• using R Under development (unstable) (2025-12-07 r89119)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.6 (2)     Debian flang version 21.1.6 (2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘GPCERF/DESCRIPTION’ ... OK
• this is package ‘GPCERF’ version ‘0.2.4’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... INFO Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’
• 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 ‘GPCERF’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 21.1.6 (2)’
• checking C++ specification ... OK
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... NOTE Author field differs from that derived from Authors@R   Author: ‘Naeem Khoshnevis [aut] (<https://orcid.org/0000-0003-4315-1426>, HUIT), Boyu Ren [aut, cre] (<https://orcid.org/0000-0002-5300-1184>, McLean Hospital), Tanujit Dey [ctb] (<https://orcid.org/0000-0001-5559-211X>, HMS), Danielle Braun [aut] (<https://orcid.org/0000-0002-5177-8598>, HSPH)’   Authors@R: ‘Naeem Khoshnevis [aut] (ORCID: <https://orcid.org/0000-0003-4315-1426>, AFFILIATION: HUIT), Boyu Ren [aut, cre] (ORCID: <https://orcid.org/0000-0002-5300-1184>, AFFILIATION: McLean Hospital), Tanujit Dey [ctb] (ORCID: <https://orcid.org/0000-0001-5559-211X>, AFFILIATION: HMS), Danielle Braun [aut] (ORCID: <https://orcid.org/0000-0002-5177-8598>, AFFILIATION: HSPH)’
• 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 ... [4s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
• checking loading without being on the library search path ... [3s/4s] OK
• checking whether startup messages can be suppressed ... [4s/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 ... [21s/27s] OK
• checking Rd files ... [0s/1s] 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 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 pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/5s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [47s/24s] ERROR   Running ‘testthat.R’ [47s/24s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(GPCERF)   >   > test_check("GPCERF")   2025-12-08 17:32:44.415647 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   Loading required package: nnls   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-compute_deriv_nn-8.R   2025-12-08 17:32:45.979507 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-compute_deriv_weights_gp-8.R   2025-12-08 17:32:47.273114 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-compute_m_sigma-12.R   2025-12-08 17:32:48.306992 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-compute_posterior_m_nn-10.R   2025-12-08 17:32:49.655882 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-compute_posterior_sd_nn-10.R   2025-12-08 17:32:50.877581 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-compute_rl_deriv_gp-8.R   2025-12-08 17:32:52.054721 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-compute_rl_deriv_nn-8.R   2025-12-08 17:32:53.069899 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-compute_sd_gp-17.R   Saving _problems/test-compute_weight_gp-49.R   2025-12-08 17:32:54.520828 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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_cerf_gp-10.R   2025-12-08 17:32:55.574835 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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_cerf_nngp-10.R   2025-12-08 17:32:56.672843 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-10.R   2025-12-08 17:32:57.796367 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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_mean_sd_nn-10.R   2025-12-08 17:32:59.142388 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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_noise_gp-11.R   2025-12-08 17:33:00.278211 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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_noise_nn-10.R   2025-12-08 17:33:01.21995 gimli2 603761 GPCERF estimate_gps INFO: Started estimating GPS values ...   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-find_optimal_nn-9.R   [ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4    2. └─SuperLearner::SuperLearner(...)   ── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────   Expected `weight$weight[28]` to equal 0.0002182767.   Differences:     `actual`: 0.00000   `expected`: 0.00022      ── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3    2. └─SuperLearner::SuperLearner(...)   ── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────   Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library   Backtrace:       ▆    1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3    2. └─SuperLearner::SuperLearner(...)      [ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [26s/36s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’ --- re-building ‘Developers-Guide.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Developers-Guide.Rmd’ --- re-building ‘GPCERF.Rmd’ using rmarkdown 2025-12-08 17:33:15.87726 gimli2 613988 GPCERF estimate_gps INFO: Started estimating GPS values ... Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `SuperLearner::SuperLearner()`: ! All algorithms dropped from library --- Backtrace:     ▆  1. └─GPCERF::estimate_gps(...)  2. └─SuperLearner::SuperLearner(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'GPCERF.Rmd' failed with diagnostics: All algorithms dropped from library --- failed re-building ‘GPCERF.Rmd’ --- re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’ using rmarkdown 2025-12-08 17:33:29.041041 gimli2 615446 GPCERF estimate_gps INFO: Started estimating GPS values ... Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `SuperLearner::SuperLearner()`: ! All algorithms dropped from library --- Backtrace:     ▆  1. └─GPCERF::estimate_gps(...)  2. └─SuperLearner::SuperLearner(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics: All algorithms dropped from library --- failed re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’ --- re-building ‘Standard-Gaussian-Processes.Rmd’ using rmarkdown 2025-12-08 17:33:40.707059 gimli2 618538 GPCERF estimate_gps INFO: Started estimating GPS values ... Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `SuperLearner::SuperLearner()`: ! All algorithms dropped from library --- Backtrace:     ▆  1. └─GPCERF::estimate_gps(...)  2. └─SuperLearner::SuperLearner(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics: All algorithms dropped from library --- failed re-building ‘Standard-Gaussian-Processes.Rmd’ SUMMARY: processing the following files failed:   ‘GPCERF.Rmd’ ‘Nearest-neighbor-Gaussian-Processes.Rmd’   ‘Standard-Gaussian-Processes.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [2s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE