[ci] [docs] readthedocs build broken: Could not find LibR

[jameslamb]

Copied from https://github.com/microsoft/LightGBM/pull/2963#issuecomment-623204453

-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check for working C compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++
-- Check for working CXX compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring incomplete, errors occurred!
See also "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/lightgbm_r/src/build/CMakeFiles/CMakeOutput.log".

Updating lightgbm documentation
Loading lightgbm
Re-compiling lightgbm
'/home/docs/.conda/envs/r_env/lib/R/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/lightgbm_r'  \
  --library='/tmp/RtmpT7BLvD/devtools_install_be97189381e' --no-R --no-data  \
  --no-help --no-demo --no-inst --no-docs --no-exec --no-multiarch  \
  --no-test-load --preclean 

* installing *source* package ‘lightgbm’ ...
** libs
installing via 'install.libs.R' to /tmp/RtmpT7BLvD/devtools_install_be97189381e/lightgbm
R version passed into FindLibR.cmake: 3.5.1
CMake Error at /home/docs/.conda/envs/r_env/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find LibR (missing: LIBR_CORE_LIBRARY)
Call Stack (most recent call first):
  /home/docs/.conda/envs/r_env/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
  cmake/modules/FindLibR.cmake:221 (find_package_handle_standard_args)
  CMakeLists.txt:76 (find_package)

make: *** No rule to make target '_lightgbm'.  Stop.
Error in eval(ei, envir) : Cannot find lib_lightgbm.so
* removing ‘/tmp/RtmpT7BLvD/devtools_install_be97189381e/lightgbm’
Error: Command failed (1)
Execution halted

Full logs (clickable):

``` Read the Docs build information Build id: 10956193 Project: lightgbm Version: latest Commit: 6823af945390ba89b66d7e579501dc87e3cc6162 Date: 2020-05-03T02:56:29.295286Z State: finished Success: False [rtd-command-info] start-time: 2020-05-03T02:56:35.508728Z, end-time: 2020-05-03T02:56:37.804356Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/Microsoft/LightGBM . Cloning into '.'... [rtd-command-info] start-time: 2020-05-03T02:56:38.204370Z, end-time: 2020-05-03T02:56:38.583519Z, 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 6823af9 [docs] updated bug report template (#3032) [rtd-command-info] start-time: 2020-05-03T02:56:38.743686Z, end-time: 2020-05-03T02:56:38.995877Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-03T02:56:42.124059Z, end-time: 2020-05-03T02:56:46.975182Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-05-03T02:56:47.163401Z, end-time: 2020-05-03T02:56:48.094174Z, duration: 0, exit-code: 0 /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/bin/python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (20.1) [rtd-command-info] start-time: 2020-05-03T02:56:48.266392Z, end-time: 2020-05-03T02:57:00.822122Z, duration: 12, exit-code: 0 /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/bin/python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.3-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=5601b03737041e5d5a8c8732009ed529e541f800f4cdab9015b1af084706c3cc Stored in directory: /tmp/pip-ephem-wheel-cache-aeax0maq/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=26bc0027006814813dafa7eade050d3d9c14d0a1d3080ae9dc4f94638829de36 Stored in directory: /tmp/pip-ephem-wheel-cache-aeax0maq/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, certifi, chardet, urllib3, idna, requests, imagesize, six, pyparsing, packaging, pytz, babel, sphinxcontrib-websupport, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.1.3 Uninstalling setuptools-46.1.3: Successfully uninstalled setuptools-46.1.3 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.3 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.2 urllib3-1.25.9 [rtd-command-info] start-time: 2020-05-03T02:57:00.954635Z, end-time: 2020-05-03T02:57:05.325175Z, duration: 4, exit-code: 0 /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r docs/requirements_rtd.txt Ignoring mock: markers 'python_version < "3"' don't match your environment Collecting sphinx>=3.0.2 Downloading Sphinx-3.0.3-py3-none-any.whl (2.8 MB) Requirement already satisfied: sphinx_rtd_theme>=0.3 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from -r docs/requirements_rtd.txt (line 2)) (0.4.3) Collecting breathe Downloading breathe-4.18.0-py3-none-any.whl (76 kB) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2.11.2) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2.3.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (41.0.1) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2.8.0) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (1.2.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (20.3) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (0.14) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2.0.0) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2.23.0) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (0.7.12) Requirement already satisfied: six>=1.9 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from breathe->-r docs/requirements_rtd.txt (line 4)) (1.14.0) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (1.1.1) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2020.1) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from packaging->sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2.4.7) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2020.4.5.1) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (2.9) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (3.0.4) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=3.0.2->-r docs/requirements_rtd.txt (line 1)) (1.25.9) Installing collected packages: sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-devhelp, sphinx, breathe Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed breathe-4.18.0 sphinx-3.0.3 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 [rtd-command-info] start-time: 2020-05-03T02:57:06.498301Z, end-time: 2020-05-03T02:57:06.732298Z, duration: 0, exit-code: 0 cat docs/conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # LightGBM documentation build configuration file, created by # sphinx-quickstart on Thu May 4 14:30:58 2017. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # 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. """Sphinx configuration file.""" import datetime import os import sys import sphinx from distutils.dir_util import copy_tree from docutils.parsers.rst import Directive from sphinx.errors import VersionRequirementError from subprocess import PIPE, Popen CURR_PATH = os.path.abspath(os.path.dirname(__file__)) LIB_PATH = os.path.join(CURR_PATH, os.path.pardir, 'python-package') sys.path.insert(0, LIB_PATH) # -- mock out modules try: from unittest.mock import Mock # Python 3.x except ImportError: from mock import Mock # Python 2.x MOCK_MODULES = ['numpy', 'scipy', 'scipy.sparse', 'sklearn', 'matplotlib', 'pandas', 'graphviz'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() class IgnoredDirective(Directive): """Stub for unknown directives.""" has_content = True def run(self): """Do nothing.""" return [] # -- General configuration ------------------------------------------------ os.environ['LIGHTGBM_BUILD_DOC'] = '1' C_API = os.environ.get('C_API', '').lower().strip() != 'no' RTD = bool(os.environ.get('READTHEDOCS', '')) # If your documentation needs a minimal Sphinx version, state it here. needs_sphinx = '1.3' # Due to sphinx.ext.napoleon if needs_sphinx > sphinx.