* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/CausalGPS.Rcheck’ * using R Under development (unstable) (2025-12-02 r89085) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘CausalGPS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CausalGPS’ version ‘0.5.0’ * 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 ‘CausalGPS’ can be installed ... [29s/29s] OK * used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’ * 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 loading without being on the library search path ... OK * checking whether 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 ... [14s/14s] OK * checking Rd files ... OK * 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 data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... 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 $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘CausalGPS-Ex.R’ failed The error most likely occurred in: > ### Name: check_covar_balance > ### Title: Check covariate balance > ### Aliases: check_covar_balance > > ### ** Examples > > ## No test: > set.seed(422) > n <- 100 > mydata <- generate_syn_data(sample_size=n) > year <- sample(x=c("2001","2002","2003","2004","2005"),size = n, + replace = TRUE) > region <- sample(x=c("North", "South", "East", "West"),size = n, + replace = TRUE) > mydata$year <- as.factor(year) > mydata$region <- as.factor(region) > mydata$cf5 <- as.factor(mydata$cf5) > > m_xgboost <- function(nthread = 1, + ntrees = 35, + shrinkage = 0.3, + max_depth = 5, + ...) {SuperLearner::SL.xgboost( + nthread = nthread, + ntrees = ntrees, + shrinkage=shrinkage, + max_depth=max_depth, + ...)} > > data_with_gps <- estimate_gps(.data = mydata, + .formula = w ~ cf1 + cf2 + cf3 + cf4 + cf5 + + cf6 + year + region, + sl_lib = c("m_xgboost"), + gps_density = "kernel") Loading required package: nnls 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) 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 = objective, nrounds = ntrees, : argument "y" is missing, with no default Warning in FUN(X[[i]], ...) : Error in algorithm m_xgboost The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in SuperLearner::SuperLearner(Y = target, X = data.frame(input), : All algorithms dropped from library Calls: estimate_gps -> train_it -> Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CausalGPS) > > Sys.setenv("R_TESTS" = "") > library(testthat) > test_check("CausalGPS") Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Saving _problems/test-estimate_erf-22.R Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Saving _problems/test-estimate_gps-29.R Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Saving _problems/test-generate_pseudo_pop-35.R Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, : argument "y" is missing, with no default Saving _problems/test-trim_it-34.R [ FAIL 4 | WARN 200 | SKIP 19 | PASS 68 ] ══ Skipped tests (19) ══════════════════════════════════════════════════════════ • On CRAN (17): 'test-CausalGPS_smooth.R:3:4', 'test-absolute_corr_fun.R:4:3', 'test-absolute_weighted_corr_fun.R:4:3', 'test-check_covar_balance.R:2:1', 'test-check_kolmogorov_smirnov.R:2:3', 'test-compile_pseudo_pop.R:3:3', 'test-compute_density.R:3:3', 'test-compute_minmax.R:3:3', 'test-compute_resid.R:3:3', 'test-create_weighting.R:3:3', 'test-estimate_gps.R:63:3', 'test-estimate_gps.R:92:3', 'test-estimate_hat_vals.R:3:3', 'test-matching_fn.R:3:3', 'test-set_logger.R:3:5', 'test-train_it.R:3:3', 'test-train_it.R:18:3' • empty test (2): 'test-estimate_npmetric_erf.R:1:1', 'test-estimate_npmetric_erf.R:89:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-estimate_erf.R:19:3'): estimate erf works as expected ────────── Error in `SuperLearner::SuperLearner(Y = target, X = data.frame(input), SL.library = sl_lib_internal)`: All algorithms dropped from library Backtrace: ▆ 1. └─CausalGPS::estimate_gps(...) at test-estimate_erf.R:19:3 2. └─CausalGPS:::train_it(...) 3. └─SuperLearner::SuperLearner(...) ── Error ('test-estimate_gps.R:26:3'): estimate_gps works as expected. ───────── Error in `SuperLearner::SuperLearner(Y = target, X = data.frame(input), SL.library = sl_lib_internal)`: All algorithms dropped from library Backtrace: ▆ 1. └─CausalGPS::estimate_gps(...) at test-estimate_gps.R:26:3 2. └─CausalGPS:::train_it(...) 3. └─SuperLearner::SuperLearner(...) ── Error ('test-generate_pseudo_pop.R:31:3'): generate_pseudo_pop works as expected. ── Error in `SuperLearner::SuperLearner(Y = target, X = data.frame(input), SL.library = sl_lib_internal)`: All algorithms dropped from library Backtrace: ▆ 1. └─CausalGPS::estimate_gps(...) at test-generate_pseudo_pop.R:31:3 2. └─CausalGPS:::train_it(...) 3. └─SuperLearner::SuperLearner(...) ── Error ('test-trim_it.R:31:3'): trim_it works as expected ──────────────────── Error in `SuperLearner::SuperLearner(Y = target, X = data.frame(input), SL.library = sl_lib_internal)`: All algorithms dropped from library Backtrace: ▆ 1. └─CausalGPS::estimate_gps(...) at test-trim_it.R:31:3 2. └─CausalGPS:::train_it(...) 3. └─SuperLearner::SuperLearner(...) [ FAIL 4 | WARN 200 | SKIP 19 | PASS 68 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [20s/20s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 2 ERRORs See ‘/data/blackswan/ripley/R/packages/tests-devel/CausalGPS.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:27.88, 122.89 + 23.74