.rst, triton/3-jobs/1-lsf.rst, triton/3-jobs/2-queues.rst, triton/3-jobs/3-commands.rst, triton/3-jobs/4-scripts.rst, triton/3-jobs/5-interactive.rst, triton/3-jobs/README.rst, triton/README.rst loading intersphinx inventory 'rtd' from https://docs.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... loading intersphinx inventory 'sphinx' from https://www.sphinx-doc.org/en/master/objects.inv ... intersphinx inventory has moved: https://docs.readthedocs.io/en/stable/objects.inv -> https://docs.readthedocs.com/platform/stable/objects.inv building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 68 source files that are out of date updating environment: [new config] 68 added, 0 changed, 0 removed reading sources... 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[100%] triton/README /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:2: WARNING: Title underline too short. **Introduction to Apptainer on Pegasus** ======================================= [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:90: WARNING: Title underline too short. **Overview of the Apptainer Interface** -------------------------------------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:427: WARNING: Title underline too short. **Running GUI Jupyter notebook through apptainer container** ==================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:427: WARNING: Title underline too short. **Running GUI Jupyter notebook through apptainer container** ==================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:465: WARNING: Title underline too short. **Apptainer Matlab Interactive:** ==================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:465: WARNING: Title underline too short. **Apptainer Matlab Interactive:** ==================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:509: WARNING: Title underline too short. **Apptainer R Interactive:** ==================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:509: WARNING: Title underline too short. **Apptainer R Interactive:** ==================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:568: WARNING: Title underline too short. **Apptainer Definition Files** ============================ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:568: WARNING: Title underline too short. **Apptainer Definition Files** ============================ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:1122: WARNING: Title underline too short. **GPU Support with PyTorch** =========================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:1122: WARNING: Title underline too short. **GPU Support with PyTorch** =========================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst:2: WARNING: Title underline too short. Pegasus QuickStart Guide ======================= [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst:142: WARNING: Title underline too short. 3. Installing dependent libraries on Pegasus ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst:142: WARNING: Title underline too short. 3. Installing dependent libraries on Pegasus ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/5-sccc_quickstart.rst:21: WARNING: Literal block expected; none found. 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[docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/p_faqs.rst:100: WARNING: duplicate label pegasus job scheduling, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/jobs/README.rst [autosectionlabel.pegasus/p_faqs] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/soft/Jupyterhub.rst:45: WARNING: Title underline too short. Switching between JupyterLab & JupyterHub ----------------------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/soft/Jupyterhub.rst:45: WARNING: Title underline too short. 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Setup your $RSTUDIO_WORK_DIR ------------------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/soft/RStudio.rst:23: WARNING: Title underline too short. Edit your rstudio_lsf.job Script ---------------------------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/soft/RStudio.rst:23: WARNING: Title underline too short. Edit your rstudio_lsf.job Script ---------------------------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/policies/README.rst:2: WARNING: Title underline too short. IDSC ACS Policies ================ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/policies/policies.rst:4: WARNING: Title underline too short. 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IDSC Onboarding Training Videos ============ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:5: WARNING: duplicate label before you get started:, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:17: WARNING: duplicate label basic concepts, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:20: WARNING: duplicate label home directory vs. scratch directory (scratch space), other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:39: WARNING: duplicate label login node vs. compute node, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:52: WARNING: duplicate label basic steps, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:60: WARNING: duplicate label 1. preparing the code you would like to run, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:123: WARNING: duplicate label 2. preparing the input data, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:185: WARNING: duplicate label 4. preparing the job script, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:247: WARNING: duplicate label 5. submitting and monitoring the job, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:278: WARNING: duplicate label 6. checking the job output, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/1-env/4-triton_quickstart.rst:336: WARNING: duplicate label 7. chao, other instance in /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/env/4-pegasus_quickstart.rst [autosectionlabel.triton/1-env/4-triton_quickstart] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/2-sw/README.rst:4: WARNING: toctree contains reference to nonexisting document 'triton/2-sw/rPackages' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/2-sw/R_Through_Anaconda.rst:2: WARNING: Title underline too short. Using R through miniforge ============ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/2-sw/R_Through_Anaconda.rst:11: WARNING: Title underline too short. Load Miniforge software module ------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/2-sw/R_Through_Anaconda.rst:21: WARNING: Title underline too short. Create the R conda environment ------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/2-sw/R_Through_Anaconda.rst:21: WARNING: Title underline too short. Create the R conda environment ------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/triton/2-sw/R_Through_Anaconda.rst:43: WARNING: Title underline too short. 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[100%] triton/README generating indices... /home/docs/checkouts/readthedocs.org/user_builds/um-advanced-computing-acs-docs/checkouts/latest/docs/pegasus/Singularity/apptainerinfo.rst:1629: WARNING: Lexing literal_block "$ nf-core list\n\nnf-core list\n ,--./,-.\n ___ __ __ __ ___ /,-._.--~\\\n|\\ | |__ __ / ` / \\ |__) |__ } {\n| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,\n `._,._,'\nnf-core/tools version 2.9 - https://nf-co.re\nThere is a new version of nf-core/tools available! (2.10)\n\n┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┓\n┃ Pipeline Name ┃ Stars ┃ Latest Release ┃ Released ┃ Last Pulled ┃ Have latest release? ┃\n┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━┩\n│ pixelator │ 1 │ dev │ 24 hours ago │ - │ - │\n│ pangenome │ 33 │ dev │ yesterday │ - │ - │\n│ taxprofiler │ 66 │ dev │ yesterday │ - │ - │\n│ rnavar │ 20 │ dev │ yesterday │ - │ - │\n│ rnaseq │ 670 │ dev │ yesterday │ - │ - │\n│ epitopeprediction │ 25 │ dev │ yesterday │ - │ - │\n│ bacass │ 46 │ dev │ yesterday │ - │ - │\n│ sarek │ 276 │ dev │ 2 days ago │ - │ - │\n│ metatdenovo │ 3 │ dev │ 2 days ago │ - │ - │\n│ mag │ 145 │ dev │ 2 days ago │ - │ - │\n│ differentialabundance │ 27 │ dev │ 3 days ago │ - │ - │\n│ readsimulator │ 0 │ dev │ 3 days ago │ - │ - │\n│ mhcquant │ 27 │ dev │ 3 days ago │ - │ - │\n│ rnasplice │ 9 │ dev │ 4 days ago │ - │ - │\n│ metaboigniter │ 11 │ dev │ 4 days ago │ - │ - │\n│ rnadnavar │ 0 │ dev │ 4 days ago │ - │ - │\n│ dualrnaseq │ 13 │ dev │ 4 days ago │ - │ - │\n│ fetchngs │ 87 │ dev │ 4 days ago │ - │ - │\n│ phageannotator │ 4 │ dev │ 6 days ago │ - │ - │\n│ bamtofastq │ 10 │ dev │ 6 days ago │ - │ - │\n│ sammyseq │ 0 │ dev │ 6 days ago │ - │ - │\n│ eager │ 103 │ dev │ 1 week ago │ - │ - │\n│ funcscan │ 43 │ dev │ 1 weeks ago │ - │ - │\n│ nascent │ 10 │ dev │ 1 weeks ago │ - │ - │\n│ raredisease │ 59 │ dev │ 1 weeks ago │ - │ - │\n│ proteinfold │ 27 │ dev │ 1 weeks ago │ - │ - │\n│ rnafusion │ 114 │ dev │ 1 weeks ago │ - │ - │\n│ scrnaseq │ 102 │ dev │ 1 weeks ago │ - │ - │\n│ circrna │ 31 │ dev │ 2 weeks ago │ - │ - │\n│ multiplesequencealign │ 4 │ dev │ 2 weeks ago │ - │ - │\n│ ampliseq │ 131 │ dev │ 2 weeks ago │ - │ - │\n│ crisprseq │ 11 │ dev │ 2 weeks ago │ - │ - │\n│ mcmicro │ 0 │ dev │ 2 weeks ago │ - │ - │\n│ chipseq │ 153 │ dev │ 2 weeks ago │ - │ - │\n│ atacseq │ 148 │ dev │ 2 weeks ago │ - │ - │\n│ molkart │ 2 │ dev │ 2 weeks ago │ - │ - │\n│ metapep │ 4 │ dev │ 2 weeks ago │ - │ - │\n│ methylseq │ 117 │ dev │ 3 weeks ago │ - │ - │\n│ viralrecon │ 101 │ dev │ 3 weeks ago │ - │ - │\n│ pathogensurveillance │ 6 │ dev │ 1 months ago │ - │ - │\n│ createpanelrefs │ 3 │ dev │ 1 months ago │ - │ - │\n│ quantms │ 14 │ dev │ 1 months ago │ - │ - │\n│ smrnaseq │ 58 │ dev │ 1 months ago │ - │ - │\n│ nanostring │ 6 │ dev │ 1 months ago │ - │ - │\n│ cutandrun │ 51 │ dev │ 1 months ago │ - │ - │\n│ demultiplex │ 28 │ dev │ 2 months ago │ 1 weeks ago │ No (v1.3.2) │\n│ isoseq │ 16 │ dev │ 2 months ago │ - │ - │\n│ airrflow │ 32 │ dev │ 3 months ago │ - │ - │\n│ viralintegration │ 11 │ dev │ 3 months ago │ - │ - │\n│ hicar │ 4 │ dev │ 3 months ago │ - │ - │\n│ circdna │ 17 │ dev │ 3 months ago │ - │ - │\n│ marsseq │ 4 │ dev │ 3 months ago │ - │ - │\n│ spatialtranscriptomics │ 28 │ dev │ 3 months ago │ - │ - │\n│ hic │ 60 │ dev │ 4 months ago │ - │ - │\n│ nanoseq │ 123 │ dev │ 5 months ago │ - │ - │\n│ callingcards │ 2 │ dev │ 5 months ago │ - │ - │\n│ gwas │ 15 │ dev │ 5 months ago │ - │ - │\n│ hgtseq │ 18 │ dev │ 5 months ago │ - │ - │\n│ genomeassembler │ 13 │ dev │ 5 months ago │ - │ - │\n│ spinningjenny │ 0 │ dev │ 7 months ago │ - │ - │\n│ variantcatalogue │ 4 │ dev │ 7 months ago │ - │ - │\n│ phyloplace │ 3 │ dev │ 7 months ago │ - │ - │\n│ clipseq │ 16 │ dev │ 7 months ago │ - │ - │\n│ radseq │ 3 │ dev │ 8 months ago │ - │ - │\n│ hlatyping │ 47 │ dev │ 9 months ago │ - │ - │\n│ fastquorum │ 8 │ dev │ 11 months ago │ - │ - │\n│ coproid │ 8 │ dev │ 11 months ago │ - │ - │\n│ lncpipe │ 26 │ dev │ 1 years ago │ - │ - │\n│ imcyto │ 23 │ dev │ 1 years ago │ - │ - │\n│ mnaseseq │ 10 │ dev │ 1 years ago │ - │ - │\n│ genomeannotator │ 12 │ dev │ 2 years ago │ - │ - │\n│ proteomicslfq │ 32 │ dev │ 2 years ago │ - │ - │\n│ cageseq │ 9 │ dev │ 2 years ago │ - │ - │\n│ scflow │ 21 │ dev │ 2 years ago │ - │ - │\n│ bactmap │ 45 │ dev │ 2 years ago │ - │ - │\n│ diaproteomics │ 12 │ dev │ 2 years ago │ - │ - │\n│ pgdb │ 5 │ dev │ 2 years ago │ - │ - │\n│ slamseq │ 4 │ dev │ 2 years ago │ - │ - │\n└────────────────────────┴───────┴────────────────┴───────────────┴─────────────┴──────────────────────┘" as "bash" resulted in an error at token: "'". Retrying in relaxed mode. [misc.highlighting_failure] genindex done writing additional pages... search done copying images... [ 7%] pegasus/Singularity/apptainerhelp1.png copying images... [ 13%] pegasus/Singularity/apptainerverify2.png copying images... [ 20%] pegasus/Singularity/apptainerjupyter3.png copying images... [ 27%] pegasus/Singularity/Apptainerdeffile4.png copying images... [ 33%] pegasus/Singularity/ruserid5.png copying images... [ 40%] pegasus/Singularity/RGUIstudioserver6.png copying images... [ 47%] pegasus/Singularity/apptainergpu7.png copying images... [ 53%] pegasus/Singularity/mcmicroresult8.png copying images... [ 60%] pegasus/Singularity/apptainerresult9.png copying images... [ 67%] pegasus/Singularity/apptainertest10.png copying images... [ 73%] pegasus/soft/assets/MatlabParallel1.png copying images... [ 80%] pegasus/soft/assets/MatlabParallel2.png copying images... [ 87%] pegasus/soft/assets/MatlabParallel3.png copying images... [ 93%] services/assets/putty_1.png copying images... [100%] services/assets/putty_2.png dumping search index in English (code: en)... done dumping object inventory... done ====================== slowest reading durations ======================= 0.078 pegasus/Singularity/apptainerinfo 0.038 policies/terms_conditions 0.021 services/svn 0.020 pegasus/soft/amazon_cli 0.016 linux/2-files build succeeded, 91 warnings. The HTML pages are in ../_readthedocs/html.