• using R Under development (unstable) (2025-12-31 r89265)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (1)     Debian flang version 21.1.8 (1)
• 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/3s] 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 21.1.8 (1)’
• 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/4s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
• checking loading without being on the library search path ... [3s/5s] OK
• checking whether startup messages can be suppressed ... [4s/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 ... [21s/30s] 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/6s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [125s/130s] ERROR   Running ‘testthat.R’ [125s/130s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(GPCERF)   >   > test_check("GPCERF")   2026-01-01 17:33:58.857158 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   Loading required package: nnls   Saving _problems/test-compute_deriv_nn-21.R   2026-01-01 17:34:03.286137 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_deriv_weights_gp-17.R   2026-01-01 17:34:07.211 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_m_sigma-32.R   2026-01-01 17:34:14.40131 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:34:18.239591 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:34:21.860912 gimli2 4070234 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=4077433 on localhost:11284 at 17:34:22.207   2026-01-01 17:34:26.136291 gimli2 4070234 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.276 s.   2026-01-01 17:34:26.234057 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:34:29.863106 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:34:33.52433 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_weight_gp-49.R   2026-01-01 17:34:37.573389 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:34:41.181707 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:44.609673 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:34:46.793419 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:46.820531 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:34:50.619113 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:50.651681 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:50.678051 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:50.710994 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:50.74674 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:50.783682 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:50.819642 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:34:50.862305 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:34:54.561219 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   starting worker pid=4085123 on localhost:11284 at 17:34:54.964   starting worker pid=4085122 on localhost:11284 at 17:34:55.086   2026-01-01 17:35:03.241241 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:35:06.796136 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:35:06.81112 gimli2 4070234 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-01 17:35:06.820058 gimli2 4070234 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=4088122 on localhost:11284 at 17:35:07.168   2026-01-01 17:35:11.341286 gimli2 4070234 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.515 s.} ...   2026-01-01 17:35:11.348966 gimli2 4070234 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=4089010 on localhost:11284 at 17:35:11.660   2026-01-01 17:35:16.043855 gimli2 4070234 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.7 s.   2026-01-01 17:35:16.046621 gimli2 4070234 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=4090328 on localhost:11284 at 17:35:16.319   2026-01-01 17:35:20.915447 gimli2 4070234 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 4.869 s.   2026-01-01 17:35:20.917757 gimli2 4070234 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 14.107 s.   2026-01-01 17:35:20.92345 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:35:20.935056 gimli2 4070234 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-01 17:35:20.96871 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:35:20.981395 gimli2 4070234 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-01 17:35:21.120071 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:35:21.128463 gimli2 4070234 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-01 17:35:21.155816 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:35:23.522751 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:35:23.535557 gimli2 4070234 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-01 17:35:23.562869 gimli2 4070234 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-31 r89265), detected cores: 32   2026-01-01 17:35:23.575354 gimli2 4070234 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-01 17:35:23.630141 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-estimate_gps-15.R   2026-01-01 17:35:27.455985 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:35:31.423687 gimli2 4070234 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=4094524 on localhost:11284 at 17:35:31.756   2026-01-01 17:35:35.813134 gimli2 4070234 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.38900000000001 s.   2026-01-01 17:35:35.816724 gimli2 4070234 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=4095698 on localhost:11284 at 17:35:36.228   2026-01-01 17:35:41.620733 gimli2 4070234 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 5.804 s.   Saving _problems/test-estimate_mean_sd_nn-37.R   2026-01-01 17:35:41.749959 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:35:44.371631 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:35:48.046754 gimli2 4070234 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=4099960 on localhost:11284 at 17:35:48.591   2026-01-01 17:35:51.995698 gimli2 4070234 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.949 s.   2026-01-01 17:35:52.025778 gimli2 4070234 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-01 17:35:55.782105 gimli2 4070234 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=4101923 on localhost:11284 at 17:35:56.200   2026-01-01 17:36:02.56278 gimli2 4070234 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 6.77799999999999 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 ... [94s/147s] OK
• 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: 1 ERROR, 1 NOTE