[R-package] require lgb.Dataset, remove support for passing 'colnames' and 'categorical_feature' for lgb.train() and lgb.cv()

[jameslamb]

Fixes #6435

Enforces deprecations that have been in {lightgbm} sinvce v4.4.0:

• removes support for passing anything other than an lgb.Dataset to data argument of lgb.cv()
• removes colnames and categorical_feature arguments from lgb.train() and lgb.cv()

Also fixes some new warnings from {lintr} 3.2.0: #6714 (comment)

Notes for Reviewers

Still need to do reverse dependency checks

Before this is merged, we should check that it won't break any projects on CRAN that depend on {lightgbm}. I might propose introducing a comment-triggered CI job we can use for this purpose, maybe with https://github.com/r-lib/revdepcheck.

Looks like no reverse dependencies would be broken by the v4.6.0 release!

#6714 (comment)

xgboost did something similar recently

As @mayer79 mentioned on #6435. See dmlc/xgboost#10031

[jameslamb]

Setting up a CI job to run reverse dependency checks is taking too long (#6734), let's not block this on that.

Tomorrow, I will just test all the reverse dependencies manually. I won't merge this until I've done that and posted a comment here summarizing that.

But opening this up now for review... @StrikerRUS or @jmoralez could you review? This + #5010 are the last 2 things I'd like to try to get into v4.6.0, and as a reminder we only have 5 more days to put up a v4.6.0 release on CRAN (#6791).

Neither of those is critical, so if you do not have time to review please just let me know and we can skip them for this release.

[StrikerRUS]

LGTM, thank you for removing deprecated args!

[jameslamb]

Reverse dependency checks

Listing out the reverse dependencies (from https://cran.r-project.org/web/packages/lightgbm/index.html). I'll update this comment as I run the tests (probably tomorrow, my timezone, at this point, sorry).

Setup details

• R 4.3.3
  • for all but {ubair}... {ubair} was run on R 4.4.2 (it requires R>=4.4.0)
• macOS (arm64, M2 macbook pro, macOS 14.4.1)

Downloaded all the source tarballs of the latest releases from CRAN.

get-reverse-deps.R (click me)

loadNamespace("crandep")

PKG_DIR <- "~/repos/LightGBM/delete-me"

.log <- function(msg) {
    cat(sprintf("[download-revdeps] %s\n", msg))
}

# get all of lightgbm's reverse dependencies
depDF <- crandep::get_dep(
    name = "lightgbm"
    , type = "all"
    , reverse = TRUE
)
reverse_deps <- depDF[["to"]]
.log(sprintf("found %i reverse deps", length(reverse_deps)))

# skip some dependencies with known issues:
#
#   * 'misspi' (https://github.com/microsoft/LightGBM/issues/6741)
#   * 'qeML'   (checks take 45+ minutes to run)
# deps_to_skip <- c(
#     "misspi"
#     , "qeML"
# )
# .log(sprintf("excluding %i reverse deps: %s", length(deps_to_skip), toString(deps_to_skip)))
# reverse_deps <- reverse_deps[!reverse_deps %in% deps_to_skip]

.log(sprintf("checking the following packages: %s", toString(reverse_deps)))

# get the superset of all their dependencies
# (all of the packages needed to run 'R CMD check' on lightgbm's reverse deps)
their_deps <- unlist(
    unname(
        sapply(
            X = reverse_deps
            , FUN = function(pkg) {
                return(
                    crandep::get_dep(
                        name = pkg
                        , type = "all"
                        , reverse = FALSE
                    )[["to"]]
                )
            }
        )
    )
)

all_deps <- sort(unique(c(their_deps, reverse_deps)))

# don't try to install 'lightgbm', or packages that ship with the R standard library
all_deps <- all_deps[!all_deps %in% c("grid", "methods", "lightgbm", "parallel", "stats", "utils")]

# https://catboost.ai/docs/en/installation/r-installation-binary-installation
remotes::install_url(
    "https://github.com/catboost/catboost/releases/download/v1.2.7/catboost-R-darwin-universal2-1.2.7.tgz"
    , INSTALL_opts = c("--no-multiarch", "--no-staged-install", "--no-test-load")
)

