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[ci] [R-package] upgrade to R 4.0.4 in CI #4042

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merged 1 commit into from Mar 3, 2021
Merged

[ci] [R-package] upgrade to R 4.0.4 in CI #4042

merged 1 commit into from Mar 3, 2021

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jameslamb
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@jameslamb jameslamb commented Mar 3, 2021 •
edited

R Windows CI jobs are currently failing on master (logs) and #4027 (logs) with the following:

* checking whether package 'lightgbm' can be installed ... WARNING

Found the following significant warnings:

  Warning: package 'R6' was built under R version 4.0.4

See 'C:/tmp-r-cmd-check/lightgbm.Rcheck/00install.out' for details.

Status: 1 WARNING

There has not been a release of {R6} since October 2020 (https://cran.r-project.org/web/packages/R6/index.html), but CRAN does create new package binaries when a new version of R is released. R version 4.0.4 was released about two weeks ago: https://twitter.com/pdalgd/status/1361246911378960391, but right now LightGBM's CI uses 4.0.3.

This PR proposes resolving the warning by updating R to 4.0.4.

Notes for Reviewers

I did look into whether this warning could be disabled in R CMD CHECK with an environment variable, and it doesn't look like it.

Linking to #3763

@jameslamb jameslamb requested a review from Laurae2 as a code owner March 3, 2021 03:46
@shiyu1994 shiyu1994 merged commit 87c37bf into master Mar 3, 2021
@jameslamb jameslamb deleted the fix/r4.0.4 branch March 3, 2021 06:22
@jameslamb jameslamb mentioned this pull request Mar 3, 2021
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Thanks a lot for the prompt fix!

StrikerRUS added a commit that referenced this pull request Mar 25, 2021
@akshitadixit @jameslamb
@subhamagrawal7 @shiyu1994 @StrikerRUS @jmoralez @marcelonieva7 @hcho3 @deddyjobson @AlbertoEAF @mjmckp @guolinke @ashok-ponnuswami-msft
[docs] Add alt text on images (related to #4036) (#4038)
6ad3e6e 
* [docs]Add alt text on images

* Update docs/GPU-Windows.rst

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update docs/GPU-Windows.rst

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Apply suggestions from code review

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Apply suggestions from code review

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Merge main branch commit updates (#1)

* [docs] Add alt text to image in Parameters-Tuning.rst (#4035)

* [docs] Add alt text to image in Parameters-Tuning.rst

Add alt text to Leaf-wise growth image, as part of #4028

* Update docs/Parameters-Tuning.rst

Co-authored-by: James Lamb <jaylamb20@gmail.com>

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* [ci] [R-package] upgrade to R 4.0.4 in CI (#4042)

* [docs] update description of deterministic parameter (#4027)

* update description of deterministic parameter to require using with force_row_wise or force_col_wise

* Update include/LightGBM/config.h

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* update docs

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [dask] Include support for init_score (#3950)

* include support for init_score

* use dataframe from init_score and test difference with and without init_score in local model

* revert refactoring

* initial docs. test between distributed models with and without init_score

* remove ranker from tests

* test value for root node and change docs

* comma

* re-include parametrize

* fix incorrect merge

* use single init_score and the booster_ attribute

* use np.float64 instead of float

* [ci] ignore untitle Jupyter notebooks in .gitignore (#4047)

* [ci] prevent getting incompatible dask and distributed versions (#4054)

* [ci] prevent getting incompatible dask and distributed versions

* Update .ci/test.sh

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* empty commit

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [ci] fix R CMD CHECK note about example timings (fixes #4049) (#4055)

* [ci] fix R CMD CHECK note about example timings (fixes #4049)

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* empty commit

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [ci] add CMake + R 3.6 test back (fixes #3469) (#4053)

* [ci] add CMake + R 3.6 test back (fixes #3469)

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Update .ci/test_r_package_windows.ps1

* -Wait and remove rtools40

* empty commit

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [dask] include multiclass-classification task in tests (#4048)

* include multiclass-classification task and task_to_model_factory dicts

* define centers coordinates. flatten init_scores within each partition for multiclass-classification

* include issue comment and fix linting error

* Update index.rst (#4029)

Add alt text to logo image

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* [dask] raise more informative error for duplicates in 'machines' (fixes #4057) (#4059)

* [dask] raise more informative error for duplicates in 'machines'

* uncomment

* avoid test failure

* Revert "avoid test failure"

This reverts commit 9442bdf.

