Read the Docs build information
Build id: 145131
Project: cyverse-dnasubway-guide
Version: latest
Commit: cf54bba02acd4aaf27c51d095073175a2835519e
Date: 2018-09-26T16:29:47.212900Z
State: finished
Success: True
[rtd-command-info] start-time: 2018-09-26T21:29:47.692518Z, end-time: 2018-09-26T21:29:47.698197Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/CyVerse-learning-materials/dnasubway_guide.git
[rtd-command-info] start-time: 2018-09-26T21:29:47.755481Z, end-time: 2018-09-26T21:29:48.008194Z, duration: 0, exit-code: 0
git fetch --tags --prune
From https://github.com/CyVerse-learning-materials/dnasubway_guide
1c5e76c..cf54bba master -> origin/master
[rtd-command-info] start-time: 2018-09-26T21:29:48.074683Z, end-time: 2018-09-26T21:29:48.082385Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 1c5e76c... test metadata link
HEAD is now at cf54bba... test metadata link
[rtd-command-info] start-time: 2018-09-26T21:29:48.139090Z, end-time: 2018-09-26T21:29:48.160020Z, duration: 0, exit-code: 0
git clean -d -f -f
Removing _build/
Removing misc/__init__.pyc
Removing misc/cyverse_sphinx_conf.pyc
[rtd-command-info] start-time: 2018-09-26T21:29:48.256396Z, end-time: 2018-09-26T21:29:48.262306Z, duration: 0, exit-code: 0
git branch -r
origin/HEAD -> origin/master
origin/master
[rtd-command-info] start-time: 2018-09-26T21:29:48.841782Z, end-time: 2018-09-26T21:29:50.463681Z, duration: 1, exit-code: 0
python2.7 -mvirtualenv --no-site-packages --no-download
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python2.7
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python2.7)
Installing setuptools, pip, wheel...done.
[rtd-command-info] start-time: 2018-09-26T21:29:50.522330Z, end-time: 2018-09-26T21:29:52.895194Z, duration: 2, exit-code: 0
python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: setuptools<40 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: commonmark==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinx<1.8 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: idna<2.8,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8)
Requirement already up-to-date: urllib3<1.24,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8)
Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8)
Requirement already up-to-date: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8)
Requirement already up-to-date: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<1.8)
Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx<1.8)
Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<1.8)
You are using pip version 9.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
[rtd-command-info] start-time: 2018-09-26T21:29:53.404887Z, end-time: 2018-09-26T21:29:53.469090Z, duration: 0, exit-code: 0
cat conf.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# General information about the project.
import sys
import os
sys.path.insert(0, os.path.dirname(__file__))
from misc.cyverse_sphinx_conf import * # noqa
project = 'DNA Subway Guide'
copyright = '2016, CyVerse'
author = 'CyVerse'
version = '1.0'
release = '1.0'
epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright
###########################################################################
# 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 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
else:
SUFFIX = source_suffix[0]
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')
html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static')
# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = False
if 'html_theme' in globals():
if html_theme in ['default']:
# Allow people to bail with a hack of having an html_style
if not 'html_style' in globals():
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'
html_style = None
html_theme_options = {}
if 'html_theme_path' in globals():
html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
else:
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
using_rtd_theme = True
else:
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'
html_style = None
html_theme_options = {}
if 'html_theme_path' in globals():
html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
else:
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
using_rtd_theme = True
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/"),
],
'downloads': [
("htmlzip", "//readthedocs.com/projects/cyverse-dnasubway-guide/downloads/htmlzip/latest/"),
],
'subprojects': [
],
'slug': 'cyverse-dnasubway-guide',
'name': u'dnasubway_guide',
'rtd_language': u'en',
'programming_language': u'words',
'canonical_url': 'https://learning.cyverse.org/projects/dnasubway_guide/en/latest/',
'analytics_code': '',
'single_version': False,
'conf_py_path': '/./',
'api_host': 'https://readthedocs.com',
'github_user': 'CyVerse-learning-materials',
'github_repo': 'dnasubway_guide',
'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': 'cf54bba0',
}
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"]
[rtd-command-info] start-time: 2018-09-26T21:29:53.537649Z, end-time: 2018-09-26T21:29:55.799187Z, duration: 2, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 11 source files that are out of date
updating environment: 11 added, 0 changed, 0 removed
reading sources... [ 9%] Contributors_maintainers
reading sources... [ 18%] License
reading sources... [ 27%] index
reading sources... [ 36%] step1
reading sources... [ 45%] step2
reading sources... [ 54%] step3
reading sources... [ 63%] step4
reading sources... [ 72%] step5
reading sources... [ 81%] step6
reading sources... [ 90%] step7
reading sources... [100%] step8
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:180: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:182: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:64: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:699: WARNING: Substitution definition "QIIME2 documentation" empty or invalid.