# mixOmics moved to Bioconductor
# ref: https://www.bioconductor.org/packages/release/bioc/html/mixOmics.html
install.packages("BiocManager")

# this installs about 50 million other packages, ugh
bioconductor_deps <- "mixOmics"
BiocManager::install(
    bioconductor_deps
    , lib = .libPaths()[1]
    , update = TRUE
    , ask = FALSE
)

.log(sprintf("CRAN packages required to run these checks: %i", length(all_deps)))
.log(sprintf("Biocondutor packages required to run these checks: %i", length(bioconductor_deps)))

.log("installing all packages required to check reverse dependencies")

# install only the strong dependencies of all those packages
install.packages(  # nolint: undesirable_function
    pkgs = all_deps
    , repos = "https://cran.r-project.org"
    , dependencies = c("Depends", "Imports", "LinkingTo")
    , type = "both"
    , Ncpus = parallel::detectCores()
)

# get source tarballs, to be checked with 'R CMD check'
print(sprintf("--- downloading reverse dependencies to check (%i)", length(reverse_deps)))
download.packages(
    pkgs = reverse_deps
    , destdir = PKG_DIR
    , repos = "https://cran.r-project.org"
    , type = "source"
)

Ran R CMD check --no-manual --run-donttest on each of them.

run-checks.sh (click me)

#!/bin/bash

# Fix issues like the following that can show up running 'R CMD check' on
# specific clang versions:
#
#   * checking for detritus in the temp directory ... NOTE
#   Found the following files/directories:
#     ‘dsymutil-63923a’ ‘dsymutil-9aa721’ ‘dsymutil-b7e1bb’
#
# These are unlikely to show up in CRAN's checks. They come from
# 'dsymutil ---gen-reproducer' being run (not something LightGBM explicitly does).
#
# ref:
#   - https://github.com/llvm/llvm-project/issues/61920
#   - https://github.com/golang/go/issues/59026#issuecomment-1520487072
export DSYMUTIL_REPRODUCER_PATH=/dev/null

# parallelize compilation (extra important for Linux, where CRAN doesn't supply pre-compiled binaries)
export MAKEFLAGS="-j4"

# hack to get around this:
# https://stat.ethz.ch/pipermail/r-package-devel/2020q3/005930.html
export _R_CHECK_SYSTEM_CLOCK_=0

# ignore R CMD CHECK NOTE checking how long it has
# been since the last submission
export _R_CHECK_CRAN_INCOMING_REMOTE_=0

# to skip errors like this in {sae.projection}:
# Error in .check_ncores(length(names)) : 8 simultaneous processes spawned
export _R_CHECK_LIMIT_CORES_=false

# CRAN ignores the "installed size is too large" NOTE
export _R_CHECK_PKG_SIZES_THRESHOLD_=100

# ensure that the locally-installed version of 'tidy' is used
# ref: https://cran.r-project.org/doc/manuals/R-exts.html#Checking-packages
export R_TIDYCMD='/usr/local/bin/tidy'

Rscript -e "remove.packages('lightgbm')"
sh build-cran-package.sh --no-build-vignettes
R CMD INSTALL --with-keep.source ./lightgbm_*.tar.gz

pushd ./delete-me
rm -rf *.Rcheck

# install Java and tell R about it
# brew install openjdk
# R CMD javareconf
# export JAVA_HOME=/opt/homebrew/Cellar/openjdk/23.0.2/libexec/openjdk.jdk/Contents/Home

# Imports

# NOTE: cbl has 0 tests (https://github.com/cran/cbl)
R CMD check --no-manual --run-donttest ./cbl_*.tar.gz || true
R CMD check --no-manual --run-donttest ./misspi_*.tar.gz || true
R CMD check --no-manual --run-donttest ./predhy_*.tar.gz || true
R CMD check --no-manual --run-donttest ./predhy.GUI_*.tar.gz || true
R CMD check --no-manual --run-donttest ./sae.projection_*.tar.gz || true
R CMD check --no-manual --run-donttest ./ubair_*.tar.gz || true

