• using R Under development (unstable) (2026-01-10 r89298)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-12) 15.2.0     GNU Fortran (Debian 15.2.0-12) 15.2.0
• 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: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
• checking C++ specification ... INFO   specified C++17
• 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 ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [2s/3s] OK
• checking whether startup messages can be suppressed ... [2s/3s] 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 ... [13s/15s] OK
• checking Rd files ... [0s/0s] 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 ... [2s/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [70s/99s] ERROR   Running ‘testthat.R’ [70s/99s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(GPCERF)   >   > test_check("GPCERF")   2026-01-11 13:23:54.719216 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   Loading required package: nnls   Saving _problems/test-compute_deriv_nn-21.R   2026-01-11 13:23:58.092369 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_deriv_weights_gp-17.R   2026-01-11 13:24:01.796921 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_m_sigma-32.R   2026-01-11 13:24:07.594402 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:10.810829 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:14.294202 gimli1 3181068 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=3195317 on localhost:11258 at 13:24:14.622   2026-01-11 13:24:16.880079 gimli1 3181068 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.586 s.   2026-01-11 13:24:16.907819 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:19.88448 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:23.569129 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_weight_gp-49.R   2026-01-11 13:24:27.07703 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:30.191596 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:32.382421 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:34.899933 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:34.939927 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:38.094106 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:38.131172 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:38.158776 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:38.189667 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:38.216478 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:38.240955 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:38.269964 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:38.301205 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:41.327774 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   starting worker pid=3216499 on localhost:11258 at 13:24:41.679   starting worker pid=3216501 on localhost:11258 at 13:24:41.715   2026-01-11 13:24:47.408525 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:24:50.748382 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:24:50.766242 gimli1 3181068 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-11 13:24:50.772877 gimli1 3181068 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=3225309 on localhost:11258 at 13:24:51.117   2026-01-11 13:24:54.217204 gimli1 3181068 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 3.443 s.} ...   2026-01-11 13:24:54.219234 gimli1 3181068 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=3228753 on localhost:11258 at 13:24:54.525   2026-01-11 13:24:57.304408 gimli1 3181068 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.08499999999999 s.   2026-01-11 13:24:57.308022 gimli1 3181068 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=3231350 on localhost:11258 at 13:24:57.565   2026-01-11 13:25:00.621734 gimli1 3181068 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.31399999999999 s.   2026-01-11 13:25:00.623459 gimli1 3181068 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 9.857 s.   2026-01-11 13:25:00.626593 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:25:00.642406 gimli1 3181068 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-11 13:25:00.655929 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:25:00.674866 gimli1 3181068 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-11 13:25:00.757696 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:25:00.777152 gimli1 3181068 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-11 13:25:00.790485 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:25:03.164173 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:25:03.182313 gimli1 3181068 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-11 13:25:03.19954 gimli1 3181068 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-10 r89298), detected cores: 64   2026-01-11 13:25:03.212884 gimli1 3181068 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-11 13:25:03.231138 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-estimate_gps-15.R   2026-01-11 13:25:06.475257 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:25:09.642612 gimli1 3181068 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=3243037 on localhost:11258 at 13:25:09.895   2026-01-11 13:25:12.137145 gimli1 3181068 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.494 s.   2026-01-11 13:25:12.139302 gimli1 3181068 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=3244913 on localhost:11258 at 13:25:12.535   2026-01-11 13:25:15.291545 gimli1 3181068 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.152 s.   Saving _problems/test-estimate_mean_sd_nn-37.R   2026-01-11 13:25:15.335648 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:25:17.45114 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:25:20.497377 gimli1 3181068 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=3251213 on localhost:11258 at 13:25:20.779   2026-01-11 13:25:23.243449 gimli1 3181068 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.74600000000001 s.   2026-01-11 13:25:23.281597 gimli1 3181068 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-11 13:25:26.150746 gimli1 3181068 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=3254565 on localhost:11258 at 13:25:26.493   2026-01-11 13:25:30.013587 gimli1 3181068 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 3.861 s.} ...   [ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──   Expected `deriv_val[1, 1]` to equal 1.558466.   Differences:     `actual`: -1.0   `expected`: 1.6      ── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──   Expected `weights[37]` to equal 3.307249e-05.   Differences:     `actual`: -0.00011   `expected`: 0.00003      ── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──   Expected `gp_cerf[10]` to equal 2.105425.   Differences:     `actual`: -6.1   `expected`: 2.1      ── 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      ── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────   Expected `gps_m$gps[4, 1]` to equal 8.74310154.   Differences:     `actual`: 7.3   `expected`: 8.7      ── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──   Expected `val[10]` to equal 5.031225.   Differences:     `actual`: 5.067   `expected`: 5.031         [ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [60s/104s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE