* using log directory 'd:/Rcompile/CRANpkg/local/4.4/nlpred.Rcheck' * using R version 4.4.3 (2025-02-28 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'nlpred/DESCRIPTION' ... OK * this is package 'nlpred' version '1.0.1' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'nlpred' 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 ... [5s] OK * checking whether the package can be loaded with stated dependencies ... [5s] OK * checking whether the package can be unloaded cleanly ... [4s] OK * checking whether the namespace can be loaded with stated dependencies ... [5s] OK * checking whether the namespace can be unloaded cleanly ... [5s] OK * checking loading without being on the library search path ... [5s] OK * checking use of S3 registration ... 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 ... [17s] OK * checking Rd files ... [1s] NOTE checkRd: (-1) dot-make_long_data.Rd:44: Lost braces; missing escapes or markup? 44 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)), | ^ checkRd: (-1) dot-make_long_data_nested_cv.Rd:49: Lost braces; missing escapes or markup? 49 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)), | ^ * 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 ... [1s] 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 ... [21s] ERROR Running examples in 'nlpred-Ex.R' failed The error most likely occurred in: > ### Name: xgboost_wrapper > ### Title: Wrapper for fitting eXtreme gradient boosting via 'xgboost' > ### Aliases: xgboost_wrapper > > ### ** Examples > > # simulate data > # make list of training data > train_X <- data.frame(x1 = runif(50)) > train_Y <- rbinom(50, 1, plogis(train_X$x1)) > train <- list(Y = train_Y, X = train_X) > # make list of test data > test_X <- data.frame(x1 = runif(50)) > test_Y <- rbinom(50, 1, plogis(train_X$x1)) > test <- list(Y = test_Y, X = test_X) > # fit xgboost > xgb_wrap <- xgboost_wrapper(train = train, test = test) Warning in throw_err_or_depr_msg("Parameter(s) have been removed from this function: ", : Parameter(s) have been removed from this function: params, save_period. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), : Passed unrecognized parameters: verbose. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version. Error in xgboost::xgboost(data = xgmat, objective = "binary:logistic", : argument "y" is missing, with no default Calls: xgboost_wrapper ... -> process.y.margin.and.objective -> NROW Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [17s] ERROR Running 'testthat.R' [16s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(nlpred) Loading required package: data.table > > test_check("nlpred") Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 | Multistart 1 of 1 / Multistart 1 of 1 | Multistart 1 of 1 | Saving _problems/testWrappers-13.R [ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('testWrappers.R:12:3'): wrappers work ──────────────────────────────── Error in `xgboost::xgboost(data = xgmat, objective = "binary:logistic", nrounds = ntrees, max_depth = max_depth, min_child_weight = minobspernode, eta = shrinkage, verbose = verbose, nthread = nthread, params = params, save_period = save_period)`: argument "y" is missing, with no default Backtrace: ▆ 1. └─nlpred (local) check_wrapper(paste0(wrap, "_wrapper"), test = test, train = train) at testWrappers.R:31:17 2. ├─base::do.call(wrapper, args = list(train = train, test = test)) at testWrappers.R:12:17 3. └─nlpred::xgboost_wrapper(train = ``, test = ``) 4. └─xgboost::xgboost(...) 5. └─xgboost:::process.y.margin.and.objective(...) 6. └─base::NROW(y) [ FAIL 1 | WARN 4 | SKIP 0 | PASS 40 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [58s] OK * checking PDF version of manual ... [19s] OK * checking HTML version of manual ... [8s] OK * DONE Status: 2 ERRORs, 1 NOTE