• using R Under development (unstable) (2025-12-21 r89216)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 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 ... [2s/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 15.2.0-11) 15.2.0’
• 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 ... [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/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [2s/3s] OK
• checking whether startup messages can be suppressed ... [3s/4s] 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/18s] 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 ... [2s/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [75s/122s] ERROR   Running ‘testthat.R’ [75s/122s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(GPCERF)   >   > test_check("GPCERF")   2025-12-22 13:25:06.977654 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   Loading required package: nnls   Saving _problems/test-compute_deriv_nn-21.R   2025-12-22 13:25:10.803294 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_deriv_weights_gp-17.R   2025-12-22 13:25:14.41837 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_m_sigma-32.R   2025-12-22 13:25:21.542795 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:25:25.232571 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:25:28.520417 gimli1 1205118 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1221548 on localhost:11506 at 13:25:28.883   2025-12-22 13:25:32.280155 gimli1 1205118 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.76 s.   2025-12-22 13:25:32.328753 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:25:36.099696 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:25:39.926719 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_weight_gp-49.R   2025-12-22 13:25:44.256474 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:25:47.861706 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:50.913461 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:25:54.249911 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:54.288521 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:25:58.98271 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:59.022422 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:59.053864 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:59.089866 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:59.121526 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:59.153443 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:59.185348 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:25:59.222335 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:26:03.328084 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   starting worker pid=1252335 on localhost:11506 at 13:26:03.722   starting worker pid=1252336 on localhost:11506 at 13:26:03.753   2025-12-22 13:26:10.845284 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:26:14.887266 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:26:14.905638 gimli1 1205118 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 13:26:14.913406 gimli1 1205118 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=1269002 on localhost:11506 at 13:26:15.269   2025-12-22 13:26:19.356684 gimli1 1205118 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.441 s.} ...   2025-12-22 13:26:19.358822 gimli1 1205118 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1275269 on localhost:11506 at 13:26:19.712   2025-12-22 13:26:22.116186 gimli1 1205118 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.75800000000001 s.   2025-12-22 13:26:22.123759 gimli1 1205118 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=1278284 on localhost:11506 at 13:26:22.521   2025-12-22 13:26:26.282246 gimli1 1205118 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 4.164 s.   2025-12-22 13:26:26.284165 gimli1 1205118 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 11.379 s.   2025-12-22 13:26:26.287191 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:26:26.309251 gimli1 1205118 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 13:26:26.322292 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:26:26.341229 gimli1 1205118 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 13:26:26.37863 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:26:26.409191 gimli1 1205118 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 13:26:26.422073 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:26:29.562257 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:26:29.585655 gimli1 1205118 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 13:26:29.603158 gimli1 1205118 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 64   2025-12-22 13:26:29.62554 gimli1 1205118 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 13:26:29.67267 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-estimate_gps-15.R   2025-12-22 13:26:33.236902 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:26:37.993601 gimli1 1205118 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1296985 on localhost:11506 at 13:26:38.453   2025-12-22 13:26:41.360134 gimli1 1205118 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.367 s.   2025-12-22 13:26:41.362061 gimli1 1205118 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=1301069 on localhost:11506 at 13:26:41.755   2025-12-22 13:26:45.369355 gimli1 1205118 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 4.00700000000001 s.   Saving _problems/test-estimate_mean_sd_nn-37.R   2025-12-22 13:26:45.435167 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:26:49.074649 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:26:53.437855 gimli1 1205118 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1318501 on localhost:11506 at 13:26:53.883   2025-12-22 13:26:56.966675 gimli1 1205118 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.52800000000001 s.   2025-12-22 13:26:56.99273 gimli1 1205118 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 13:27:00.667006 gimli1 1205118 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=1325635 on localhost:11506 at 13:27:01.105   2025-12-22 13:27:05.512449 gimli1 1205118 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.842 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 ... [61s/111s] 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