__version__: message = 'This project needs at least Sphinx v%s' % needs_sphinx raise VersionRequirementError(message) # 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', 'sphinx.ext.autosummary', 'sphinx.ext.todo', 'sphinx.ext.viewcode', 'sphinx.ext.napoleon', ] autodoc_default_flags = ['members', 'inherited-members', 'show-inheritance'] autodoc_default_options = { "members": True, "inherited-members": True, "show-inheritance": True, } # Generate autosummary pages. Output should be set with: `:toctree: pythonapi/` autosummary_generate = ['Python-API.rst'] # Only the class' docstring is inserted. autoclass_content = 'class' # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # The master toctree document. master_doc = 'index' # General information about the project. project = 'LightGBM' copyright = '%s, Microsoft Corporation' % str(datetime.datetime.now().year) author = 'Microsoft Corporation' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. with open(os.path.join(CURR_PATH, os.path.pardir, 'VERSION.txt'), 'r') as f: # The short X.Y version. version = f.read().strip() # The full version, including alpha/beta/rc tags. release = version # 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 patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'default' # -- Configuration for C API docs generation ------------------------------ if C_API: extensions.extend([ 'breathe', ]) breathe_projects = { "LightGBM": os.path.join(CURR_PATH, 'doxyoutput', 'xml') } breathe_default_project = "LightGBM" breathe_domain_by_extension = { "h": "c", } breathe_show_define_initializer = True c_id_attributes = ['LIGHTGBM_C_EXPORT'] # -- 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' # 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 = { 'includehidden': False, } # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # -- Options for HTMLHelp output ------------------------------------------ # Output file base name for HTML help builder. htmlhelp_basename = 'LightGBMdoc' def generate_doxygen_xml(app): """Generate XML documentation for C API by Doxygen. Parameters ---------- app : object The application object representing the Sphinx process. """ doxygen_args = [ "INPUT={}".format(os.path.join(CURR_PATH, os.path.pardir, 'include', 'LightGBM', 'c_api.h')), "OUTPUT_DIRECTORY={}".format(os.path.join(CURR_PATH, 'doxyoutput')), "GENERATE_HTML=NO", "GENERATE_LATEX=NO", "GENERATE_XML=YES", "XML_OUTPUT=xml", "XML_PROGRAMLISTING=YES", r'ALIASES="rst=\verbatim embed:rst:leading-asterisk"', r'ALIASES+="endrst=\endverbatim"', "ENABLE_PREPROCESSING=YES", "MACRO_EXPANSION=YES", "EXPAND_ONLY_PREDEF=NO", "SKIP_FUNCTION_MACROS=NO", "SORT_BRIEF_DOCS=YES", "WARN_AS_ERROR=YES", ] doxygen_input = '\n'.join(doxygen_args) is_py3 = sys.version[0] == "3" if is_py3: doxygen_input = bytes(doxygen_input, "utf-8") if not os.path.exists(os.path.join(CURR_PATH, 'doxyoutput')): os.makedirs(os.path.join(CURR_PATH, 'doxyoutput')) try: # Warning! The following code can cause buffer overflows on RTD. # Consider suppressing output completely if RTD project silently fails. # Refer to https://github.com/svenevs/exhale # /blob/fe7644829057af622e467bb529db6c03a830da99/exhale/deploy.py#L99-L111 process = Popen(["doxygen", "-"], stdin=PIPE, stdout=PIPE, stderr=PIPE) stdout, stderr = process.communicate(doxygen_input) output = '\n'.join([i.decode('utf-8') if is_py3 else i for i in (stdout, stderr) if i is not None]) if process.returncode != 0: raise RuntimeError(output) else: print(output) except BaseException as e: raise Exception("An error has occurred while executing Doxygen\n" + str(e)) def generate_r_docs(app): """Generate documentation for R-package. Parameters ---------- app : object The application object representing the Sphinx process. """ commands = """ echo 'options(repos = "https://cran.rstudio.com")' > $HOME/.Rprofile /home/docs/.conda/bin/conda create -q -y -n r_env \ r-base=3.5.1=h1e0a451_2 \ r-devtools=1.13.6=r351h6115d3f_0 \ r-jsonlite=1.5=r351h96ca727_0 \ r-matrix=1.2_14=r351h96ca727_0 \ r-testthat=2.0.0=r351h29659fb_0 \ cmake=3.14.0=h52cb24c_0 \ ca-certificates=2019.11.27=0 /home/docs/.conda/bin/conda install -q -y -n r_env -c conda-forge \ r-data.table=1.12.8=r35hcdcec82_0 \ r-pkgdown=1.3.0=r35h6115d3f_1001 \ r-roxygen2=6.1.1=r35h0357c0b_1001 source /home/docs/.conda/bin/activate r_env export TAR=/bin/tar cd {0} sed -i'.bak' '/# Build the package (do not touch this line!)/q' build_r.R Rscript build_r.R Rscript build_r_site.R """.format(os.path.join(CURR_PATH, os.path.pardir)) try: # Warning! The following code can cause buffer overflows on RTD. # Consider suppressing output completely if RTD project silently fails. # Refer to https://github.com/svenevs/exhale # /blob/fe7644829057af622e467bb529db6c03a830da99/exhale/deploy.py#L99-L111 process = Popen(['/bin/bash'], stdin=PIPE, stdout=PIPE, stderr=PIPE, universal_newlines=True) stdout, stderr = process.communicate(commands) output = '\n'.join([i for i in (stdout, stderr) if i is not None]) if process.returncode != 0: raise RuntimeError(output) else: print(output) except BaseException as e: raise Exception("An error has occurred while generating documentation for R-package\n" + str(e)) def setup(app): """Add new elements at Sphinx initialization time. Parameters ---------- app : object The application object representing the Sphinx process. """ first_run = not os.path.exists(os.path.join(CURR_PATH, '_FIRST_RUN.flag')) if first_run and RTD: open(os.path.join(CURR_PATH, '_FIRST_RUN.flag'), 'w').close() if C_API: app.connect("builder-inited", generate_doxygen_xml) else: app.add_directive('doxygenfile', IgnoredDirective) if RTD: # build R docs only on Read the Docs site if first_run: app.connect("builder-inited", generate_r_docs) app.connect("build-finished", lambda app, exception: copy_tree(os.path.join(CURR_PATH, os.path.pardir, "lightgbm_r", "docs"), os.path.join(app.outdir, "R"), verbose=0)) add_js_file = getattr(app, 'add_js_file', False) or app.add_javascript add_js_file("js/script.js") ########################################################################### # 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.org/websupport' websupport2_static_url = 'https://assets.readthedocs.org/static/' #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.org/", 'STATIC_URL': "https://assets.readthedocs.org/static/", 'PRODUCTION_DOMAIN': "readthedocs.org", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//lightgbm.readthedocs.io/_/downloads/en/latest/pdf/"), ], 'subprojects': [ ], 'slug': 'lightgbm', 'name': u'lightgbm', 'rtd_language': u'en', 'programming_language': u'cpp', 'canonical_url': 'https://lightgbm.readthedocs.io/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.org', 'github_user': 'Microsoft', 'github_repo': 'LightGBM', '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-17997319-1', 'commit': '6823af94', } 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: 2020-05-03T02:57:06.861359Z, end-time: 2020-05-03T03:00:33.319705Z, duration: 206, exit-code: 2 python /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/bin/sphinx-build -T -E -W -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.0.3 loading translations [en]... done making output directory... done [autosummary] generating autosummary for: Python-API.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.Booster.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.LGBMClassifier.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.LGBMModel.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.LGBMRanker.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.LGBMRegressor.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.create_tree_digraph.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.cv.