* For CRAN submission, remove all #pragma's that suppress compiler warnings
A few headers in dmlc-core contain #pragma's that disable compiler warnings,
which is against the CRAN submission policy. Fix the problem by removing
the offending #pragma's as part of the command `make Rbuild`.
This addresses issue #3322.
* Fix script to improve Cygwin/MSYS compatibility
We need this to pass rmingw CI test
* Remove remove_warning_suppression_pragma.sh from packaged tarball
* rank_metric: add AUC-PR
Implementation of the AUC-PR calculation for weighted data, proposed by Keilwagen, Grosse and Grau (https://doi.org/10.1371/journal.pone.0092209)
* rank_metric: fix lint warnings
* Implement tests for AUC-PR and fix implementation
* add aucpr to documentation for other languages
* fix rebase conflict
* [core] additional gblinear improvements
* [R] callback for gblinear coefficients history
* force eta=1 for gblinear python tests
* add top_k to GreedyFeatureSelector
* set eta=1 in shotgun test
* [core] fix SparsePage processing in gblinear; col-wise multithreading in greedy updater
* set sorted flag within TryInitColData
* gblinear tests: use scale, add external memory test
* fix multiclass for greedy updater
* fix whitespace
* fix typo
* [R] fix finding R.exe with cmake on WIN when it is in PATH
* [R] appveyor config for R package
* [R] wrap the lines to make R check happier
* [R] install only binary dep-packages in appveyor
* [R] for MSVC appveyor, also build a binary for R package and keep as an artifact
* [R] fix predict contributions for data with no colnames
* [R] add a render parameter for xgb.plot.multi.trees; fixes#2628
* [R] update Rd's
* [R] remove unnecessary dep-package from R cmake install
* silence type warnings; readability
* [R] silence complaint about incomplete line at the end
* [R] initial version of xgb.plot.shap()
* [R] more work on xgb.plot.shap
* [R] enforce black font in xgb.plot.tree; fixes#2640
* [R] if feature names are available, check in predict that they are the same; fixes#2857
* [R] cran check and lint fixes
* remove tabs
* [R] add references; a test for plot.shap
* SHAP values for feature contributions
* Fix commenting error
* New polynomial time SHAP value estimation algorithm
* Update API to support SHAP values
* Fix merge conflicts with updates in master
* Correct submodule hashes
* Fix variable sized stack allocation
* Make lint happy
* Add docs
* Fix typo
* Adjust tolerances
* Remove unneeded def
* Fixed cpp test setup
* Updated R API and cleaned up
* Fixed test typo
* [R] MSVC compatibility
* [GPU] allow seed in BernoulliRng up to size_t and scale to uint32_t
* R package build with cmake and CUDA
* R package CUDA build fixes and cleanups
* always export the R package native initialization routine on windows
* update the install instructions doc
* fix lint
* use static_cast directly to set BernoulliRng seed
* [R] demo for GPU accelerated algorithm
* tidy up the R package cmake stuff
* R pack cmake: installs main dependency packages if needed
* [R] version bump in DESCRIPTION
* update NEWS
* added short missing/sparse values explanations to FAQ
for loop in create.new.tree.features was referencing length(trees) as the upper bound of the loop. trees is a base R dataset and not the model that the code is generating. Changed loop boundary to model$niter which should be the number of trees.