* [dask] add tutorial documentation (fixes #3814, fixes #3838) (#4030)

* [dask] add tutorial documentation (fixes #3814, fixes #3838)

* add notes on saving the model

* quick start examples

* add examples

* fix timeouts in examples

* remove notebook

* fill out prediction section

* table of contents

* add line back

* linting

* isort

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* move examples under python-guide

* remove unused pickle import

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* set 'pending' commit status for R Solaris optional workflow (#4061)

* [docs] add Yu Shi to repo maintainers (#4060)

* Update FAQ.rst

* Update CODEOWNERS

* set is_linear_ to false when it is absent from the model file (fix #3778) (#4056)

* Add CMake option to enable sanitizers and build gtest (#3555)

* Add CMake option to enable sanitizer

* Set up gtest

* Address reviewer's feedback

* Address reviewer's feedback

* Update CMakeLists.txt

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* added type hint (#4070)

* [ci] run Dask examples on CI (#4064)

* Update Parallel-Learning-Guide.rst

* Update test.sh

* fix path

* address review comments

* [python-package] add type hints on Booster.set_network() (#4068)

* [python-package] add type hints on Booster.set_network()

* change behavior

* [python-package] Some mypy fixes (#3916)

* Some mypy fixes

* address James' comments

* Re-introduce pass in empty classes

* Update compat.py

Remove extra lines

* [dask] [ci] fix flaky network-setup test (#4071)

* [tests][dask] simplify code in Dask tests (#4075)

* simplify Dask tests code

* enable CI

* disable CI

* Revert "[ci] prevent getting incompatible dask and distributed versions (#4054)" (#4076)

This reverts commit 4e9c976.

* Fix parsing of non-finite values (#3942)

* Fix index out-of-range exception generated by BaggingHelper on small datasets.

Prior to this change, the line "score_t threshold = tmp_gradients[top_k - 1];" would generate an exception, since tmp_gradients would be empty when the cnt input value to the function is zero.

* Update goss.hpp

* Update goss.hpp

* Add API method LGBM_BoosterPredictForMats which runs prediction on a data set given as of array of pointers to rows (as opposed to existing method LGBM_BoosterPredictForMat which requires data given as contiguous array)

* Fix incorrect upstream merge

* Add link to LightGBM.NET

* Fix indenting to 2 spaces

* Dummy edit to trigger CI

* Dummy edit to trigger CI

* remove duplicate functions from merge

* Fix parsing of non-finite values.  Current implementation silently returns zero when input string is "inf", "-inf", or "nan" when compiled with VS2017, so instead just explicitly check for these values and fail if there is no match.  No attempt to optimise string allocations in this implementation since it is usually rarely invoked.

* Dummy commit to trigger CI

* Also handle -nan in double parsing method

* Update include/LightGBM/utils/common.h

Remove trailing whitespace to pass linting tests

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

Co-authored-by: matthew-peacock <matthew.peacock@whiteoakam.com>
Co-authored-by: Guolin Ke <guolin.ke@outlook.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [dask] remove unused imports from typing (#4079)

* Range check for DCG position discount lookup (#4069)

* Add check to prevent out of index lookup in the position discount table. Add debug logging to report number of queries found in the data.

* Change debug logging location so that we can print the data file name as well.

* Revert "Change debug logging location so that we can print the data file name as well."

This reverts commit 3981b34.

* Add data file name to debug logging.

* Move log line to a place where it is output even when query IDs are read from a separate file.

* Also add the out-of-range check to rank metrics.

* Perform check after number of queries is initialized.

