1026 Commits

Author SHA1 Message Date
James Lamb
3cca1c5fa1
[R] remove uses of exists() (#6387) 2020-11-17 15:06:23 +08:00
Philip Hyunsu Cho
5a33c2f3a0
[CI] Add noLD R test (#6382)
* [CI] Add noLD test

* Make noLD test only trigger with a PR comment

* [CI] Don't install stringi

* Add the Titanic example as a unit test

* Document trigger

* add to index

* Clarify that it needs to be a review comment
2020-11-12 12:41:25 -08:00
Philip Hyunsu Cho
c5645180a6
[R] Fix a crash that occurs with noLD R (#6378) 2020-11-11 21:09:08 -08:00
Jiaming Yuan
debeae2509
[R] Fix warnings from R check --as-cran (#6374)
* Remove exit and printf.

* Fix warnings.
2020-11-11 18:39:37 +08:00
James Lamb
6383757dca
[R] allow xgb.plot.importance() calls to fill a grid (#6294) 2020-10-28 14:37:28 -07:00
Jiaming Yuan
bcfab4d726
Revert "Disable JSON full serialization for now. (#6248)" (#6266)
This reverts commit 6d293020fbfa2c67b532d550fe5d55689662caac.
2020-10-27 03:30:47 +08:00
Jiaming Yuan
b5c2a47b20
Drop single point model recovery (#6262)
* Pass rabit params in JVM package.
* Implement timeout using poll timeout parameter.
* Remove OOB data check.
2020-10-21 15:27:03 +08:00
Jiaming Yuan
6d293020fb
Disable JSON full serialization for now. (#6248)
* Disable JSON serialization for now.

* Multi-class classification is checkpointing for each iteration.
This brings significant overhead.

Revert: 90355b4f007ae

* Set R tests to use binary.
2020-10-16 17:59:54 +08:00
Christian Lorentzen
cf4f019ed6
[Breaking] Change default evaluation metric for classification to logloss / mlogloss (#6183)
* Change DefaultEvalMetric of classification from error to logloss

* Change default binary metric in plugin/example/custom_obj.cc

* Set old error metric in python tests

* Set old error metric in R tests

* Fix missed eval metrics and typos in R tests

* Fix setting eval_metric twice in R tests

* Add warning for empty eval_metric for classification

* Fix Dask tests

Co-authored-by: Hyunsu Cho <chohyu01@cs.washington.edu>
2020-10-02 12:06:47 -07:00
James Lamb
c686bc0461
[R] remove warning in configure.ac (fixes #6151) (#6152)
* [R] remove warning in configure.ac (fixes #6151)

* update configure
2020-09-22 22:47:38 -07:00
Philip Hyunsu Cho
9e955fb9b0
[R] Check warnings explicitly for model compatibility tests (#6114)
* [R] Check warnings explicitly for model compatibility tests

* Address reviewer's feedback
2020-09-15 10:49:48 -07:00
Philip Hyunsu Cho
33577ef5d3
Add MAPE metric (#6119) 2020-09-14 18:45:27 -07:00
Jiaming Yuan
b5f52f0b1b
Validate weights are positive values. (#6115) 2020-09-15 09:03:55 +08:00
Vitalie Spinu
1453bee3e7
[R] Remove stringi dependency (#6109)
* [R] Fix empty empty tests and a test warnings

* [R] Remove stringi dependency (fix #5905)

* Fix R lint check

* [R] Fix automatic conversion to factor in R < 4.0.0 in xgb.model.dt.tree

* Add `R` Makefile variable

Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
2020-09-12 13:18:08 -07:00
Jiaming Yuan
c92d751ad1
Enable building rabit on Windows (#6105) 2020-09-11 11:54:46 +08:00
Tong He
3912f3de06
Updates from 1.2.0 cran submission (#6077)
* update for 1.2.0 cran submission

* recover cmakelists

* fix unittest from the shap PR

* trigger CI
2020-09-02 20:50:23 +08:00
Jiaming Yuan
20c95be625
Expand categorical node. (#6028)
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
2020-08-25 18:53:57 +08:00
Philip Hyunsu Cho
b3193052b3
Bump version to 1.3.0 snapshot in master (#6052) 2020-08-23 17:13:46 -07:00
Cuong Duong
e51cba6195
Add SHAP summary plot using ggplot2 (#5882)
* add SHAP summary plot using ggplot2

* Update xgb.plot.shap

* Update example in xgb.plot.shap documentation

* update logic, add tests

* whitespace fixes

* whitespace fixes for test_helpers

* namespace for sd function

* explicitly declare variables that are automatically evaluated by data.table

* Fix R lint

Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
2020-08-18 18:04:09 -07:00
James Lamb
589b385ec6
[R] fix uses of 1:length(x) and other small things (#5992) 2020-08-09 03:31:33 +08:00
Philip Hyunsu Cho
5a2dcd1c33
[R] Provide better guidance for persisting XGBoost model (#5964)
* [R] Provide better guidance for persisting XGBoost model

* Update saving_model.rst

* Add a paragraph about xgb.serialize()
2020-07-31 20:00:26 -07:00
Jiaming Yuan
18349a7ccf
[Breaking] Fix custom metric for multi output. (#5954)
* Set output margin to true for custom metric.  This fixes only R and Python.
2020-07-29 19:25:27 +08:00
Philip Hyunsu Cho
5879acde9a
[CI] Improve R linter script (#5944)
* [CI] Move lint to a separate script

* [CI] Improved lintr launcher

* Add lintr as a separate action

* Add custom parsing logic to print out logs

* Fix lintr issues in demos

* Run R demos

* Fix CRAN checks

* Install XGBoost into R env before running lintr

* Install devtools (needed to run demos)
2020-07-27 00:55:35 -07:00
Philip Hyunsu Cho
6347fa1c2e
[R] Enable weighted learning to rank (#5945)
* [R] enable weighted learning to rank

* Add R unit test for ranking

* Fix lint
2020-07-26 21:10:36 -07:00
Philip Hyunsu Cho
ace7fd328b
[R] Add a compatibility layer to load Booster object from an old RDS file (#5940)
* [R] Add a compatibility layer to load Booster from an old RDS
* Modify QuantileHistMaker::LoadConfig() to be backward compatible with 1.1.x
* Add a big warning about compatibility in QuantileHistMaker::LoadConfig()
* Add testing suite
* Discourage use of saveRDS() in CRAN doc
2020-07-26 00:06:49 -07:00
Jiaming Yuan
fbfbd525d8
Cache dependencies on Github Action. (#5928) 2020-07-23 14:00:19 +08:00
Jiaming Yuan
bc1d3ee230
Fix r early stop with custom objective. (#5923)
* Specify `ntreelimit`.
2020-07-23 03:28:17 +08:00
Philip Hyunsu Cho
627cf41a60
Add option to enable all compiler warnings in GCC/Clang (#5897)
* Add option to enable all compiler warnings in GCC/Clang

* Fix -Wall for CUDA sources

* Make -Wall private req for xgboost-r
2020-07-21 23:34:03 -07:00
Jiaming Yuan
8b1afce316
Add Github Action for R. (#5911)
* Fix lintr errors.
2020-07-20 19:23:36 +08:00
Philip Hyunsu Cho
7aee0e51ed
Fix R package build with CMake 3.13 (#5895)
* Fix R package build with CMake 3.13

* Require OpenMP for xgboost-r target
2020-07-15 20:22:11 -07:00
Philip Hyunsu Cho
0d411b0397
[CI] Simplify CMake build with modern CMake techniques (#5871)
* [CI] Simplify CMake build

