Read the Docs build information Build id: 236431 Project: life-epigenetics-methylprep Version: latest Commit: ec640cca9ea9d7774b8f20fe347dbc85e6904e0c Date: 2019-08-27T16:48:50.758399Z State: finished Success: False [rtd-command-info] start-time: 2019-08-27T16:48:51.220209Z, end-time: 2019-08-27T16:48:55.362991Z, duration: 4, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylprep.git . Cloning into '.'... [rtd-command-info] start-time: 2019-08-27T16:48:55.635259Z, end-time: 2019-08-27T16:48:56.235409Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out '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 performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at ec640cc Update README.md [rtd-command-info] start-time: 2019-08-27T16:48:56.313690Z, end-time: 2019-08-27T16:48:56.328821Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-08-27T16:48:57.873037Z, end-time: 2019-08-27T16:49:01.285682Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.7.1' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl Collecting pyrsistent>=0.14.0 (from jsonschema!=2.5.0,>=2.4->nbformat->nbsphinx->-r requirements.txt (line 10)) Downloading https://files.pythonhosted.org/packages/b9/66/b2638d96a2d128b168d0dba60fdc77b7800a9b4a5340cefcc5fc4eae6295/pyrsistent-0.15.4.tar.gz (107kB) Building wheels for collected packages: coveralls-python, m2r, pandocfilters, pyrsistent Building wheel for coveralls-python (setup.py): started Building wheel for coveralls-python (setup.py): finished with status 'done' Created wheel for coveralls-python: filename=coveralls_python-0.0.1-cp37-none-any.whl size=1153 sha256=e2baf056e5c2cfa96fdb56a5d08df56d8e6b2fef3fbe4e69f9ef1770612da090 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip/wheels/5d/cd/a1/f3b05c5cadb3e18d779b3d86c3bda0276d59a098c8b3379447 Building wheel for m2r 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for pyrsistent: filename=pyrsistent-0.15.4-cp37-cp37m-linux_x86_64.whl size=115875 sha256=17a6282d7602b44c8c5ce5aee9c86792323cf8d2fa44d4352ba571b234d83665 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip/wheels/bb/46/00/6d471ef0b813e3621f0abe6cb723c20d529d39a061de3f7c51 Successfully built coveralls-python m2r pandocfilters pyrsistent Installing collected packages: numpy, python-dateutil, pandas, scipy, patsy, statsmodels, more-itertools, atomicwrites, wcwidth, zipp, importlib-metadata, pluggy, py, pytest, coverage, coveralls-python, pbr, sphinxcontrib-apidoc, mistune, m2r, entrypoints, testpath, ipython-genutils, decorator, traitlets, pandocfilters, jupyter-core, pyrsistent, jsonschema, nbformat, webencodings, bleach, defusedxml, nbconvert, nbsphinx, tqdm Successfully installed atomicwrites-1.3.0 bleach-3.1.0 coverage-4.5.4 coveralls-python-0.0.1 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-0.19 ipython-genutils-0.2.0 jsonschema-3.0.2 jupyter-core-4.5.0 m2r-0.2.1 mistune-0.8.4 more-itertools-7.2.0 nbconvert-5.6.0 nbformat-4.4.0 nbsphinx-0.4.2 numpy-1.17.1 pandas-0.25.1 pandocfilters-1.4.2 patsy-0.5.1 pbr-5.4.2 pluggy-0.12.0 py-1.8.0 pyrsistent-0.15.4 pytest-5.1.1 python-dateutil-2.8.0 scipy-1.3.1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.10.1 testpath-0.4.2 tqdm-4.35.0 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1 zipp-0.6.0 [rtd-command-info] start-time: 2019-08-27T16:49:44.026058Z, end-time: 2019-08-27T16:49:44.372657Z, duration: 0, exit-code: 0 cat conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # -- 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 = 'methylprep' copyright = '2019, Life Epigenetics' author = 'Life Epigenetics' # The short X.Y version version = '' # The full version, including alpha/beta/rc tags release = '1.0' # -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinxcontrib.apidoc', 'm2r', 'nbsphinx' ] # instead of CLI "sphinx-autodoc . _build/html" you write this apidoc_module_dir = '.' apidoc_output_dir = '_sphinx_build' apidoc_excluded_paths = ['tests'] apidoc_separate_modules = False # Add any paths that contain templates here, relative to this directory. templates_path = ['_sphinx_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # source_suffix = '.rst' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # 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 = ['_sphinx_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # -- 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' #'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # 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 = ['_sphinx_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'methylpredoc' # -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'methylprep.tex', 'methylprep Documentation', 'Life Epigenetics', 'manual'), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'methylprep', 'methylprep Documentation', [author], 1) ] # -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'methylprep', 'methylprep Documentation', author, 'methylprep', 'One line description of project.', 'Miscellaneous'), ] # -- Extension configuration ------------------------------------------------- ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("renamed", "/en/renamed/"), ], 'downloads': [ ("html", "//readthedocs.com/projects/life-epigenetics-methylprep/downloads/htmlzip/latest/"), ("epub", "//readthedocs.com/projects/life-epigenetics-methylprep/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylprep', 'name': u'methylprep', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://life-epigenetics-methylprep.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'LifeEGX', 'github_repo': 'methylprep', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'ec640cca', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2019-08-27T16:49:44.466905Z, end-time: 2019-08-27T16:49:48.722467Z, duration: 4, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst. building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 13 source files that are out of date updating environment: 13 added, 0 changed, 0 removed reading sources... [ 7%] README reading sources... [ 15%] docs/README reading sources... [ 23%] docs/cli reading sources... [ 30%] docs/installation reading sources... [ 38%] docs/methylprep_tutorial reading sources... [ 46%] docs/package reading sources... [ 53%] docs/source/methpype reading sources... [ 61%] docs/source/methpype.arrays reading sources... [ 69%] docs/source/methpype.preprocess reading sources... [ 76%] docs/source/methpype.samples reading sources... [ 84%] docs/source/methpype.utils reading sources... [ 92%] docs/source/modules reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:188: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:218: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:252: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methqc". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:362: WARNING: Title level inconsistent: Filtering by Probes ~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:433: WARNING: Title level inconsistent: Visual Filtering Functions ~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:2: WARNING: Title underline too short. methylprep package ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.utils' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short. methylprep.cli module ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short. methylprep.cli module ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:2: WARNING: Title underline too short. methylprep.arrays package ======================= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short. methylprep.arrays.arrays module ----------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short. methylprep.arrays.arrays module ----------------------------- WARNING: autodoc: failed to import module 'arrays.arrays' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short. methylprep.arrays.controls module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short. methylprep.arrays.controls module ------------------------------- WARNING: autodoc: failed to import module 'arrays.controls' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short. methylprep.arrays.manifest module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short. methylprep.arrays.manifest module ------------------------------- WARNING: autodoc: failed to import module 'arrays.manifest' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short. methylprep.arrays.probes module ----------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short. methylprep.arrays.probes module ----------------------------- WARNING: autodoc: failed to import module 'arrays.probes' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' WARNING: autodoc: failed to import module 'arrays' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:2: WARNING: Title underline too short. methylprep.preprocess package =========================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short. methylprep.preprocess.idat module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short. methylprep.preprocess.idat module ------------------------------- WARNING: autodoc: failed to import module 'preprocess.idat' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short. methylprep.preprocess.meth\_dataset module ---------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short. methylprep.preprocess.meth\_dataset module ---------------------------------------- WARNING: autodoc: failed to import module 'preprocess.meth_dataset' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short. methylprep.preprocess.noob module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short. methylprep.preprocess.noob module ------------------------------- WARNING: autodoc: failed to import module 'preprocess.noob' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short. methylprep.preprocess.pipeline module ----------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short. methylprep.preprocess.pipeline module ----------------------------------- WARNING: autodoc: failed to import module 'preprocess.pipeline' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short. methylprep.preprocess.raw\_dataset module --------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short. methylprep.preprocess.raw\_dataset module --------------------------------------- WARNING: autodoc: failed to import module 'preprocess.raw_dataset' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short. methylprep.preprocess.utils module -------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short. methylprep.preprocess.utils module -------------------------------- WARNING: autodoc: failed to import module 'preprocess.utils' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' WARNING: autodoc: failed to import module 'preprocess' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:2: WARNING: Title underline too short. methylprep.samples package ======================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short. methylprep.samples.sample module ------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short. methylprep.samples.sample module ------------------------------ WARNING: autodoc: failed to import module 'samples.sample' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short. methylprep.samples.sample\_sheet module ------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short. methylprep.samples.sample\_sheet module ------------------------------------- WARNING: autodoc: failed to import module 'samples.sample_sheet' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' WARNING: autodoc: failed to import module 'samples' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:2: WARNING: Title underline too short. methylprep.utils package ====================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short. methylprep.utils.data module -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short. methylprep.utils.data module -------------------------- WARNING: autodoc: failed to import module 'data' from module 'methylprep.utils'; the following exception was raised: No module named 'methylprep.utils.data' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short. methylprep.utils.decorators module -------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short. methylprep.utils.decorators module -------------------------------- WARNING: autodoc: failed to import module 'decorators' from module 'methylprep.utils'; the following exception was raised: No module named 'methylprep.utils.decorators' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short. methylprep.utils.files module --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short. methylprep.utils.files module --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Title underline too short. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Unexpected section title. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Title underline too short. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Unexpected section title. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:2: WARNING: Title underline too short. methylprep ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:4: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:7: WARNING: Title underline too short. Welcome to methylprep's documentation! ==================================== README.md:188: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ README.md:218: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ README.md:252: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/installation.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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[ 94%] docs/tutorial_figs/fig17.png copying images... [100%] docs/tutorial_figs/fig18.png copying static files... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 86 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-08-27T16:49:48.867730Z, end-time: 2019-08-27T16:49:52.890337Z, duration: 4, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst. 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:188: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:218: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:252: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methqc". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:362: WARNING: Title level inconsistent: Filtering by Probes ~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:433: WARNING: Title level inconsistent: Visual Filtering Functions ~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:2: WARNING: Title underline too short. methylprep package ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.utils' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short. methylprep.cli module ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short. methylprep.cli module ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:2: WARNING: Title underline too short. methylprep.arrays package ======================= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short. methylprep.arrays.arrays module ----------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short. methylprep.arrays.arrays module ----------------------------- WARNING: autodoc: failed to import module 'arrays.arrays' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short. methylprep.arrays.controls module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short. methylprep.arrays.controls module ------------------------------- WARNING: autodoc: failed to import module 'arrays.controls' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short. methylprep.arrays.manifest module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short. methylprep.arrays.manifest module ------------------------------- WARNING: autodoc: failed to import module 'arrays.manifest' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short. methylprep.arrays.probes module ----------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short. methylprep.arrays.probes module ----------------------------- WARNING: autodoc: failed to import module 'arrays.probes' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' WARNING: autodoc: failed to import module 'arrays' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:2: WARNING: Title underline too short. methylprep.preprocess package =========================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short. methylprep.preprocess.idat module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short. methylprep.preprocess.idat module ------------------------------- WARNING: autodoc: failed to import module 'preprocess.idat' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short. methylprep.preprocess.meth\_dataset module ---------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short. methylprep.preprocess.meth\_dataset module ---------------------------------------- WARNING: autodoc: failed to import module 'preprocess.meth_dataset' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short. methylprep.preprocess.noob module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short. methylprep.preprocess.noob module ------------------------------- WARNING: autodoc: failed to import module 'preprocess.noob' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short. methylprep.preprocess.pipeline module ----------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short. methylprep.preprocess.pipeline module ----------------------------------- WARNING: autodoc: failed to import module 'preprocess.pipeline' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short. methylprep.preprocess.raw\_dataset module --------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short. methylprep.preprocess.raw\_dataset module --------------------------------------- WARNING: autodoc: failed to import module 'preprocess.raw_dataset' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short. methylprep.preprocess.utils module -------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short. methylprep.preprocess.utils module -------------------------------- WARNING: autodoc: failed to import module 'preprocess.utils' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' WARNING: autodoc: failed to import module 'preprocess' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:2: WARNING: Title underline too short. methylprep.samples package ======================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short. methylprep.samples.sample module ------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short. methylprep.samples.sample module ------------------------------ WARNING: autodoc: failed to import module 'samples.sample' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short. methylprep.samples.sample\_sheet module ------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short. methylprep.samples.sample\_sheet module ------------------------------------- WARNING: autodoc: failed to import module 'samples.sample_sheet' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' WARNING: autodoc: failed to import module 'samples' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:2: WARNING: Title underline too short. methylprep.utils package ====================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short. methylprep.utils.data module -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short. methylprep.utils.data module -------------------------- WARNING: autodoc: failed to import module 'data' from module 'methylprep.utils'; the following exception was raised: No module named 'methylprep.utils.data' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short. methylprep.utils.decorators module -------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short. methylprep.utils.decorators module -------------------------------- WARNING: autodoc: failed to import module 'decorators' from module 'methylprep.utils'; the following exception was raised: No module named 'methylprep.utils.decorators' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short. methylprep.utils.files module --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short. methylprep.utils.files module --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Title underline too short. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Unexpected section title. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Title underline too short. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Unexpected section title. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:2: WARNING: Title underline too short. methylprep ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:4: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:7: WARNING: Title underline too short. Welcome to methylprep's documentation! ==================================== README.md:188: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ README.md:218: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ README.md:252: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/installation.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... docs/methylprep_tutorial docs/cli docs/source/modules writing... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:278: WARNING: Could not lex literal_block as "bash". 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[ 83%] docs/tutorial_figs/fig15.png copying images... [ 88%] docs/tutorial_figs/fig16.png copying images... [ 94%] docs/tutorial_figs/fig17.png copying images... [100%] docs/tutorial_figs/fig18.png copying static files... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 86 warnings. The HTML page is in _build/localmedia. [rtd-command-info] start-time: 2019-08-27T16:49:53.021133Z, end-time: 2019-08-27T16:49:59.286902Z, duration: 6, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst. 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:188: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:218: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:252: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methqc". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:362: WARNING: Title level inconsistent: Filtering by Probes ~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:433: WARNING: Title level inconsistent: Visual Filtering Functions ~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:2: WARNING: Title underline too short. methylprep package ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.utils' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short. methylprep.cli module ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short. methylprep.cli module ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:2: WARNING: Title underline too short. methylprep.arrays package ======================= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short. methylprep.arrays.arrays module ----------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short. methylprep.arrays.arrays module ----------------------------- WARNING: autodoc: failed to import module 'arrays.arrays' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short. methylprep.arrays.controls module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short. methylprep.arrays.controls module ------------------------------- WARNING: autodoc: failed to import module 'arrays.controls' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short. methylprep.arrays.manifest module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short. methylprep.arrays.manifest module ------------------------------- WARNING: autodoc: failed to import module 'arrays.manifest' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short. methylprep.arrays.probes module ----------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short. methylprep.arrays.probes module ----------------------------- WARNING: autodoc: failed to import module 'arrays.probes' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' WARNING: autodoc: failed to import module 'arrays' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:2: WARNING: Title underline too short. methylprep.preprocess package =========================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short. methylprep.preprocess.idat module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short. methylprep.preprocess.idat module ------------------------------- WARNING: autodoc: failed to import module 'preprocess.idat' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short. methylprep.preprocess.meth\_dataset module ---------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short. methylprep.preprocess.meth\_dataset module ---------------------------------------- WARNING: autodoc: failed to import module 'preprocess.meth_dataset' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short. methylprep.preprocess.noob module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short. methylprep.preprocess.noob module ------------------------------- WARNING: autodoc: failed to import module 'preprocess.noob' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short. methylprep.preprocess.pipeline module ----------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short. methylprep.preprocess.pipeline module ----------------------------------- WARNING: autodoc: failed to import module 'preprocess.pipeline' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short. methylprep.preprocess.raw\_dataset module --------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short. methylprep.preprocess.raw\_dataset module --------------------------------------- WARNING: autodoc: failed to import module 'preprocess.raw_dataset' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short. methylprep.preprocess.utils module -------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short. methylprep.preprocess.utils module -------------------------------- WARNING: autodoc: failed to import module 'preprocess.utils' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' WARNING: autodoc: failed to import module 'preprocess' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:2: WARNING: Title underline too short. methylprep.samples package ======================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short. methylprep.samples.sample module ------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short. methylprep.samples.sample module ------------------------------ WARNING: autodoc: failed to import module 'samples.sample' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short. methylprep.samples.sample\_sheet module ------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short. methylprep.samples.sample\_sheet module ------------------------------------- WARNING: autodoc: failed to import module 'samples.sample_sheet' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' WARNING: autodoc: failed to import module 'samples' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:2: WARNING: Title underline too short. methylprep.utils package ====================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short. methylprep.utils.data module -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short. methylprep.utils.data module -------------------------- WARNING: autodoc: failed to import module 'data' from module 'methylprep.utils'; the following exception was raised: No module named 'methylprep.utils.data' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short. methylprep.utils.decorators module -------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short. methylprep.utils.decorators module -------------------------------- WARNING: autodoc: failed to import module 'decorators' from module 'methylprep.utils'; the following exception was raised: No module named 'methylprep.utils.decorators' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short. methylprep.utils.files module --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short. methylprep.utils.files module --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Title underline too short. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Unexpected section title. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Title underline too short. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Unexpected section title. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:2: WARNING: Title underline too short. methylprep ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:4: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:7: WARNING: Title underline too short. Welcome to methylprep's documentation! ==================================== README.md:188: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ README.md:218: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ README.md:252: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/installation.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst: WARNING: document isn't included in any toctree done processing methylprep.tex...index docs/methylprep_tutorial docs/cli docs/source/modules resolving references... 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' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2019-08-27T16:50:08.252113Z, end-time: 2019-08-27T16:50:10.578518Z, duration: 2, exit-code: 12 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylprep -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. 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Type H for immediate help. ... l.227 ...85bf0d887fe833c6ebc1cdb73fdc/badge}.svg}} ^^M [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 296--298 \T1/ptm/m/n/10 val-ues are \T1/pcr/m/n/10 custom\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 296--298 \T1/pcr/m/n/10 450k\T1/ptm/m/n/10 , \T1/pcr/m/n/10 epic\T1/ptm/m/n/10 , and Underfull \hbox (badness 5302) in paragraph at lines 296--298 \T1/ptm/m/n/10 to de-ter-mine the ar-ray Overfull \hbox (21.06123pt too wide) in paragraph at lines 317--318 []|\T1/pcr/m/n/10 sample_sheet_filepath| [2] [3] Overfull \hbox (21.06123pt too wide) in paragraph at lines 472--473 []|\T1/pcr/m/n/10 sample_sheet_filepath| Underfull \hbox (badness 10000) in paragraph at lines 526--528 \T1/ptm/m/n/10 val-ues are \T1/pcr/m/n/10 custom\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 526--528 \T1/pcr/m/n/10 450k\T1/ptm/m/n/10 , \T1/pcr/m/n/10 epic\T1/ptm/m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 526--528 \T1/ptm/m/n/10 the pacak-age will at- Underfull \hbox (badness 10000) in paragraph at lines 526--528 \T1/ptm/m/n/10 pro-vided Raw-Dataset [4] LaTeX Warning: Hyper reference `docs/methylprep_tutorial:minfi' on page 5 undef ined on input line 596. [5] LaTeX Warning: Hyper reference `docs/methylprep_tutorial:27K' on page 6 undefin ed on input line 605. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:infinium' on page 6 un defined on input line 614. [6 <./1-s2.0-S0888754311001807-gr1.jpg>] LaTeX Warning: Hyper reference `docs/methylprep_tutorial:du' on page 7 undefine d on input line 621. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:triche' on page 7 unde fined on input line 633. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:chen' on page 7 undefi ned on input line 638. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:chen' on page 7 undefi ned on input line 641. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:zhou' on page 7 undefi ned on input line 644. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:naeem' on page 7 undef ined on input line 647. [7] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. 