# Suggests
R CMD check --no-manual --run-donttest ./bonsai_*.tar.gz || true
R CMD check --no-manual --run-donttest ./EIX_*.tar.gz || true
R CMD check --no-manual --run-donttest ./fastml_*.tar.gz || true
R CMD check --no-manual --run-donttest ./mllrnrs_*.tar.gz || true
R CMD check --no-manual --run-donttest ./PatientLevelPrediction_*.tar.gz || true
R CMD check --no-manual --run-donttest ./qeML_*.tar.gz || true
R CMD check --no-manual --run-donttest ./r2pmml_*.tar.gz || true
R CMD check --no-manual --run-donttest ./SHAPforxgboost_*.tar.gz || true
R CMD check --no-manual --run-donttest ./stackgbm_*.tar.gz || true
R CMD check --no-manual --run-donttest ./treeshap_*.tar.gz || true

# Enhances
R CMD check --no-manual --run-donttest ./fastshap_*.tar.gz || true
R CMD check --no-manual --run-donttest ./shapviz_*.tar.gz || true
R CMD check --no-manual --run-donttest ./vip_*.tar.gz || true

Those scripts are a little rough, will clean them up in #6734.

Reverse Imports

✅ cbl - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/cbl.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘cbl/DESCRIPTION’ ... OK
* this is package ‘cbl’ version ‘0.1.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cbl’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* DONE
Status: OK

❌ misspi - 1 ERROR (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/misspi.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘misspi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘misspi’ version ‘0.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘misspi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘misspi-Ex.R’ failed
The error most likely occurred in:

> ### Name: misspi
> ### Title: Missing Value Imputation in Parallel
> ### Aliases: misspi
> 
> ### ** Examples
> 
> 
> ## No test: 
> # Quick example 1
> # Load a small data
> data(iris)
> # Keep numerical columns
> num.col <- which(sapply(iris, is.numeric))
> iris.numeric <- as.matrix(iris[, num.col])
> set.seed(0)
> iris.miss <- missar(iris.numeric, 0.3, 1)
> iris.impute <- misspi(iris.miss)
Set number of cores used to 4 necessary ... 
Parallel computing using 4 cores ...
Imputing a matrix with  150  rows and  4  columns ... 
Highest missing rate is 0.326666666666667 ... 
Initializing ... 

  |                                                                           
  |                                                                     |   0%
  |                                                                           
  | *  *  *  *  *  *                                                    |  25%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *                                  |  50%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *                   |  75%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  * | 100%
Iteration 1 ... 

  |                                                                           
  | *  *  *  *  *  *                                                    |  25%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *                                  |  50%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *                   |  75%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  * | 100%
Relative squared difference is 0.0114309991586331 ... 

Iteration 2 ... 

  |                                                                           
  | *  *  *  *  *  *                                                    |  25%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *                                  |  50%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *                   |  75%
  |                                                                           
  | *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  * | 100%
Relative squared difference is 0.0116804139169135 ... 
Early stopping invoked ... 
> iris.impute
$x.imputed
       Sepal.Length Sepal.Width Petal.Length Petal.Width
  [1,]     5.100000    3.100000     1.366667   0.2000000
...
[150,]     6.266667    3.000000     5.100000   1.8000000

$time.elapsed
Time difference of 1.268682 secs

$niter
[1] 2

> 
> # Quick example 2
> # Load a high dimensional data
> data(toxicity, package = "misspi")
> set.seed(0)
> toxicity.miss <- missar(toxicity, 0.4, 0.2)
> toxicity.impute <- misspi(toxicity.miss)
We highly recommend activate viselect since your data is in high dimension. This may highly improve the speed and imputation accuracy ...