* [gblinear] add features contribution prediction; fix DumpModel bug
* [gbtree] minor changes to PredContrib
* [R] add feature contribution prediction to R
* [R] bump up version; update NEWS
* [gblinear] fix the base_margin issue; fixes#1969
* [R] list of matrices as output of multiclass feature contributions
* [gblinear] make order of DumpModel coefficients consistent: group index changes the fastest
* [R] add native routines registration
* c_api.h needs to include <cstdint> since it uses fixed width integer types
* [R] use registered native routines from R code
* [R] bump version; add info on native routine registration to the contributors guide
* make lint happy
* [R] make sure things work for a single split model; fixes#2191
* [R] add option use_int_id to xgb.model.dt.tree
* [R] add example of exporting tree plot to a file
* [R] set save_period = NULL as default in xgboost() to be the same as in xgb.train; fixes#2182
* [R] it's a good practice after CRAN releases to bump up package version in dev
* [R] allow xgb.DMatrix construction from integer dense matrices
* [R] xgb.DMatrix: silent parameter; improve documentation
* [R] xgb.model.dt.tree code style changes
* [R] update NEWS with parameter changes
* [R] code safety & style; handle non-strict matrix and inherited classes of input and model; fixes#2242
* [R] change to x.y.z.p R-package versioning scheme and set version to 0.6.4.3
* [R] add an R package versioning section to the contributors guide
* [R] R-package/README.md: clean up the redundant old installation instructions, link the contributors guide
* [R] xgb.save must work when handle in nil but raw exists
* [R] print.xgb.Booster should still print other info when handle is nil
* [R] rename internal function xgb.Booster to xgb.Booster.handle to make its intent clear
* [R] rename xgb.Booster.check to xgb.Booster.complete and make it visible; more docs
* [R] storing evaluation_log should depend only on watchlist, not on verbose
* [R] reduce the excessive chattiness of unit tests
* [R] only disable some tests in windows when it's not 64-bit
* [R] clean-up xgb.DMatrix
* [R] test xgb.DMatrix loading from libsvm text file
* [R] store feature_names in xgb.Booster, use them from utility functions
* [R] remove non-functional co-occurence computation from xgb.importance
* [R] verbose=0 is enough without a callback
* [R] added forgotten xgb.Booster.complete.Rd; cran check fixes
* [R] update installation instructions
* fix cran check
* change required R version because of utils::globalVariables
* temporary commit, monotone not working
* fix test
* fix doc
* fix doc
* fix cran note and warning
* improve checks
* fix urls
* fix cran check
* add cleanup and bump up version number
* use clean in build
* Update Makefile
* [R-package] JSON tree dump interface
* [R-package] precision bugfix in xgb.attributes
* [R-package] bugfix for cb.early.stop called from xgb.cv
* [R-package] a bit more clarity on labels checking in xgb.cv
* [R-package] test JSON dump for gblinear as well
* whitespace lint
* [CORE] allow updating trees in an existing model
* [CORE] in refresh updater, allow keeping old leaf values and update stats only
* [R-package] xgb.train mod to allow updating trees in an existing model
* [R-package] added check for nrounds when is_update
* [CORE] merge parameter declaration changes; unify their code style
* [CORE] move the update-process trees initialization to Configure; rename default process_type to 'default'; fix the trees and trees_to_update sizes comparison check
* [R-package] unit tests for the update process type
* [DOC] documentation for process_type parameter; improved docs for updater, Gamma and Tweedie; added some parameter aliases; metrics indentation and some were non-documented
* fix my sloppy merge conflict resolutions
* [CORE] add a TreeProcessType enum
* whitespace fix
* fix cran check
* change required R version because of utils::globalVariables
* temporary commit, monotone not working
* fix test
* fix doc
* fix doc
* fix cran note and warning
* improve checks
* fix urls
* add support for tweedie regression
* added back readme line that was accidentally deleted
* fixed linting errors
* add support for tweedie regression
* added back readme line that was accidentally deleted
* fixed linting errors
* rebased with upstream master and added R example
* changed parameter name to tweedie_variance_power
* linting error fix
* refactored tweedie-nloglik metric to be more like the other parameterized metrics
* added upper and lower bound check to tweedie metric
* add support for tweedie regression
* added back readme line that was accidentally deleted
* fixed linting errors
* added upper and lower bound check to tweedie metric
* added back readme line that was accidentally deleted
* rebased with upstream master and added R example
* rebased again on top of upstream master
* linting error fix
* added upper and lower bound check to tweedie metric
* rebased with master
* lint fix
* removed whitespace at end of line 186 - elementwise_metric.cc