* Update

* [ci] upgrade R CI scripts to work on Ubuntu 20.04 (#4084)

* [ci] install additional LaTeX packages in R CI jobs

* update autoconf version

* bump upper limit on package size to 100

* [SWIG] Add streaming data support + cpp tests (#3997)

* [feature] Add ChunkedArray to SWIG

* Add ChunkedArray
* Add ChunkedArray_API_extensions.i
* Add SWIG class wrappers

* Address some review comments

* Fix linting issues

* Move test to tests/test_ChunkedArray_manually.cpp

* Add test note

* Move ChunkedArray to include/LightGBM/utils/

* Declare more explicit types of ChunkedArray in the SWIG API.

* Port ChunkedArray tests to googletest

* Please C++ linter

* Address StrikerRUS' review comments

* Update SWIG doc & disable ChunkedArray<int64_t>

* Use CHECK_EQ instead of assert

* Change include order (linting)

* Rename ChunkedArray -> chunked_array files

* Change header guards

* Address last comments from StrikerRUS

* store all CMake files in one place (#4087)

* v3.2.0 release (#3872)

* Update VERSION.txt

* update appveyor.yml and configure

* fix Appveyor builds

Co-authored-by: James Lamb <jaylamb20@gmail.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: StrikerRUS <nekit94-12@hotmail.com>

* [ci] Bump version for development (#4094)

* Update .appveyor.yml

* Update cran-comments.md

* Update VERSION.txt

* update configure

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* [ci] fix flaky Azure Pipelines jobs (#4095)

* Update test.sh

* Update setup.sh

* Update .vsts-ci.yml

* Update test.sh

* Update setup.sh

* Update .vsts-ci.yml

* Update setup.sh

* Update setup.sh

Co-authored-by: Subham Agrawal <34346812+subhamagrawal7@users.noreply.github.com>
Co-authored-by: James Lamb <jaylamb20@gmail.com>
Co-authored-by: shiyu1994 <shiyu_k1994@qq.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: jmoralez <jmoralz92@gmail.com>
Co-authored-by: marcelonieva7 <72712805+marcelonieva7@users.noreply.github.com>
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
Co-authored-by: Deddy Jobson <dedjob@hotmail.com>
Co-authored-by: Alberto Ferreira <AlbertoEAF@users.noreply.github.com>
Co-authored-by: mjmckp <mjmckp@users.noreply.github.com>
Co-authored-by: matthew-peacock <matthew.peacock@whiteoakam.com>
Co-authored-by: Guolin Ke <guolin.ke@outlook.com>
Co-authored-by: ashok-ponnuswami-msft <57648631+ashok-ponnuswami-msft@users.noreply.github.com>
Co-authored-by: StrikerRUS <nekit94-12@hotmail.com>

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

Co-authored-by: James Lamb <jaylamb20@gmail.com>
Co-authored-by: Subham Agrawal <34346812+subhamagrawal7@users.noreply.github.com>
Co-authored-by: shiyu1994 <shiyu_k1994@qq.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: jmoralez <jmoralz92@gmail.com>
Co-authored-by: marcelonieva7 <72712805+marcelonieva7@users.noreply.github.com>
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
Co-authored-by: Deddy Jobson <dedjob@hotmail.com>
Co-authored-by: Alberto Ferreira <AlbertoEAF@users.noreply.github.com>
Co-authored-by: mjmckp <mjmckp@users.noreply.github.com>
Co-authored-by: matthew-peacock <matthew.peacock@whiteoakam.com>
Co-authored-by: Guolin Ke <guolin.ke@outlook.com>
Co-authored-by: ashok-ponnuswami-msft <57648631+ashok-ponnuswami-msft@users.noreply.github.com>
Co-authored-by: StrikerRUS <nekit94-12@hotmail.com>
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@shiyu1994 shiyu1994 shiyu1994 approved these changes

@StrikerRUS StrikerRUS Awaiting requested review from StrikerRUS

@Laurae2 Laurae2 Awaiting requested review from Laurae2

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