.. |QIIME2 documentation| raw::html
QIIME 2 documentation
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:51: WARNING: Undefined substitution referenced: "QIIME2 documentation".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 9%] Contributors_maintainers
writing output... [ 18%] License
writing output... [ 27%] index
writing output... [ 36%] step1
writing output... [ 45%] step2
writing output... [ 54%] step3
writing output... [ 63%] step4
writing output... [ 72%] step5
writing output... [ 81%] step6
writing output... [ 90%] step7
writing output... [100%] step8
generating indices... genindex
writing additional pages... search
copying images... [ 2%] ./img/dna_subway/sleuth_heatmap_1.png
copying images... [ 5%] ./img/dna_subway/blue_trace.png
copying images... [ 8%] ./img/dna_subway/histogram_poor.png
copying images... [ 11%] ./img/dna_subway/sleuth_bootstrap_1.png
copying images... [ 13%] ./img/dna_subway/sleuth_pca_1.png
copying images... [ 16%] ./img/dna_subway/apollo_2.png
copying images... [ 19%] ./img/dna_subway/sleuth_results_1.png
copying images... [ 22%] ./img/dna_subway/dnasubway-icon.png
copying images... [ 25%] ./img/dna_subway/project_info_tab.png
copying images... [ 27%] ./img/dna_subway/private_projects.png
copying images... [ 30%] ./img/dna_subway/blue_align.png
copying images... [ 33%] ./img/dna_subway/faith_group.png
copying images... [ 36%] ./img/dna_subway/taxonomy.png
copying images... [ 38%] ./img/dna_subway/taxabar.png
copying images... [ 41%] ./img/dna_subway/yellow_tree.png
copying images... [ 44%] ./img/dna_subway/blue_blast.png
copying images... [ 47%] ./img/dna_subway/core_matrix.png
copying images... [ 50%] ./img/dna_subway/blue_ml.png
copying images... [ 52%] ./img/dna_subway/apollo_4.png
copying images... [ 55%] ./img/dna_subway/even_cor.png
copying images... [ 58%] ./img/dna_subway/histogram_good.png
copying images... [ 61%] ./img/dna_subway/sleuth_volcano_1.png
copying images... [ 63%] ./img/dna_subway/group_sig.png
copying images... [ 66%] ./img/dna_subway/yellow_alignment.png
copying images... [ 69%] ./img/dna_subway/blue_nj.png
copying images... [ 72%] ./img/dna_subway/apollo_1.png
copying images... [ 75%] ./img/dna_subway/apollo_5.png
copying images... [ 77%] ./img/dna_subway/apollo_3.png
copying images... [ 80%] ./img/homeicon.png
copying images... [ 83%] ./img/dna_subway/bray.png
copying images... [ 86%] ./img/dna_subway/jbrowse.png
copying images... [ 88%] ./img/dna_subway/repeat_results.png
copying images... [ 91%] ./img/cyverse_rgb.png
copying images... [ 94%] ./img/dna_subway/sleuth_loadings_1.png
copying images... [ 97%] ./img/dna_subway/faith.png
copying images... [100%] ./img/dna_subway/unweighted.png
copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/_static' does not exist
WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist
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, 12 warnings.
The HTML pages are in _build/html.
[rtd-command-info] start-time: 2018-09-26T21:29:55.903916Z, end-time: 2018-09-26T21:29:57.910651Z, duration: 2, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
loading pickled environment... not yet created
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 11 added, 0 changed, 0 removed
reading sources... [ 9%] Contributors_maintainers
reading sources... [ 18%] License
reading sources... [ 27%] index
reading sources... [ 36%] step1
reading sources... [ 45%] step2
reading sources... [ 54%] step3
reading sources... [ 63%] step4
reading sources... [ 72%] step5
reading sources... [ 81%] step6
reading sources... [ 90%] step7
reading sources... [100%] step8
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:180: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:182: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:8: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:64: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:699: WARNING: Substitution definition "QIIME2 documentation" empty or invalid.
.. |QIIME2 documentation| raw::html
QIIME 2 documentation
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step8.rst:51: WARNING: Undefined substitution referenced: "QIIME2 documentation".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... step1 step2 step3 step4 step5 step6 step7 step8
writing... done
writing additional files...
copying images... [ 2%] ./img/dna_subway/sleuth_heatmap_1.png
copying images... [ 5%] ./img/dna_subway/blue_trace.png
copying images... [ 8%] ./img/dna_subway/histogram_poor.png
copying images... [ 11%] ./img/dna_subway/sleuth_bootstrap_1.png
copying images... [ 13%] ./img/dna_subway/sleuth_pca_1.png
copying images... [ 16%] ./img/dna_subway/apollo_2.png
copying images... [ 19%] ./img/dna_subway/sleuth_results_1.png
copying images... [ 22%] ./img/dna_subway/dnasubway-icon.png
copying images... [ 25%] ./img/dna_subway/project_info_tab.png
copying images... [ 27%] ./img/dna_subway/private_projects.png
copying images... [ 30%] ./img/dna_subway/blue_align.png
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copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/_static' does not exist
WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist
done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 12 warnings.
The HTML page is in _build/localmedia.