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Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} (That makes 100 errors; please try again.) ! ==> Fatal error occurred, no output PDF file produced! Transcript written on life-epigenetics-methylprep.log. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Rule 'makeindex life-epigenetics-methylprep.idx': File changes, etc: Non-existent destination files: 'life-epigenetics-methylprep.ind' ------------ Run number 1 of rule 'makeindex life-epigenetics-methylprep.idx' ------------ ------------ Running 'makeindex -s python.ist -o "life-epigenetics-methylprep.ind" "life-epigenetics-methylprep.idx"' ------------ Latexmk: applying rule 'makeindex life-epigenetics-methylprep.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file life-epigenetics-methylprep.idx...done (0 entries accepted, 0 rejected). Nothing written in life-epigenetics-methylprep.ind. Transcript written in life-epigenetics-methylprep.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylprep.aux' 'life-epigenetics-methylprep.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylprep" "methylprep.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./methylprep.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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Type H for immediate help. ... l.227 ...85bf0d887fe833c6ebc1cdb73fdc/badge}.svg}} ^^M [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 296--298 \T1/ptm/m/n/10 val-ues are \T1/pcr/m/n/10 custom\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 296--298 \T1/pcr/m/n/10 450k\T1/ptm/m/n/10 , \T1/pcr/m/n/10 epic\T1/ptm/m/n/10 , and Underfull \hbox (badness 5302) in paragraph at lines 296--298 \T1/ptm/m/n/10 to de-ter-mine the ar-ray Overfull \hbox (21.06123pt too wide) in paragraph at lines 317--318 []|\T1/pcr/m/n/10 sample_sheet_filepath| [2] [3] Overfull \hbox (21.06123pt too wide) in paragraph at lines 472--473 []|\T1/pcr/m/n/10 sample_sheet_filepath| Underfull \hbox (badness 10000) in paragraph at lines 526--528 \T1/ptm/m/n/10 val-ues are \T1/pcr/m/n/10 custom\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 526--528 \T1/pcr/m/n/10 450k\T1/ptm/m/n/10 , \T1/pcr/m/n/10 epic\T1/ptm/m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 526--528 \T1/ptm/m/n/10 the pacak-age will at- Underfull \hbox (badness 10000) in paragraph at lines 526--528 \T1/ptm/m/n/10 pro-vided Raw-Dataset [4] LaTeX Warning: Hyper reference `docs/methylprep_tutorial:minfi' on page 5 undef ined on input line 596. [5] LaTeX Warning: Hyper reference `docs/methylprep_tutorial:27K' on page 6 undefin ed on input line 605. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:infinium' on page 6 un defined on input line 614. [6 <./1-s2.0-S0888754311001807-gr1.jpg>] LaTeX Warning: Hyper reference `docs/methylprep_tutorial:du' on page 7 undefine d on input line 621. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:triche' on page 7 unde fined on input line 633. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:chen' on page 7 undefi ned on input line 638. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:chen' on page 7 undefi ned on input line 641. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:zhou' on page 7 undefi ned on input line 644. LaTeX Warning: Hyper reference `docs/methylprep_tutorial:naeem' on page 7 undef ined on input line 647. [7] ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. 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Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} (That makes 100 errors; please try again.) ! ==> Fatal error occurred, no output PDF file produced! Transcript written on life-epigenetics-methylprep.log. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylprep.out' 'life-epigenetics-methylprep.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylprep" "methylprep.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./methylprep.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} ! Package inputenc Error: Unicode char █ (U+2588) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.680 ...m}{00}:00, \PYG{l+m}{18}.08s/it\PYG{o}{]} (That makes 100 errors; please try again.) ! ==> Fatal error occurred, no output PDF file produced! Transcript written on life-epigenetics-methylprep.log. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Failure to make 'life-epigenetics-methylprep.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2019-08-27T16:50:10.718527Z, end-time: 2019-08-27T16:50:25.690904Z, duration: 14, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst. building [mo]: targets for 0 po files that are out of date building [epub]: targets for 13 source files that are out of date updating environment: 13 added, 0 changed, 0 removed reading sources... [ 7%] README reading sources... [ 15%] docs/README reading sources... 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:188: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:218: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:252: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methqc". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:362: WARNING: Title level inconsistent: Filtering by Probes ~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:433: WARNING: Title level inconsistent: Visual Filtering Functions ~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:2: WARNING: Title underline too short. methylprep package ================ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.utils' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short. methylprep.cli module ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short. methylprep.cli module ------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:2: WARNING: Title underline too short. methylprep.arrays package ======================= /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short. methylprep.arrays.arrays module ----------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short. methylprep.arrays.arrays module ----------------------------- WARNING: autodoc: failed to import module 'arrays.arrays' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short. methylprep.arrays.controls module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short. methylprep.arrays.controls