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.early_stopping.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.plot_importance.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.plot_metric.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.plot_split_value_histogram.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.plot_tree.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.print_evaluation.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.record_evaluation.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.reset_parameter.rst, /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/pythonapi/lightgbm.train.rst /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages/sphinx/deprecation.py:52: RemovedInSphinx40Warning: sphinx.builders.html.DirectoryHTMLBuilder is deprecated. Check CHANGES for Sphinx API modifications. return getattr(self._module, name) /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages/readthedocs_ext/readthedocs.py:14: RemovedInSphinx40Warning: sphinx.builders.html.SingleFileHTMLBuilder is deprecated. Check CHANGES for Sphinx API modifications. from sphinx.builders.html import (DirectoryHTMLBuilder, SingleFileHTMLBuilder, Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/conf.py", line 258, in generate_r_docs raise RuntimeError(output) RuntimeError: Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/docs/.conda/envs/r_env added / updated specs: - ca-certificates==2019.11.27=0 - cmake==3.14.0=h52cb24c_0 - r-base==3.5.1=h1e0a451_2 - r-devtools==1.13.6=r351h6115d3f_0 - r-jsonlite==1.5=r351h96ca727_0 - r-matrix==1.2_14=r351h96ca727_0 - r-testthat==2.0.0=r351h29659fb_0 The following packages will be downloaded: package | build ---------------------------|----------------- _r-mutex-1.0.0 | anacondar_1 3 KB binutils_impl_linux-64-2.33.1| he6710b0_7 3.7 MB binutils_linux-64-2.33.1 | h9595d00_15 26 KB bwidget-1.9.11 | 1 116 KB bzip2-1.0.8 | h7b6447c_0 78 KB ca-certificates-2019.11.27 | 0 124 KB cairo-1.14.12 | h8948797_3 906 KB cmake-3.14.0 | h52cb24c_0 5.5 MB curl-7.67.0 | hbc83047_0 134 KB expat-2.2.6 | he6710b0_0 146 KB fontconfig-2.13.0 | h9420a91_0 227 KB freetype-2.9.1 | h8a8886c_1 550 KB fribidi-1.0.5 | h7b6447c_0 101 KB gcc_impl_linux-64-7.3.0 | habb00fd_1 41.9 MB gcc_linux-64-7.3.0 | h553295d_15 27 KB gfortran_impl_linux-64-7.3.0| hdf63c60_1 7.8 MB gfortran_linux-64-7.3.0 | h553295d_15 27 KB glib-2.63.1 | h5a9c865_0 2.9 MB graphite2-1.3.13 | h23475e2_0 98 KB gsl-2.4 | h14c3975_4 1.8 MB gxx_impl_linux-64-7.3.0 | hdf63c60_1 15.0 MB gxx_linux-64-7.3.0 | h553295d_15 26 KB harfbuzz-1.8.8 | hffaf4a1_0 507 KB icu-58.2 | he6710b0_3 10.5 MB jpeg-9b | h024ee3a_2 214 KB krb5-1.16.4 | h173b8e3_0 1.2 MB ld_impl_linux-64-2.33.1 | h53a641e_7 568 KB libcurl-7.67.0 | h20c2e04_0 426 KB libgfortran-ng-7.3.0 | hdf63c60_0 1006 KB libpng-1.6.37 | hbc83047_0 278 KB libssh2-1.9.0 | h1ba5d50_1 269 KB libtiff-4.1.0 | h2733197_0 447 KB libuuid-1.0.3 | h1bed415_2 15 KB libxcb-1.13 | h1bed415_1 421 KB libxml2-2.9.9 | hea5a465_1 1.6 MB make-4.2.1 | h1bed415_1 415 KB ncurses-6.2 | he6710b0_1 817 KB openssl-1.1.1g | h7b6447c_0 2.5 MB pango-1.42.4 | h049681c_0 464 KB pcre-8.43 | he6710b0_0 209 KB pixman-0.38.0 | h7b6447c_0 364 KB r-assertthat-0.2.0 | r351h6115d3f_0 55 KB r-base-3.5.1 | h1e0a451_2 26.5 MB r-cli-1.0.0 | r351h6115d3f_1 310 KB r-crayon-1.3.4 | r351h6115d3f_0 729 KB r-curl-3.2 | r351hadc6856_1 374 KB r-devtools-1.13.6 | r351h6115d3f_0 665 KB r-digest-0.6.15 | r351h96ca727_0 138 KB r-git2r-0.23.0 | r351h96ca727_1 804 KB r-httr-1.3.1 | r351h6115d3f_1 421 KB r-jsonlite-1.5 | r351h96ca727_0 632 KB r-lattice-0.20_35 | r351h96ca727_0 1.1 MB r-magrittr-1.5 | r351h6115d3f_4 157 KB r-matrix-1.2_14 | r351h96ca727_0 3.3 MB r-memoise-1.1.0 | r351h6115d3f_0 38 KB r-mime-0.5 | r351h96ca727_0 37 KB r-openssl-1.0.2 | r351h96ca727_1 588 KB r-praise-1.0.0 | r351h6115d3f_4 21 KB r-r6-2.2.2 | r351h6115d3f_0 245 KB r-rlang-0.2.1 | r351h96ca727_0 744 KB r-rstudioapi-0.7 | r351h6115d3f_0 126 KB r-testthat-2.0.0 | r351h29659fb_0 879 KB r-whisker-0.3_2 | r351hf348343_4 63 KB r-withr-2.1.2 | r351h6115d3f_0 149 KB rhash-1.3.8 | h1ba5d50_0 188 KB tktable-2.10 | h14c3975_0 86 KB xz-5.2.5 | h7b6447c_0 438 KB zstd-1.3.7 | h0b5b093_0 401 KB ------------------------------------------------------------ Total: 142.0 MB The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _r-mutex pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1 binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.33.1-he6710b0_7 binutils_linux-64 pkgs/main/linux-64::binutils_linux-64-2.33.1-h9595d00_15 bwidget pkgs/main/linux-64::bwidget-1.9.11-1 bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 ca-certificates pkgs/main/linux-64::ca-certificates-2019.11.27-0 cairo pkgs/main/linux-64::cairo-1.14.12-h8948797_3 cmake pkgs/main/linux-64::cmake-3.14.0-h52cb24c_0 curl pkgs/main/linux-64::curl-7.67.0-hbc83047_0 expat pkgs/main/linux-64::expat-2.2.6-he6710b0_0 fontconfig pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0 freetype pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1 fribidi pkgs/main/linux-64::fribidi-1.0.5-h7b6447c_0 gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-7.3.0-habb00fd_1 gcc_linux-64 pkgs/main/linux-64::gcc_linux-64-7.3.0-h553295d_15 gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_1 gfortran_linux-64 pkgs/main/linux-64::gfortran_linux-64-7.3.0-h553295d_15 glib pkgs/main/linux-64::glib-2.63.1-h5a9c865_0 graphite2 pkgs/main/linux-64::graphite2-1.3.13-h23475e2_0 gsl pkgs/main/linux-64::gsl-2.4-h14c3975_4 gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_1 gxx_linux-64 pkgs/main/linux-64::gxx_linux-64-7.3.0-h553295d_15 harfbuzz pkgs/main/linux-64::harfbuzz-1.8.8-hffaf4a1_0 icu pkgs/main/linux-64::icu-58.2-he6710b0_3 jpeg pkgs/main/linux-64::jpeg-9b-h024ee3a_2 krb5 pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libcurl pkgs/main/linux-64::libcurl-7.67.0-h20c2e04_0 libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0 libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0 libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0 libssh2 pkgs/main/linux-64::libssh2-1.9.0-h1ba5d50_1 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_0 libuuid pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2 libxcb pkgs/main/linux-64::libxcb-1.13-h1bed415_1 libxml2 pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1 make pkgs/main/linux-64::make-4.2.1-h1bed415_1 ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0 pango pkgs/main/linux-64::pango-1.42.4-h049681c_0 pcre pkgs/main/linux-64::pcre-8.43-he6710b0_0 pixman pkgs/main/linux-64::pixman-0.38.0-h7b6447c_0 r-assertthat pkgs/r/linux-64::r-assertthat-0.2.0-r351h6115d3f_0 r-base pkgs/r/linux-64::r-base-3.5.1-h1e0a451_2 r-cli pkgs/r/linux-64::r-cli-1.0.0-r351h6115d3f_1 r-crayon pkgs/r/linux-64::r-crayon-1.3.4-r351h6115d3f_0 r-curl pkgs/r/linux-64::r-curl-3.2-r351hadc6856_1 r-devtools pkgs/r/linux-64::r-devtools-1.13.6-r351h6115d3f_0 r-digest pkgs/r/linux-64::r-digest-0.6.15-r351h96ca727_0 r-git2r pkgs/r/linux-64::r-git2r-0.23.0-r351h96ca727_1 r-httr pkgs/r/linux-64::r-httr-1.3.1-r351h6115d3f_1 r-jsonlite pkgs/r/linux-64::r-jsonlite-1.5-r351h96ca727_0 r-lattice pkgs/r/linux-64::r-lattice-0.20_35-r351h96ca727_0 r-magrittr pkgs/r/linux-64::r-magrittr-1.5-r351h6115d3f_4 r-matrix pkgs/r/linux-64::r-matrix-1.2_14-r351h96ca727_0 r-memoise pkgs/r/linux-64::r-memoise-1.1.0-r351h6115d3f_0 r-mime pkgs/r/linux-64::r-mime-0.5-r351h96ca727_0 r-openssl pkgs/r/linux-64::r-openssl-1.0.2-r351h96ca727_1 r-praise pkgs/r/linux-64::r-praise-1.0.0-r351h6115d3f_4 r-r6 pkgs/r/linux-64::r-r6-2.2.2-r351h6115d3f_0 r-rlang