Parallel computing using 8 cores ...
Imputing a matrix with  171  rows and  1203  columns ... 
Highest missing rate is 0.491228070175439 ... 
Initializing ... 
...
...thousands of lines of logs printing progress bars and a big matrix ...
...
 [83,]       1 0.0000000        -0.0472  0.0000
 [ reached getOption("max.print") -- omitted 88 rows ]

$time.elapsed
Time difference of 28.0371 secs

$niter
[1] 1

> 
> # Change cores
> iris.impute.5core <- misspi(iris.miss, ncore = 5)
Set number of cores used to 4 necessary ... 
Parallel computing using 4 cores ...
...
  | *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  * | 100%Error in { : 
  task 97 failed - "Forced splits file includes feature index 0, but maximum feature index in dataset is -1
"
Calls: misspi -> %dopar% -> <Anonymous>
Execution halted
* DONE
Status: 1 ERROR

* checking examples ... ERROR
Running examples in ‘misspi-Ex.R’ failed
The error most likely occurred in:
...
Error in { : 
  task 97 failed - "Forced splits file includes feature index 0, but maximum feature index in dataset is -1
"

This is reproducible with {lightgbm} 4.5.0 too, so doesn't need to be fixed to submit to CRAN. ref: #6741

✅ predhy - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/predhy.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘predhy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘predhy’ version ‘2.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘predhy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* DONE
Status: OK

✅ predhy.GUI - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/predhy.GUI.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘predhy.GUI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘predhy.GUI’ version ‘2.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘predhy.GUI’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* DONE
Status: OK

✅ sae.projection - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/sae.projection.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-donttest --no-manual’
* checking for file ‘sae.projection/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sae.projection’ version ‘0.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sae.projection’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* DONE
Status: OK

✅ ubair - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/ubair.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-donttest --no-manual’
* checking for file ‘ubair/DESCRIPTION’ ... OK
* this is package ‘ubair’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ubair’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

Reverse Suggests

✅ bonsai - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/bonsai.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘bonsai/DESCRIPTION’ ... OK
* this is package ‘bonsai’ version ‘0.3.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bonsai’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘bonsai.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ EIX - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/EIX.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘EIX/DESCRIPTION’ ... OK
* this is package ‘EIX’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EIX’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘EIX.Rmd’ using ‘UTF-8’... OK
  ‘titanic_data.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ fastml - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/fastshap.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘fastshap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastshap’ version ‘0.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘fastshap’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
* used SDK: ‘MacOSX14.4.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘tinytest.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... NONE
  ‘fastshap.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ mllrnrs - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/mllrnrs.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘mllrnrs/DESCRIPTION’ ... OK
* this is package ‘mllrnrs’ version ‘0.0.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mllrnrs’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘mllrnrs_glmnet_binary.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_glmnet_multiclass.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_glmnet_regression.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_lightgbm_binary.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_lightgbm_multiclass.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_lightgbm_regression.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_ranger_binary.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_ranger_multiclass.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_ranger_regression.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_xgboost_binary.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_xgboost_multiclass.qmd’ using ‘UTF-8’... OK
  ‘mllrnrs_xgboost_regression.qmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ PatientLevelPrediction - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/PatientLevelPrediction.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-donttest --no-manual’
* checking for file ‘PatientLevelPrediction/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PatientLevelPrediction’ version ‘6.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PatientLevelPrediction’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘AddingCustomFeatureEngineering.Rmd’ using ‘UTF-8’... OK
  ‘AddingCustomModels.Rmd’ using ‘UTF-8’... OK
  ‘AddingCustomSamples.Rmd’ using ‘UTF-8’... OK
  ‘AddingCustomSplitting.Rmd’ using ‘UTF-8’... OK
  ‘BenchmarkTasks.Rmd’ using ‘UTF-8’... OK
  ‘BestPractices.Rmd’ using ‘UTF-8’... OK
  ‘BuildingMultiplePredictiveModels.Rmd’ using ‘UTF-8’... OK
  ‘BuildingPredictiveModels.Rmd’ using ‘UTF-8’... OK
  ‘ClinicalModels.Rmd’ using ‘UTF-8’... OK
  ‘ConstrainedPredictors.Rmd’ using ‘UTF-8’... OK
  ‘CreatingLearningCurves.Rmd’ using ‘UTF-8’... OK
  ‘CreatingNetworkStudies.Rmd’ using ‘UTF-8’... OK
  ‘GISExample.Rmd’ using ‘UTF-8’... OK
  ‘InstallationGuide.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ qeML - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/qeML.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-donttest --no-manual’
* checking for file ‘qeML/DESCRIPTION’ ... OK
* this is package ‘qeML’ version ‘1.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘qeML’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘Feature_Selection.Rmd’ using ‘UTF-8’... OK
  ‘Function_List.Rmd’ using ‘UTF-8’... OK
  ‘ML_Overview.Rmd’ using ‘UTF-8’... OK
  ‘NoPValues.Rmd’ using ‘UTF-8’... OK
  ‘Overfitting.Rmd’ using ‘UTF-8’... OK
  ‘PCA_and_UMAP.Rmd’ using ‘UTF-8’... OK
  ‘Quick_Start.Rmd’ using ‘UTF-8’... OK
  ‘Unbalanced_Classes.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ r2pmml - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/r2pmml.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘r2pmml/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘r2pmml’ version ‘0.30.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘r2pmml’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* DONE
Status: OK