module ------------------------------- WARNING: autodoc: failed to import module 'arrays.controls' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short. methylprep.arrays.manifest module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short. methylprep.arrays.manifest module ------------------------------- WARNING: autodoc: failed to import module 'arrays.manifest' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short. methylprep.arrays.probes module ----------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short. methylprep.arrays.probes module ----------------------------- WARNING: autodoc: failed to import module 'arrays.probes' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' WARNING: autodoc: failed to import module 'arrays' from module 'methylprep'; the following exception was raised: No module named 'methylprep.arrays' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:2: WARNING: Title underline too short. methylprep.preprocess package =========================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short. methylprep.preprocess.idat module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short. methylprep.preprocess.idat module ------------------------------- WARNING: autodoc: failed to import module 'preprocess.idat' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short. methylprep.preprocess.meth\_dataset module ---------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short. methylprep.preprocess.meth\_dataset module ---------------------------------------- WARNING: autodoc: failed to import module 'preprocess.meth_dataset' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short. methylprep.preprocess.noob module ------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short. methylprep.preprocess.noob module ------------------------------- WARNING: autodoc: failed to import module 'preprocess.noob' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short. methylprep.preprocess.pipeline module ----------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short. methylprep.preprocess.pipeline module ----------------------------------- WARNING: autodoc: failed to import module 'preprocess.pipeline' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short. methylprep.preprocess.raw\_dataset module --------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short. methylprep.preprocess.raw\_dataset module --------------------------------------- WARNING: autodoc: failed to import module 'preprocess.raw_dataset' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short. methylprep.preprocess.utils module -------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short. methylprep.preprocess.utils module -------------------------------- WARNING: autodoc: failed to import module 'preprocess.utils' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' WARNING: autodoc: failed to import module 'preprocess' from module 'methylprep'; the following exception was raised: No module named 'methylprep.preprocess' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:2: WARNING: Title underline too short. methylprep.samples package ======================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short. methylprep.samples.sample module ------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short. methylprep.samples.sample module ------------------------------ WARNING: autodoc: failed to import module 'samples.sample' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short. methylprep.samples.sample\_sheet module ------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short. methylprep.samples.sample\_sheet module ------------------------------------- WARNING: autodoc: failed to import module 'samples.sample_sheet' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' WARNING: autodoc: failed to import module 'samples' from module 'methylprep'; the following exception was raised: No module named 'methylprep.samples' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:2: WARNING: Title underline too short. methylprep.utils package ====================== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short. methylprep.utils.data module -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short. methylprep.utils.data module -------------------------- WARNING: autodoc: failed to import module 'data' from module 'methylprep.utils'; the following exception was raised: No module named 'methylprep.utils.data' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short. methylprep.utils.decorators module -------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short. methylprep.utils.decorators module -------------------------------- WARNING: autodoc: failed to import module 'decorators' from module 'methylprep.utils'; the following exception was raised: No module named 'methylprep.utils.decorators' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short. methylprep.utils.files module --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short. methylprep.utils.files module --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Title underline too short. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Unexpected section title. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Title underline too short. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Unexpected section title. Examples: -------- /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:2: WARNING: Title underline too short. methylprep ======== /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:4: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep' /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:7: WARNING: Title underline too short. Welcome to methylprep's documentation! ==================================== README.md:188: WARNING: Title level inconsistent: ``get_sample_sheet`` ~~~~~~~~~~~~~~~~~~~~~~~~ README.md:218: WARNING: Title level inconsistent: ``get_manifest`` ~~~~~~~~~~~~~~~~~~~~ README.md:252: WARNING: Title level inconsistent: ``get_raw_datasets`` ~~~~~~~~~~~~~~~~~~~~~~~~ looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/README.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/installation.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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