pkgs/r/linux-64::r-rlang-0.2.1-r351h96ca727_0 r-rstudioapi pkgs/r/linux-64::r-rstudioapi-0.7-r351h6115d3f_0 r-testthat pkgs/r/linux-64::r-testthat-2.0.0-r351h29659fb_0 r-whisker pkgs/r/linux-64::r-whisker-0.3_2-r351hf348343_4 r-withr pkgs/r/linux-64::r-withr-2.1.2-r351h6115d3f_0 readline pkgs/main/linux-64::readline-7.0-h7b6447c_5 rhash pkgs/main/linux-64::rhash-1.3.8-h1ba5d50_0 tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0 tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/docs/.conda/envs/r_env added / updated specs: - r-data.table==1.12.8=r35hcdcec82_0 - r-pkgdown==1.3.0=r35h6115d3f_1001 - r-roxygen2==6.1.1=r35h0357c0b_1001 The following packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2020.4.5.1 | hecc5488_0 146 KB conda-forge openssl-1.1.1g | h516909a_0 2.1 MB conda-forge pandoc-2.9.2.1 | 0 18.7 MB conda-forge r-backports-1.1.6 | r35hcdcec82_1 76 KB conda-forge r-base64enc-0.1_3 | r35hcdcec82_1003 43 KB conda-forge r-brew-1.0_6 | r35h6115d3f_1002 92 KB conda-forge r-callr-3.4.3 | r35h6115d3f_0 391 KB conda-forge r-commonmark-1.7 | r35hcdcec82_1001 151 KB conda-forge r-data.table-1.12.8 | r35hcdcec82_0 1.8 MB conda-forge r-desc-1.2.0 | r35h6115d3f_1002 286 KB conda-forge r-evaluate-0.14 | r35h6115d3f_1 79 KB conda-forge r-fansi-0.4.1 | r35hcdcec82_0 195 KB conda-forge r-fs-1.4.1 | r35h0357c0b_0 483 KB conda-forge r-glue-1.4.0 | r35hcdcec82_0 143 KB conda-forge r-highlight-0.5.0 | r35h0357c0b_0 566 KB conda-forge r-highr-0.8 | r35h6115d3f_1 47 KB conda-forge r-htmltools-0.4.0 | r35h0357c0b_0 213 KB conda-forge r-knitr-1.28 | r35h6115d3f_0 1.3 MB conda-forge r-markdown-1.1 | r35hcdcec82_0 143 KB conda-forge r-mass-7.3_51.6 | r35hcdcec82_1 1.1 MB conda-forge r-packrat-0.5.0 | r35h6115d3f_1001 455 KB conda-forge r-pillar-1.3.0 | r351h6115d3f_0 152 KB r-pkgbuild-1.0.7 | r35h6115d3f_0 151 KB conda-forge r-pkgdown-1.3.0 | r35h6115d3f_1001 505 KB conda-forge r-pkgload-1.0.2 | r35h0357c0b_1001 159 KB conda-forge r-prettyunits-1.1.1 | r35h6115d3f_0 40 KB conda-forge r-processx-3.4.2 | r35hcdcec82_0 269 KB conda-forge r-ps-1.3.2 | r35hcdcec82_0 224 KB conda-forge r-purrr-0.2.5 |r351h96ca727_1002 283 KB conda-forge r-rcpp-1.0.4.6 | r35h0357c0b_0 1.9 MB conda-forge r-rematch2-2.1.2 | r35h6115d3f_0 52 KB conda-forge r-rmarkdown-2.1 | r35h6115d3f_0 3.0 MB conda-forge r-roxygen2-6.1.1 | r35h0357c0b_1001 508 KB conda-forge r-rprojroot-1.3_2 | r35h6115d3f_1002 93 KB conda-forge r-rsconnect-0.8.16 | r35h6115d3f_0 670 KB conda-forge r-stringi-1.4.3 | r35h0357c0b_2 766 KB conda-forge r-stringr-1.4.0 | r35h6115d3f_1 207 KB conda-forge r-tibble-1.4.2 |r351h96ca727_1002 229 KB conda-forge r-tinytex-0.22 | r35h6115d3f_0 110 KB conda-forge r-utf8-1.1.4 | r35hcdcec82_1002 160 KB conda-forge r-xfun-0.13 | r35h6115d3f_0 194 KB conda-forge r-xml2-1.3.2 | r35h0357c0b_0 249 KB conda-forge r-yaml-2.2.1 | r35hcdcec82_0 116 KB conda-forge ------------------------------------------------------------ Total: 38.3 MB The following NEW packages will be INSTALLED: pandoc conda-forge/linux-64::pandoc-2.9.2.1-0 r-backports conda-forge/linux-64::r-backports-1.1.6-r35hcdcec82_1 r-base64enc conda-forge/linux-64::r-base64enc-0.1_3-r35hcdcec82_1003 r-brew conda-forge/noarch::r-brew-1.0_6-r35h6115d3f_1002 r-callr conda-forge/noarch::r-callr-3.4.3-r35h6115d3f_0 r-commonmark conda-forge/linux-64::r-commonmark-1.7-r35hcdcec82_1001 r-data.table conda-forge/linux-64::r-data.table-1.12.8-r35hcdcec82_0 r-desc conda-forge/noarch::r-desc-1.2.0-r35h6115d3f_1002 r-evaluate conda-forge/noarch::r-evaluate-0.14-r35h6115d3f_1 r-fansi conda-forge/linux-64::r-fansi-0.4.1-r35hcdcec82_0 r-fs conda-forge/linux-64::r-fs-1.4.1-r35h0357c0b_0 r-glue conda-forge/linux-64::r-glue-1.4.0-r35hcdcec82_0 r-highlight conda-forge/linux-64::r-highlight-0.5.0-r35h0357c0b_0 r-highr conda-forge/noarch::r-highr-0.8-r35h6115d3f_1 r-htmltools conda-forge/linux-64::r-htmltools-0.4.0-r35h0357c0b_0 r-knitr conda-forge/noarch::r-knitr-1.28-r35h6115d3f_0 r-markdown conda-forge/linux-64::r-markdown-1.1-r35hcdcec82_0 r-mass conda-forge/linux-64::r-mass-7.3_51.6-r35hcdcec82_1 r-packrat conda-forge/noarch::r-packrat-0.5.0-r35h6115d3f_1001 r-pillar pkgs/r/linux-64::r-pillar-1.3.0-r351h6115d3f_0 r-pkgbuild conda-forge/noarch::r-pkgbuild-1.0.7-r35h6115d3f_0 r-pkgdown conda-forge/noarch::r-pkgdown-1.3.0-r35h6115d3f_1001 r-pkgload conda-forge/linux-64::r-pkgload-1.0.2-r35h0357c0b_1001 r-prettyunits conda-forge/noarch::r-prettyunits-1.1.1-r35h6115d3f_0 r-processx conda-forge/linux-64::r-processx-3.4.2-r35hcdcec82_0 r-ps conda-forge/linux-64::r-ps-1.3.2-r35hcdcec82_0 r-purrr conda-forge/linux-64::r-purrr-0.2.5-r351h96ca727_1002 r-rcpp conda-forge/linux-64::r-rcpp-1.0.4.6-r35h0357c0b_0 r-rematch2 conda-forge/noarch::r-rematch2-2.1.2-r35h6115d3f_0 r-rmarkdown conda-forge/noarch::r-rmarkdown-2.1-r35h6115d3f_0 r-roxygen2 conda-forge/linux-64::r-roxygen2-6.1.1-r35h0357c0b_1001 r-rprojroot conda-forge/noarch::r-rprojroot-1.3_2-r35h6115d3f_1002 r-rsconnect conda-forge/noarch::r-rsconnect-0.8.16-r35h6115d3f_0 r-stringi conda-forge/linux-64::r-stringi-1.4.3-r35h0357c0b_2 r-stringr conda-forge/noarch::r-stringr-1.4.0-r35h6115d3f_1 r-tibble conda-forge/linux-64::r-tibble-1.4.2-r351h96ca727_1002 r-tinytex conda-forge/noarch::r-tinytex-0.22-r35h6115d3f_0 r-utf8 conda-forge/linux-64::r-utf8-1.1.4-r35hcdcec82_1002 r-xfun conda-forge/noarch::r-xfun-0.13-r35h6115d3f_0 r-xml2 conda-forge/linux-64::r-xml2-1.3.2-r35h0357c0b_0 r-yaml conda-forge/linux-64::r-yaml-2.2.1-r35hcdcec82_0 The following packages will be UPDATED: ca-certificates pkgs/main::ca-certificates-2019.11.27~ --> conda-forge::ca-certificates-2020.4.5.1-hecc5488_0 The following packages will be SUPERSEDED by a higher-priority channel: openssl pkgs/main::openssl-1.1.1g-h7b6447c_0 --> conda-forge::openssl-1.1.1g-h516909a_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done -- The C compiler identification is GNU 7.3.0 -- The CXX compiler identification is GNU 7.3.0 -- Check for working C compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc -- Check for working C compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++ -- Check for working CXX compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring incomplete, errors occurred! See also "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/lightgbm_r/src/build/CMakeFiles/CMakeOutput.log". Updating lightgbm documentation Loading lightgbm Re-compiling lightgbm '/home/docs/.conda/envs/r_env/lib/R/bin/R' --no-site-file --no-environ \ --no-save --no-restore --quiet CMD INSTALL \ '/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/lightgbm_r' \ --library='/tmp/RtmpT7BLvD/devtools_install_be97189381e' --no-R --no-data \ --no-help --no-demo --no-inst --no-docs --no-exec --no-multiarch \ --no-test-load --preclean * installing *source* package ‘lightgbm’ ... ** libs installing via 'install.libs.R' to /tmp/RtmpT7BLvD/devtools_install_be97189381e/lightgbm R version passed into FindLibR.cmake: 3.5.1 CMake Error at /home/docs/.conda/envs/r_env/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137 (message): Could NOT find LibR (missing: LIBR_CORE_LIBRARY) Call Stack (most recent call first): /home/docs/.conda/envs/r_env/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE) cmake/modules/FindLibR.cmake:221 (find_package_handle_standard_args) CMakeLists.txt:76 (find_package) make: *** No rule to make target '_lightgbm'. Stop. Error in eval(ei, envir) : Cannot find lib_lightgbm.so * removing ‘/tmp/RtmpT7BLvD/devtools_install_be97189381e/lightgbm’ Error: Command failed (1) Execution halted During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 279, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 277, in __init__ self._init_builder() File "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 333, in _init_builder self.events.emit('builder-inited') File "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/envs/latest/lib/python3.7/site-packages/sphinx/events.py", line 107, in emit results.append(listener.handler(self.app, *args)) File "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/conf.py", line 262, in generate_r_docs raise Exception("An error has occurred while generating documentation for R-package\n" + str(e)) Exception: An error has occurred while generating documentation for R-package Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/docs/.conda/envs/r_env added / updated specs: - ca-certificates==2019.11.27=0 - cmake==3.14.0=h52cb24c_0 - r-base==3.5.1=h1e0a451_2 - r-devtools==1.13.6=r351h6115d3f_0 - r-jsonlite==1.5=r351h96ca727_0 - r-matrix==1.2_14=r351h96ca727_0 - r-testthat==2.0.0=r351h29659fb_0 The following packages will be downloaded: package | build ---------------------------|----------------- _r-mutex-1.0.0 | anacondar_1 3 KB binutils_impl_linux-64-2.33.1| he6710b0_7 3.7 MB binutils_linux-64-2.33.1 | h9595d00_15 26 KB bwidget-1.9.11 | 1 116 KB bzip2-1.0.8 | h7b6447c_0 78 KB ca-certificates-2019.11.27 | 0 124 KB cairo-1.14.12 | h8948797_3 906 KB cmake-3.14.0 | h52cb24c_0 5.5 MB curl-7.67.0 | hbc83047_0 134 KB expat-2.2.6 | he6710b0_0 146 KB fontconfig-2.13.0 | h9420a91_0 227 KB freetype-2.9.1 | h8a8886c_1 550 KB fribidi-1.0.5 | h7b6447c_0 101 KB gcc_impl_linux-64-7.3.0 | habb00fd_1 41.9 MB gcc_linux-64-7.3.0 | h553295d_15 27 KB gfortran_impl_linux-64-7.3.0| hdf63c60_1 7.8 MB gfortran_linux-64-7.3.0 | h553295d_15 27 KB glib-2.63.1 | h5a9c865_0 2.9 MB graphite2-1.3.13 | h23475e2_0 98 KB gsl-2.4 | h14c3975_4 1.8 MB gxx_impl_linux-64-7.3.0 | hdf63c60_1 15.0 MB gxx_linux-64-7.3.0 | h553295d_15 26 KB harfbuzz-1.8.8 | hffaf4a1_0 507 KB icu-58.2 | he6710b0_3 10.5 MB jpeg-9b | h024ee3a_2 214 KB krb5-1.16.4 | h173b8e3_0 1.2 MB ld_impl_linux-64-2.33.1 | h53a641e_7 568 KB libcurl-7.67.0 | h20c2e04_0 426 KB libgfortran-ng-7.3.0 | hdf63c60_0 1006 KB libpng-1.6.37 | hbc83047_0 278 KB libssh2-1.9.0 | h1ba5d50_1 269 KB libtiff-4.1.0 | h2733197_0 447 KB libuuid-1.0.3 | h1bed415_2 15 KB libxcb-1.13 | h1bed415_1 421 KB libxml2-2.9.9 | hea5a465_1 1.6 MB make-4.2.1 | h1bed415_1 415 KB ncurses-6.2 | he6710b0_1 817 KB openssl-1.1.1g | h7b6447c_0 2.5 MB pango-1.42.4 | h049681c_0 464 KB pcre-8.43 | he6710b0_0 209 KB pixman-0.38.0 | h7b6447c_0 364 KB r-assertthat-0.2.0 | r351h6115d3f_0 55 KB r-base-3.5.1 | h1e0a451_2 26.5 MB r-cli-1.0.0 | r351h6115d3f_1 310 KB r-crayon-1.3.4 | r351h6115d3f_0 729 KB r-curl-3.2 | r351hadc6856_1 374 KB r-devtools-1.13.6 | r351h6115d3f_0 665 KB r-digest-0.6.15 | r351h96ca727_0 138 KB r-git2r-0.23.0 | r351h96ca727_1 804 KB r-httr-1.3.1 | r351h6115d3f_1 421 KB r-jsonlite-1.5 | r351h96ca727_0 632 KB r-lattice-0.20_35 | r351h96ca727_0 1.1 MB r-magrittr-1.5 | r351h6115d3f_4 157 KB r-matrix-1.2_14 | r351h96ca727_0 3.3 MB r-memoise-1.1.0 | r351h6115d3f_0 38 KB r-mime-0.5 | r351h96ca727_0 37 KB r-openssl-1.0.2 | r351h96ca727_1 588 KB r-praise-1.0.0 | r351h6115d3f_4 21 KB r-r6-2.2.2 | r351h6115d3f_0 245 KB r-rlang-0.2.1 | r351h96ca727_0 744 KB r-rstudioapi-0.7 | r351h6115d3f_0 126 KB r-testthat-2.0.0 | r351h29659fb_0 879 KB r-whisker-0.3_2 | r351hf348343_4 63 KB r-withr-2.1.2 | r351h6115d3f_0 149 KB rhash-1.3.8 | h1ba5d50_0 188 KB tktable-2.10 | h14c3975_0 86 KB xz-5.2.5 | h7b6447c_0 438 KB zstd-1.3.7 | h0b5b093_0 401 KB ------------------------------------------------------------ Total: 142.0 MB The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _r-mutex pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1 binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.33.1-he6710b0_7 binutils_linux-64 pkgs/main/linux-64::binutils_linux-64-2.33.1-h9595d00_15 bwidget pkgs/main/linux-64::bwidget-1.9.11-1 bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 ca-certificates pkgs/main/linux-64::ca-certificates-2019.11.27-0 cairo pkgs/main/linux-64::cairo-1.14.12-h8948797_3 cmake pkgs/main/linux-64::cmake-3.14.0-h52cb24c_0 curl pkgs/main/linux-64::curl-7.67.0-hbc83047_0 expat pkgs/main/linux-64::expat-2.2.6-he6710b0_0 fontconfig pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0 freetype pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1 fribidi pkgs/main/linux-64::fribidi-1.0.5-h7b6447c_0 gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-7.3.0-habb00fd_1 gcc_linux-64 pkgs/main/linux-64::gcc_linux-64-7.3.0-h553295d_15 gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_1 gfortran_linux-64 pkgs/main/linux-64::gfortran_linux-64-7.3.0-h553295d_15 glib pkgs/main/linux-64::glib-2.63.1-h5a9c865_0 graphite2 pkgs/main/linux-64::graphite2-1.3.13-h23475e2_0 gsl pkgs/main/linux-64::gsl-2.4-h14c3975_4 gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_1 gxx_linux-64 pkgs/main/linux-64::gxx_linux-64-7.3.0-h553295d_15 harfbuzz pkgs/main/linux-64::harfbuzz-1.8.8-hffaf4a1_0 icu pkgs/main/linux-64::icu-58.2-he6710b0_3 jpeg pkgs/main/linux-64::jpeg-9b-h024ee3a_2 krb5 pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libcurl pkgs/main/linux-64::libcurl-7.67.0-h20c2e04_0 libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0 libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0 libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0 libssh2 pkgs/main/linux-64::libssh2-1.9.0-h1ba5d50_1 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_0 libuuid pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2 libxcb pkgs/main/linux-64::libxcb-1.13-h1bed415_1 libxml2 pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1 make pkgs/main/linux-64::make-4.2.1-h1bed415_1 ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0 pango pkgs/main/linux-64::pango-1.42.4-h049681c_0 pcre pkgs/main/linux-64::pcre-8.43-he6710b0_0 pixman pkgs/main/linux-64::pixman-0.38.0-h7b6447c_0 r-assertthat pkgs/r/linux-64::r-assertthat-0.2.0-r351h6115d3f_0 r-base pkgs/r/linux-64::r-base-3.5.1-h1e0a451_2 r-cli pkgs/r/linux-64::r-cli-1.0.0-r351h6115d3f_1 r-crayon pkgs/r/linux-64::r-crayon-1.3.4-r351h6115d3f_0 r-curl pkgs/r/linux-64::r-curl-3.2-r351hadc6856_1 r-devtools pkgs/r/linux-64::r-devtools-1.13.6-r351h6115d3f_0 r-digest pkgs/r/linux-64::r-digest-0.6.15-r351h96ca727_0 r-git2r pkgs/r/linux-64::r-git2r-0.23.0-r351h96ca727_1 r-httr pkgs/r/linux-64::r-httr-1.3.1-r351h6115d3f_1 r-jsonlite pkgs/r/linux-64::r-jsonlite-1.5-r351h96ca727_0 r-lattice pkgs/r/linux-64::r-lattice-0.20_35-r351h96ca727_0 r-magrittr pkgs/r/linux-64::r-magrittr-1.5-r351h6115d3f_4 r-matrix pkgs/r/linux-64::r-matrix-1.2_14-r351h96ca727_0 r-memoise pkgs/r/linux-64::r-memoise-1.1.0-r351h6115d3f_0 r-mime pkgs/r/linux-64::r-mime-0.5-r351h96ca727_0 r-openssl pkgs/r/linux-64::r-openssl-1.0.2-r351h96ca727_1 r-praise pkgs/r/linux-64::r-praise-1.0.0-r351h6115d3f_4 r-r6 pkgs/r/linux-64::r-r6-2.2.2-r351h6115d3f_0 r-rlang pkgs/r/linux-64::r-rlang-0.2.1-r351h96ca727_0 r-rstudioapi pkgs/r/linux-64::r-rstudioapi-0.7-r351h6115d3f_0 r-testthat pkgs/r/linux-64::r-testthat-2.0.0-r351h29659fb_0 r-whisker pkgs/r/linux-64::r-whisker-0.3_2-r351hf348343_4 r-withr pkgs/r/linux-64::r-withr-2.1.2-r351h6115d3f_0 readline pkgs/main/linux-64::readline-7.0-h7b6447c_5 rhash pkgs/main/linux-64::rhash-1.3.8-h1ba5d50_0 tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0 tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/docs/.conda/envs/r_env added / updated specs: - r-data.table==1.12.8=r35hcdcec82_0 - r-pkgdown==1.3.0=r35h6115d3f_1001 - r-roxygen2==6.1.1=r35h0357c0b_1001 The following packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2020.4.5.1 | hecc5488_0 146 KB conda-forge openssl-1.1.1g | h516909a_0 2.1 MB conda-forge pandoc-2.9.2.1 | 0 18.7 MB conda-forge r-backports-1.1.6 | r35hcdcec82_1 76 KB conda-forge r-base64enc-0.1_3 | r35hcdcec82_1003 43 KB conda-forge r-brew-1.0_6 | r35h6115d3f_1002 92 KB conda-forge r-callr-3.4.3 | r35h6115d3f_0 391 KB conda-forge r-commonmark-1.7 | r35hcdcec82_1001 151 KB conda-forge r-data.table-1.12.8 | r35hcdcec82_0 1.8 MB conda-forge r-desc-1.2.0 | r35h6115d3f_1002 286 KB conda-forge r-evaluate-0.14 | r35h6115d3f_1 79 KB conda-forge r-fansi-0.4.1 | r35hcdcec82_0 195 KB conda-forge r-fs-1.4.1 | r35h0357c0b_0 483 KB conda-forge r-glue-1.4.0 | r35hcdcec82_0 143 KB conda-forge r-highlight-0.5.0 | r35h0357c0b_0 566 KB conda-forge r-highr-0.8 | r35h6115d3f_1 47 KB conda-forge r-htmltools-0.4.0 | r35h0357c0b_0 213 KB conda-forge r-knitr-1.28 | r35h6115d3f_0 1.3 MB conda-forge r-markdown-1.1 | r35hcdcec82_0 143 KB conda-forge r-mass-7.3_51.6 | r35hcdcec82_1 1.1 MB conda-forge r-packrat-0.5.0 | r35h6115d3f_1001 455 KB conda-forge r-pillar-1.3.0 | r351h6115d3f_0 152 KB r-pkgbuild-1.0.7 | r35h6115d3f_0 151 KB conda-forge r-pkgdown-1.3.0 | r35h6115d3f_1001 505 KB conda-forge r-pkgload-1.0.2 | r35h0357c0b_1001 159 KB conda-forge r-prettyunits-1.1.1 | r35h6115d3f_0 40 KB conda-forge r-processx-3.4.2 | r35hcdcec82_0 269 KB conda-forge r-ps-1.3.2 | r35hcdcec82_0 224 KB conda-forge r-purrr-0.2.5 |r351h96ca727_1002 283 KB conda-forge r-rcpp-1.0.4.6 | r35h0357c0b_0 1.9 MB conda-forge r-rematch2-2.1.2 | r35h6115d3f_0 52 KB conda-forge r-rmarkdown-2.1 | r35h6115d3f_0 3.0 MB conda-forge r-roxygen2-6.1.1 | r35h0357c0b_1001 508 KB conda-forge r-rprojroot-1.3_2 | r35h6115d3f_1002 93 KB conda-forge r-rsconnect-0.8.16 | r35h6115d3f_0 670 KB conda-forge r-stringi-1.4.3 | r35h0357c0b_2 766 KB conda-forge r-stringr-1.4.0 | r35h6115d3f_1 207 KB conda-forge r-tibble-1.4.2 |r351h96ca727_1002 229 KB conda-forge r-tinytex-0.22 | r35h6115d3f_0 110 KB conda-forge r-utf8-1.1.4 | r35hcdcec82_1002 160 KB conda-forge r-xfun-0.13 | r35h6115d3f_0 194 KB conda-forge r-xml2-1.3.2 | r35h0357c0b_0 249 KB conda-forge r-yaml-2.2.1 | r35hcdcec82_0 116 KB conda-forge ------------------------------------------------------------ Total: 38.3 MB The following NEW packages will be INSTALLED: pandoc conda-forge/linux-64::pandoc-2.9.2.1-0 r-backports conda-forge/linux-64::r-backports-1.1.6-r35hcdcec82_1 r-base64enc conda-forge/linux-64::r-base64enc-0.1_3-r35hcdcec82_1003 r-brew conda-forge/noarch::r-brew-1.0_6-r35h6115d3f_1002 r-callr conda-forge/noarch::r-callr-3.4.3-r35h6115d3f_0 r-commonmark conda-forge/linux-64::r-commonmark-1.7-r35hcdcec82_1001 r-data.table conda-forge/linux-64::r-data.table-1.12.8-r35hcdcec82_0 r-desc conda-forge/noarch::r-desc-1.2.0-r35h6115d3f_1002 r-evaluate conda-forge/noarch::r-evaluate-0.14-r35h6115d3f_1 r-fansi conda-forge/linux-64::r-fansi-0.4.1-r35hcdcec82_0 r-fs conda-forge/linux-64::r-fs-1.4.1-r35h0357c0b_0 r-glue conda-forge/linux-64::r-glue-1.4.0-r35hcdcec82_0 r-highlight conda-forge/linux-64::r-highlight-0.5.0-r35h0357c0b_0 r-highr conda-forge/noarch::r-highr-0.8-r35h6115d3f_1 r-htmltools conda-forge/linux-64::r-htmltools-0.4.0-r35h0357c0b_0 r-knitr conda-forge/noarch::r-knitr-1.28-r35h6115d3f_0 r-markdown conda-forge/linux-64::r-markdown-1.1-r35hcdcec82_0 r-mass conda-forge/linux-64::r-mass-7.3_51.6-r35hcdcec82_1 r-packrat conda-forge/noarch::r-packrat-0.5.0-r35h6115d3f_1001 r-pillar pkgs/r/linux-64::r-pillar-1.3.0-r351h6115d3f_0 r-pkgbuild conda-forge/noarch::r-pkgbuild-1.0.7-r35h6115d3f_0 r-pkgdown conda-forge/noarch::r-pkgdown-1.3.0-r35h6115d3f_1001 r-pkgload conda-forge/linux-64::r-pkgload-1.0.2-r35h0357c0b_1001 r-prettyunits conda-forge/noarch::r-prettyunits-1.1.1-r35h6115d3f_0 r-processx conda-forge/linux-64::r-processx-3.4.2-r35hcdcec82_0 r-ps conda-forge/linux-64::r-ps-1.3.2-r35hcdcec82_0 r-purrr conda-forge/linux-64::r-purrr-0.2.5-r351h96ca727_1002 r-rcpp conda-forge/linux-64::r-rcpp-1.0.4.6-r35h0357c0b_0 r-rematch2 conda-forge/noarch::r-rematch2-2.1.2-r35h6115d3f_0 r-rmarkdown conda-forge/noarch::r-rmarkdown-2.1-r35h6115d3f_0 r-roxygen2 conda-forge/linux-64::r-roxygen2-6.1.1-r35h0357c0b_1001 r-rprojroot conda-forge/noarch::r-rprojroot-1.3_2-r35h6115d3f_1002 r-rsconnect conda-forge/noarch::r-rsconnect-0.8.16-r35h6115d3f_0 r-stringi conda-forge/linux-64::r-stringi-1.4.3-r35h0357c0b_2 r-stringr conda-forge/noarch::r-stringr-1.4.0-r35h6115d3f_1 r-tibble conda-forge/linux-64::r-tibble-1.4.2-r351h96ca727_1002 r-tinytex conda-forge/noarch::r-tinytex-0.22-r35h6115d3f_0 r-utf8 conda-forge/linux-64::r-utf8-1.1.4-r35hcdcec82_1002 r-xfun conda-forge/noarch::r-xfun-0.13-r35h6115d3f_0 r-xml2 conda-forge/linux-64::r-xml2-1.3.2-r35h0357c0b_0 r-yaml conda-forge/linux-64::r-yaml-2.2.1-r35hcdcec82_0 The following packages will be UPDATED: ca-certificates pkgs/main::ca-certificates-2019.11.27~ --> conda-forge::ca-certificates-2020.4.5.1-hecc5488_0 The following packages will be SUPERSEDED by a higher-priority channel: openssl pkgs/main::openssl-1.1.1g-h7b6447c_0 --> conda-forge::openssl-1.1.1g-h516909a_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done -- The C compiler identification is GNU 7.3.0 -- The CXX compiler identification is GNU 7.3.0 -- Check for working C compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc -- Check for working C compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++ -- Check for working CXX compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring incomplete, errors occurred! See also "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/lightgbm_r/src/build/CMakeFiles/CMakeOutput.log". Updating lightgbm documentation Loading lightgbm Re-compiling lightgbm '/home/docs/.conda/envs/r_env/lib/R/bin/R' --no-site-file --no-environ \ --no-save --no-restore --quiet CMD INSTALL \ '/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/lightgbm_r' \ --library='/tmp/RtmpT7BLvD/devtools_install_be97189381e' --no-R --no-data \ --no-help --no-demo --no-inst --no-docs --no-exec --no-multiarch \ --no-test-load --preclean * installing *source* package ‘lightgbm’ ... ** libs installing via 'install.libs.R' to /tmp/RtmpT7BLvD/devtools_install_be97189381e/lightgbm R version passed into FindLibR.cmake: 3.5.1 CMake Error at /home/docs/.conda/envs/r_env/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137 (message): Could NOT find LibR (missing: LIBR_CORE_LIBRARY) Call Stack (most recent call first): /home/docs/.conda/envs/r_env/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE) cmake/modules/FindLibR.cmake:221 (find_package_handle_standard_args) CMakeLists.txt:76 (find_package) make: *** No rule to make target '_lightgbm'. Stop. Error in eval(ei, envir) : Cannot find lib_lightgbm.so * removing ‘/tmp/RtmpT7BLvD/devtools_install_be97189381e/lightgbm’ Error: Command failed (1) Execution halted Exception occurred: File "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/docs/conf.py", line 262, in generate_r_docs raise Exception("An error has occurred while generating documentation for R-package\n" + str(e)) Exception: An error has occurred while generating documentation for R-package Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/docs/.conda/envs/r_env added / updated specs: - ca-certificates==2019.11.27=0 - cmake==3.14.0=h52cb24c_0 - r-base==3.5.1=h1e0a451_2 - r-devtools==1.13.6=r351h6115d3f_0 - r-jsonlite==1.5=r351h96ca727_0 - r-matrix==1.2_14=r351h96ca727_0 - r-testthat==2.0.0=r351h29659fb_0 The following packages will be downloaded: package | build ---------------------------|----------------- _r-mutex-1.0.0 | anacondar_1 3 KB binutils_impl_linux-64-2.33.1| he6710b0_7 3.7 MB binutils_linux-64-2.33.1 | h9595d00_15 26 KB bwidget-1.9.11 | 1 116 KB bzip2-1.0.8 | h7b6447c_0 78 KB ca-certificates-2019.11.27 | 0 124 KB cairo-1.14.12 | h8948797_3 906 KB cmake-3.14.0 | h52cb24c_0 5.5 MB curl-7.67.0 | hbc83047_0 134 KB expat-2.2.6 | he6710b0_0 146 KB fontconfig-2.13.0 | h9420a91_0 227 KB freetype-2.9.1 | h8a8886c_1 550 KB fribidi-1.0.5 | h7b6447c_0 101 KB gcc_impl_linux-64-7.3.0 | habb00fd_1 41.9 MB gcc_linux-64-7.3.0 | h553295d_15 27 KB gfortran_impl_linux-64-7.3.0| hdf63c60_1 7.8 MB gfortran_linux-64-7.3.0 | h553295d_15 27 KB glib-2.63.1 | h5a9c865_0 2.9 MB graphite2-1.3.13 | h23475e2_0 98 KB gsl-2.4 | h14c3975_4 1.8 MB gxx_impl_linux-64-7.3.0 | hdf63c60_1 15.0 MB gxx_linux-64-7.3.0 | h553295d_15 26 KB harfbuzz-1.8.8 | hffaf4a1_0 507 KB icu-58.2 | he6710b0_3 10.5 MB jpeg-9b | h024ee3a_2 214 KB krb5-1.16.4 | h173b8e3_0 1.2 MB ld_impl_linux-64-2.33.1 | h53a641e_7 568 KB libcurl-7.67.0 | h20c2e04_0 426 KB libgfortran-ng-7.3.0 | hdf63c60_0 1006 KB libpng-1.6.37 | hbc83047_0 278 KB libssh2-1.9.0 | h1ba5d50_1 269 KB libtiff-4.1.0 | h2733197_0 447 KB libuuid-1.0.3 | h1bed415_2 15 KB libxcb-1.13 | h1bed415_1 421 KB libxml2-2.9.9 | hea5a465_1 1.6 MB make-4.2.1 | h1bed415_1 415 KB ncurses-6.2 | he6710b0_1 817 KB openssl-1.1.1g | h7b6447c_0 2.5 MB pango-1.42.4 | h049681c_0 464 KB pcre-8.43 | he6710b0_0 209 KB pixman-0.38.0 | h7b6447c_0 364 KB r-assertthat-0.2.0 | r351h6115d3f_0 55 KB r-base-3.5.1 | h1e0a451_2 26.5 MB r-cli-1.0.0 | r351h6115d3f_1 310 KB r-crayon-1.3.4 | r351h6115d3f_0 729 KB r-curl-3.2 | r351hadc6856_1 374 KB r-devtools-1.13.6 | r351h6115d3f_0 665 KB r-digest-0.6.15 | r351h96ca727_0 138 KB r-git2r-0.23.0 | r351h96ca727_1 804 KB r-httr-1.3.1 | r351h6115d3f_1 421 KB r-jsonlite-1.5 | r351h96ca727_0 632 KB r-lattice-0.20_35 | r351h96ca727_0 1.1 MB r-magrittr-1.5 | r351h6115d3f_4 157 KB r-matrix-1.2_14 | r351h96ca727_0 3.3 MB r-memoise-1.1.0 | r351h6115d3f_0 38 KB r-mime-0.5 | r351h96ca727_0 37 KB r-openssl-1.0.2 | r351h96ca727_1 588 KB r-praise-1.0.0 | r351h6115d3f_4 21 KB r-r6-2.2.2 | r351h6115d3f_0 245 KB r-rlang-0.2.1 | r351h96ca727_0 744 KB r-rstudioapi-0.7 | r351h6115d3f_0 126 KB r-testthat-2.0.0 | r351h29659fb_0 879 KB r-whisker-0.3_2 | r351hf348343_4 63 KB r-withr-2.1.2 | r351h6115d3f_0 149 KB rhash-1.3.8 | h1ba5d50_0 188 KB tktable-2.10 | h14c3975_0 86 KB xz-5.2.5 | h7b6447c_0 438 KB zstd-1.3.7 | h0b5b093_0 401 KB ------------------------------------------------------------ Total: 142.0 MB The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _r-mutex pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1 binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.33.1-he6710b0_7 binutils_linux-64 pkgs/main/linux-64::binutils_linux-64-2.33.1-h9595d00_15 bwidget pkgs/main/linux-64::bwidget-1.9.11-1 bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 ca-certificates pkgs/main/linux-64::ca-certificates-2019.11.27-0 cairo pkgs/main/linux-64::cairo-1.14.12-h8948797_3 cmake pkgs/main/linux-64::cmake-3.14.0-h52cb24c_0 curl pkgs/main/linux-64::curl-7.67.0-hbc83047_0 expat pkgs/main/linux-64::expat-2.2.6-he6710b0_0 fontconfig pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0 freetype pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1 fribidi pkgs/main/linux-64::fribidi-1.0.5-h7b6447c_0 gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-7.3.0-habb00fd_1 gcc_linux-64 pkgs/main/linux-64::gcc_linux-64-7.3.0-h553295d_15 gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_1 gfortran_linux-64 pkgs/main/linux-64::gfortran_linux-64-7.3.0-h553295d_15 glib pkgs/main/linux-64::glib-2.63.1-h5a9c865_0 graphite2 pkgs/main/linux-64::graphite2-1.3.13-h23475e2_0 gsl pkgs/main/linux-64::gsl-2.4-h14c3975_4 gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_1 gxx_linux-64 pkgs/main/linux-64::gxx_linux-64-7.3.0-h553295d_15 harfbuzz pkgs/main/linux-64::harfbuzz-1.8.8-hffaf4a1_0 icu pkgs/main/linux-64::icu-58.2-he6710b0_3 jpeg pkgs/main/linux-64::jpeg-9b-h024ee3a_2 krb5 pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libcurl pkgs/main/linux-64::libcurl-7.67.0-h20c2e04_0 libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0 libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0 libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0 libssh2 pkgs/main/linux-64::libssh2-1.9.0-h1ba5d50_1 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_0 libuuid pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2 libxcb pkgs/main/linux-64::libxcb-1.13-h1bed415_1 libxml2 pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1 make pkgs/main/linux-64::make-4.2.1-h1bed415_1 ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0 pango pkgs/main/linux-64::pango-1.42.4-h049681c_0 pcre pkgs/main/linux-64::pcre-8.43-he6710b0_0 pixman pkgs/main/linux-64::pixman-0.38.0-h7b6447c_0 r-assertthat pkgs/r/linux-64::r-assertthat-0.2.0-r351h6115d3f_0 r-base pkgs/r/linux-64::r-base-3.5.1-h1e0a451_2 r-cli pkgs/r/linux-64::r-cli-1.0.0-r351h6115d3f_1 r-crayon pkgs/r/linux-64::r-crayon-1.3.4-r351h6115d3f_0 r-curl pkgs/r/linux-64::r-curl-3.2-r351hadc6856_1 r-devtools pkgs/r/linux-64::r-devtools-1.13.6-r351h6115d3f_0 r-digest pkgs/r/linux-64::r-digest-0.6.15-r351h96ca727_0 r-git2r pkgs/r/linux-64::r-git2r-0.23.0-r351h96ca727_1 r-httr pkgs/r/linux-64::r-httr-1.3.1-r351h6115d3f_1 r-jsonlite pkgs/r/linux-64::r-jsonlite-1.5-r351h96ca727_0 r-lattice pkgs/r/linux-64::r-lattice-0.20_35-r351h96ca727_0 r-magrittr pkgs/r/linux-64::r-magrittr-1.5-r351h6115d3f_4 r-matrix pkgs/r/linux-64::r-matrix-1.2_14-r351h96ca727_0 r-memoise pkgs/r/linux-64::r-memoise-1.1.0-r351h6115d3f_0 r-mime pkgs/r/linux-64::r-mime-0.5-r351h96ca727_0 r-openssl pkgs/r/linux-64::r-openssl-1.0.2-r351h96ca727_1 r-praise pkgs/r/linux-64::r-praise-1.0.0-r351h6115d3f_4 r-r6 pkgs/r/linux-64::r-r6-2.2.2-r351h6115d3f_0 r-rlang pkgs/r/linux-64::r-rlang-0.2.1-r351h96ca727_0 r-rstudioapi pkgs/r/linux-64::r-rstudioapi-0.7-r351h6115d3f_0 r-testthat pkgs/r/linux-64::r-testthat-2.0.0-r351h29659fb_0 r-whisker pkgs/r/linux-64::r-whisker-0.3_2-r351hf348343_4 r-withr pkgs/r/linux-64::r-withr-2.1.2-r351h6115d3f_0 readline pkgs/main/linux-64::readline-7.0-h7b6447c_5 rhash pkgs/main/linux-64::rhash-1.3.8-h1ba5d50_0 tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0 tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/docs/.conda/envs/r_env added / updated specs: - r-data.table==1.12.8=r35hcdcec82_0 - r-pkgdown==1.3.0=r35h6115d3f_1001 - r-roxygen2==6.1.1=r35h0357c0b_1001 The following packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2020.4.5.1 | hecc5488_0 146 KB conda-forge openssl-1.1.1g | h516909a_0 2.1 MB conda-forge pandoc-2.9.2.1 | 0 18.7 MB conda-forge r-backports-1.1.6 | r35hcdcec82_1 76 KB conda-forge r-base64enc-0.1_3 | r35hcdcec82_1003 43 KB conda-forge r-brew-1.0_6 | r35h6115d3f_1002 92 KB conda-forge r-callr-3.4.3 | r35h6115d3f_0 391 KB conda-forge r-commonmark-1.7 | r35hcdcec82_1001 151 KB conda-forge r-data.table-1.12.8 | r35hcdcec82_0 1.8 MB conda-forge r-desc-1.2.0 | r35h6115d3f_1002 286 KB conda-forge r-evaluate-0.14 | r35h6115d3f_1 79 KB conda-forge r-fansi-0.4.1 | r35hcdcec82_0 195 KB conda-forge r-fs-1.4.1 | r35h0357c0b_0 483 KB conda-forge r-glue-1.4.0 | r35hcdcec82_0 143 KB conda-forge r-highlight-0.5.0 | r35h0357c0b_0 566 KB conda-forge r-highr-0.8 | r35h6115d3f_1 47 KB conda-forge r-htmltools-0.4.0 | r35h0357c0b_0 213 KB conda-forge r-knitr-1.28 | r35h6115d3f_0 1.3 MB conda-forge r-markdown-1.1 | r35hcdcec82_0 143 KB conda-forge r-mass-7.3_51.6 | r35hcdcec82_1 1.1 MB conda-forge r-packrat-0.5.0 | r35h6115d3f_1001 