* Make sure that plugins can be built

* [CI] Install lz4 on Mac
2020-07-08 04:23:24 -07:00
James Lamb
d39da42e69
[R] Remove dependency on gendef for Visual Studio builds (fixes #5608) (#5764)
* [R-package] Remove dependency on gendef for Visual Studio builds (fixes #5608)

* clarify docs

* removed debugging print statement

* Make R CMake install more robust

* Fix doc format; add ToC

* Update build.rst

* Fix AppVeyor

Co-authored-by: Hyunsu Cho <chohyu01@cs.washington.edu>
2020-06-15 00:20:44 +00:00
James Lamb
c35be9dc40
[R] replace uses of T and F with TRUE and FALSE (#5778)
* [R-package] replace uses of T and F with TRUE and FALSE

* enable linting

* Remove skip

Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
2020-06-11 06:08:02 -04:00
Philip Hyunsu Cho
1d22a9be1c
Revert "Reorder includes. (#5749)" (#5771)
This reverts commit d3a0efbf162f3dceaaf684109e1178c150b32de3.
2020-06-09 10:29:28 -07:00
Jiaming Yuan
d3a0efbf16
Reorder includes. (#5749)
* Reorder includes.

* R.
2020-06-03 17:30:47 +12:00
Philip Hyunsu Cho
073b625bde
Bump version to 1.2.0 snapshot in master (#5733) 2020-05-31 00:11:34 -07:00
Philip Hyunsu Cho
e35ad8a074
[R] Fix duplicated libomp.dylib error on Mac OSX (#5701) 2020-05-24 23:37:33 -07:00
James Lamb
f656ef2fed
[R-package] Reduce duplication in configure.ac (#5693)
* updated configure
2020-05-22 12:15:22 +08:00
Andy Adinets
646def51e0
C++14 for xgboost (#5664) 2020-05-21 12:26:40 +12:00
Lorenz Walthert
60511a3222
Document more objective parameters in R package (#5682) 2020-05-20 14:00:55 +08:00
Jiaming Yuan
7903286961
Remove silent from R demos. (#5675)
* Remove silent from R demos.

* Vignettes.
2020-05-19 18:20:46 +08:00
Philip Hyunsu Cho
474cfddf91
[R] Address warnings to comply with CRAN submission policy (#5600)
* [R] Address warnings to comply with CRAN submission policy

* Include <xgboost/logging.h>
2020-04-25 13:34:36 -07:00
Philip Hyunsu Cho
e4f5b6c84f
Port R compatibility patches from 1.0.0 release branch (#5577)
* Don't use memset to set struct when compiling for R

* Support 32-bit Solaris target for R package
2020-04-21 22:51:18 -07:00
Jiaming Yuan
c355ab65ed
Enable parameter validation for R. (#5569)
* Enable parameter validation for R.

* Add test.
2020-04-21 11:19:09 -07:00
Jiaming Yuan
564b22cee5
Restore attributes in complete. (#5573) 2020-04-21 11:06:55 -07:00
Jiaming Yuan
9c1103e06c
[Breaking] Set output margin to True for custom objective. (#5564)
* Set output margin to True for custom objective in Python and R.

* Add a demo for writing multi-class custom objective function.

* Run tests on selected demos.
2020-04-20 20:44:12 +08:00
Jiaming Yuan
e1f22baf8c
Fix slice and get info. (#5552) 2020-04-18 18:00:13 +08:00
Jiaming Yuan
c245eb8755
Fix r interaction constraints (#5543)
* Unify the parsing code.

* Cleanup.
2020-04-18 06:53:51 +08:00
Jiaming Yuan
b56c902841
[R] R raw serialization. (#5123)
* Add bindings for serialization.
* Change `xgb.save.raw' into full serialization instead of simple model.
* Add `xgb.load.raw' for unserialization.
* Run devtools.
2020-04-11 17:16:54 +08:00
Paul Kaefer
c362125d7b
corrected spelling of 'list' (#5482) 2020-04-05 09:15:08 +08:00