✅ SHAPforxgboost - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/SHAPforxgboost.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘SHAPforxgboost/DESCRIPTION’ ... OK
* this is package ‘SHAPforxgboost’ version ‘0.1.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SHAPforxgboost’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘basic_workflow.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ stackgbm - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/stackgbm.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘stackgbm/DESCRIPTION’ ... OK
* this is package ‘stackgbm’ version ‘0.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘stackgbm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘stackgbm.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ treeshap - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/treeshap.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘treeshap/DESCRIPTION’ ... OK
* this is package ‘treeshap’ version ‘0.3.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘treeshap’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
* used SDK: ‘MacOSX14.4.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... OK
* DONE
Status: OK

Reverse Enhances

✅ fastshap - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/fastshap.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘fastshap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastshap’ version ‘0.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘fastshap’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
* used SDK: ‘MacOSX14.4.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘tinytest.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... NONE
  ‘fastshap.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ shapviz - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/shapviz.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-dontrun --run-donttest --no-manual’
* checking for file ‘shapviz/DESCRIPTION’ ... OK
* this is package ‘shapviz’ version ‘0.9.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘shapviz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
  ‘basic_use.Rmd’ using ‘UTF-8’... OK
  ‘geographic.Rmd’ using ‘UTF-8’... OK
  ‘multiple_output.Rmd’ using ‘UTF-8’... OK
  ‘tidymodels.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

✅ vip - OK (click me)

* using log directory ‘/Users/jlamb/repos/LightGBM/delete-me/vip.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using options ‘--run-donttest --no-manual’
* checking for file ‘vip/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vip’ version ‘0.4.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘vip’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘tinytest.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... NONE
  ‘vip.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK

[mayer79]

I like these changes,thanks for working on this.

[jameslamb]

Looks like a new version of {lintr} was just released: https://cran.r-project.org/web/packages/lintr/

Leading to the lint job in CI failing here, like this:

build_r.R:124:9: warning: [paste] Use paste(), not paste0(), to collapse a character vector when sep= is not used.
      , paste0(parsed_args[["make_args"]], collapse = "\", \"")
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

And this:

R-package/tests/testthat/test_lgb.Booster.R:1535:29: warning: [string_boundary] Use == to check for an exact string match. Doing so is more readable and more efficient.
      expect_true(any(grepl("^LightGBM Model$", printed_txt)))

(build link)

The for those is very non-controversial and small, so because we're getting close to release time, I just pushed them directly here.

[jameslamb]

Also posting because edits wouldn't have generated a notification.... I've finished reverse dependency checks. Details here: #6714 (comment)

Happy to say that I don't think v4.6.0 will cause any problems for projects on CRAN depending on {lightgbm}!

[jameslamb]

Going to merge this on the stale approval to keep the release moving, and because the small set of linter-related changes I made should be non-controversial.

#6796 will need to be approved anyway, so @jmoralez @StrikerRUS if you have any follow-up comments please make them there and we can incorporate them before releasing.

Thanks!