455 KB conda-forge r-pillar-1.3.0 | r351h6115d3f_0 152 KB r-pkgbuild-1.0.7 | r35h6115d3f_0 151 KB conda-forge r-pkgdown-1.3.0 | r35h6115d3f_1001 505 KB conda-forge r-pkgload-1.0.2 | r35h0357c0b_1001 159 KB conda-forge r-prettyunits-1.1.1 | r35h6115d3f_0 40 KB conda-forge r-processx-3.4.2 | r35hcdcec82_0 269 KB conda-forge r-ps-1.3.2 | r35hcdcec82_0 224 KB conda-forge r-purrr-0.2.5 |r351h96ca727_1002 283 KB conda-forge r-rcpp-1.0.4.6 | r35h0357c0b_0 1.9 MB conda-forge r-rematch2-2.1.2 | r35h6115d3f_0 52 KB conda-forge r-rmarkdown-2.1 | r35h6115d3f_0 3.0 MB conda-forge r-roxygen2-6.1.1 | r35h0357c0b_1001 508 KB conda-forge r-rprojroot-1.3_2 | r35h6115d3f_1002 93 KB conda-forge r-rsconnect-0.8.16 | r35h6115d3f_0 670 KB conda-forge r-stringi-1.4.3 | r35h0357c0b_2 766 KB conda-forge r-stringr-1.4.0 | r35h6115d3f_1 207 KB conda-forge r-tibble-1.4.2 |r351h96ca727_1002 229 KB conda-forge r-tinytex-0.22 | r35h6115d3f_0 110 KB conda-forge r-utf8-1.1.4 | r35hcdcec82_1002 160 KB conda-forge r-xfun-0.13 | r35h6115d3f_0 194 KB conda-forge r-xml2-1.3.2 | r35h0357c0b_0 249 KB conda-forge r-yaml-2.2.1 | r35hcdcec82_0 116 KB conda-forge ------------------------------------------------------------ Total: 38.3 MB The following NEW packages will be INSTALLED: pandoc conda-forge/linux-64::pandoc-2.9.2.1-0 r-backports conda-forge/linux-64::r-backports-1.1.6-r35hcdcec82_1 r-base64enc conda-forge/linux-64::r-base64enc-0.1_3-r35hcdcec82_1003 r-brew conda-forge/noarch::r-brew-1.0_6-r35h6115d3f_1002 r-callr conda-forge/noarch::r-callr-3.4.3-r35h6115d3f_0 r-commonmark conda-forge/linux-64::r-commonmark-1.7-r35hcdcec82_1001 r-data.table conda-forge/linux-64::r-data.table-1.12.8-r35hcdcec82_0 r-desc conda-forge/noarch::r-desc-1.2.0-r35h6115d3f_1002 r-evaluate conda-forge/noarch::r-evaluate-0.14-r35h6115d3f_1 r-fansi conda-forge/linux-64::r-fansi-0.4.1-r35hcdcec82_0 r-fs conda-forge/linux-64::r-fs-1.4.1-r35h0357c0b_0 r-glue conda-forge/linux-64::r-glue-1.4.0-r35hcdcec82_0 r-highlight conda-forge/linux-64::r-highlight-0.5.0-r35h0357c0b_0 r-highr conda-forge/noarch::r-highr-0.8-r35h6115d3f_1 r-htmltools conda-forge/linux-64::r-htmltools-0.4.0-r35h0357c0b_0 r-knitr conda-forge/noarch::r-knitr-1.28-r35h6115d3f_0 r-markdown conda-forge/linux-64::r-markdown-1.1-r35hcdcec82_0 r-mass conda-forge/linux-64::r-mass-7.3_51.6-r35hcdcec82_1 r-packrat conda-forge/noarch::r-packrat-0.5.0-r35h6115d3f_1001 r-pillar pkgs/r/linux-64::r-pillar-1.3.0-r351h6115d3f_0 r-pkgbuild conda-forge/noarch::r-pkgbuild-1.0.7-r35h6115d3f_0 r-pkgdown conda-forge/noarch::r-pkgdown-1.3.0-r35h6115d3f_1001 r-pkgload conda-forge/linux-64::r-pkgload-1.0.2-r35h0357c0b_1001 r-prettyunits conda-forge/noarch::r-prettyunits-1.1.1-r35h6115d3f_0 r-processx conda-forge/linux-64::r-processx-3.4.2-r35hcdcec82_0 r-ps conda-forge/linux-64::r-ps-1.3.2-r35hcdcec82_0 r-purrr conda-forge/linux-64::r-purrr-0.2.5-r351h96ca727_1002 r-rcpp conda-forge/linux-64::r-rcpp-1.0.4.6-r35h0357c0b_0 r-rematch2 conda-forge/noarch::r-rematch2-2.1.2-r35h6115d3f_0 r-rmarkdown conda-forge/noarch::r-rmarkdown-2.1-r35h6115d3f_0 r-roxygen2 conda-forge/linux-64::r-roxygen2-6.1.1-r35h0357c0b_1001 r-rprojroot conda-forge/noarch::r-rprojroot-1.3_2-r35h6115d3f_1002 r-rsconnect conda-forge/noarch::r-rsconnect-0.8.16-r35h6115d3f_0 r-stringi conda-forge/linux-64::r-stringi-1.4.3-r35h0357c0b_2 r-stringr conda-forge/noarch::r-stringr-1.4.0-r35h6115d3f_1 r-tibble conda-forge/linux-64::r-tibble-1.4.2-r351h96ca727_1002 r-tinytex conda-forge/noarch::r-tinytex-0.22-r35h6115d3f_0 r-utf8 conda-forge/linux-64::r-utf8-1.1.4-r35hcdcec82_1002 r-xfun conda-forge/noarch::r-xfun-0.13-r35h6115d3f_0 r-xml2 conda-forge/linux-64::r-xml2-1.3.2-r35h0357c0b_0 r-yaml conda-forge/linux-64::r-yaml-2.2.1-r35hcdcec82_0 The following packages will be UPDATED: ca-certificates pkgs/main::ca-certificates-2019.11.27~ --> conda-forge::ca-certificates-2020.4.5.1-hecc5488_0 The following packages will be SUPERSEDED by a higher-priority channel: openssl pkgs/main::openssl-1.1.1g-h7b6447c_0 --> conda-forge::openssl-1.1.1g-h516909a_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done -- The C compiler identification is GNU 7.3.0 -- The CXX compiler identification is GNU 7.3.0 -- Check for working C compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc -- Check for working C compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++ -- Check for working CXX compiler: /home/docs/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring incomplete, errors occurred! See also "/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/lightgbm_r/src/build/CMakeFiles/CMakeOutput.log". Updating lightgbm documentation Loading lightgbm Re-compiling lightgbm '/home/docs/.conda/envs/r_env/lib/R/bin/R' --no-site-file --no-environ \ --no-save --no-restore --quiet CMD INSTALL \ '/home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/lightgbm_r' \ --library='/tmp/RtmpT7BLvD/devtools_install_be97189381e' --no-R --no-data \ --no-help --no-demo --no-inst --no-docs --no-exec --no-multiarch \ --no-test-load --preclean * installing *source* package ‘lightgbm’ ... ** libs installing via 'install.libs.R' to /tmp/RtmpT7BLvD/devtools_install_be97189381e/lightgbm R version passed into FindLibR.cmake: 3.5.1 CMake Error at /home/docs/.conda/envs/r_env/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137 (message): Could NOT find LibR (missing: LIBR_CORE_LIBRARY) Call Stack (most recent call first): /home/docs/.conda/envs/r_env/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE) cmake/modules/FindLibR.cmake:221 (find_package_handle_standard_args) CMakeLists.txt:76 (find_package) make: *** No rule to make target '_lightgbm'. Stop. Error in eval(ei, envir) : Cannot find lib_lightgbm.so * removing ‘/tmp/RtmpT7BLvD/devtools_install_be97189381e/lightgbm’ Error: Command failed (1) Execution haltedSearching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Reading and parsing tag files Parsing files Preprocessing /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/include/LightGBM/c_api.h... Parsing file /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/include/LightGBM/c_api.h... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/include/LightGBM/c_api.h... Generating file documentation... Generating docs for file /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/include/LightGBM/c_api.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating namespace index... Generating graph info page... Generating directory documentation... finalizing index lists... writing tag file... Generating XML output... Generating XML output for file c_api.h Generate XML output for dir /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/include/ Generate XML output for dir /home/docs/checkouts/readthedocs.org/user_builds/lightgbm/checkouts/latest/include/LightGBM/ Running dot... lookup cache used 71/65536 hits=591 misses=71 finished... The full traceback has been saved in /tmp/sphinx-err-tcmutc05.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. A bug report can be filed in the tracker at . Thanks! ```

[jameslamb]

I created a conda environment with r-base in it on my laptop, and found that conda will use ${LIBR_HOME}/lib as the location for the core library. That path was removed in #2963 because /lib isn't used by any of the standard R installations. I didn't realize that's how conda did it.

[github-actions[bot]]

This issue has been automatically locked since there has not been any recent activity since it was closed. To start a new related discussion, open a new issue at https://github.com/microsoft/LightGBM/issues including a reference to this.