• using R Under development (unstable) (2025-12-02 r89085)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.6     flang version 21.1.6
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 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 ‘nlpred’ can be installed ... [29s/134s] OK See the install log for details.
• 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 ... [7s/33s] OK
• checking whether the package can be loaded with stated dependencies ... [7s/32s] OK
• checking whether the package can be unloaded cleanly ... [7s/32s] OK
• checking whether the namespace can be loaded with stated dependencies ... [7s/31s] OK
• checking whether the namespace can be unloaded cleanly ... [7s/37s] OK
• checking loading without being on the library search path ... [7s/40s] 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 ... [43s/194s] OK
• checking Rd files ... 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 line widths ... 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 ... [24s/105s] 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 ... <Anonymous> -> process.y.margin.and.objective -> NROW Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [22s/97s] ERROR   Running ‘testthat.R’ [21s/96s] 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 ────────────────────────────────   <getvarError/missingArgError/error/condition>   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 = `<list>`, test = `<list>`)    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 ... [83s/276s] OK
• checking PDF version of manual ... [9s/43s] OK
• checking HTML version of manual ... [6s/22s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE