• using R Under development (unstable) (2025-12-21 r89216)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (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 ... [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 21.1.7 (1)’
• 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/4s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/5s] 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 ... [131s/134s] ERROR   Running ‘testthat.R’ [131s/134s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(GPCERF)   >   > test_check("GPCERF")   2025-12-22 17:35:29.829303 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   Loading required package: nnls   Saving _problems/test-compute_deriv_nn-21.R   2025-12-22 17:35:34.109678 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_deriv_weights_gp-17.R   2025-12-22 17:35:37.790682 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_m_sigma-32.R   2025-12-22 17:35:44.299954 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:35:47.908548 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:35:51.436641 gimli2 1827049 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1834231 on localhost:11582 at 17:35:51.865   2025-12-22 17:35:55.585659 gimli2 1827049 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.149 s.   2025-12-22 17:35:55.681507 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:35:59.16841 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:36:02.737651 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_weight_gp-49.R   2025-12-22 17:36:06.961057 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:36:10.565609 gimli2 1827049 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: 32   2025-12-22 17:36:13.585728 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:36:16.085748 gimli2 1827049 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: 32   2025-12-22 17:36:16.114923 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:36:19.824885 gimli2 1827049 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: 32   2025-12-22 17:36:19.860352 gimli2 1827049 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: 32   2025-12-22 17:36:19.903113 gimli2 1827049 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: 32   2025-12-22 17:36:19.939092 gimli2 1827049 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: 32   2025-12-22 17:36:19.968078 gimli2 1827049 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: 32   2025-12-22 17:36:20.00903 gimli2 1827049 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: 32   2025-12-22 17:36:20.055442 gimli2 1827049 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: 32   2025-12-22 17:36:20.09087 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:36:23.905115 gimli2 1827049 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: 32   starting worker pid=1841248 on localhost:11582 at 17:36:24.314   starting worker pid=1841249 on localhost:11582 at 17:36:24.349   2025-12-22 17:36:33.655403 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:36:37.149608 gimli2 1827049 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: 32   2025-12-22 17:36:37.161491 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 17:36:37.170325 gimli2 1827049 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=1845450 on localhost:11582 at 17:36:37.616   2025-12-22 17:36:42.348456 gimli2 1827049 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 5.176 s.} ...   2025-12-22 17:36:42.350995 gimli2 1827049 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1846668 on localhost:11582 at 17:36:42.801   2025-12-22 17:36:49.093406 gimli2 1827049 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 6.74299999999999 s.   2025-12-22 17:36:49.096303 gimli2 1827049 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=1849219 on localhost:11582 at 17:36:49.546   2025-12-22 17:36:55.375616 gimli2 1827049 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 6.279 s.   2025-12-22 17:36:55.37798 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 18.216 s.   2025-12-22 17:36:55.386687 gimli2 1827049 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: 32   2025-12-22 17:36:55.395161 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 17:36:55.421263 gimli2 1827049 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: 32   2025-12-22 17:36:55.431014 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 17:36:55.502662 gimli2 1827049 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: 32   2025-12-22 17:36:55.515468 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 17:36:55.538712 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:36:57.87326 gimli2 1827049 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: 32   2025-12-22 17:36:57.88891 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 17:36:57.903723 gimli2 1827049 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: 32   2025-12-22 17:36:57.919029 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-22 17:36:57.977055 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-estimate_gps-15.R   2025-12-22 17:37:01.726438 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:37:05.319479 gimli2 1827049 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1853528 on localhost:11582 at 17:37:05.647   2025-12-22 17:37:10.394426 gimli2 1827049 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 5.075 s.   2025-12-22 17:37:10.39697 gimli2 1827049 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=1854490 on localhost:11582 at 17:37:10.816   2025-12-22 17:37:16.190782 gimli2 1827049 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 5.794 s.   Saving _problems/test-estimate_mean_sd_nn-37.R   2025-12-22 17:37:16.281108 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:37:18.723087 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:37:22.388053 gimli2 1827049 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1858166 on localhost:11582 at 17:37:22.873   2025-12-22 17:37:27.680605 gimli2 1827049 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 5.292 s.   2025-12-22 17:37:27.742444 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-22 17:37:31.796539 gimli2 1827049 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=1860652 on localhost:11582 at 17:37:32.082   2025-12-22 17:37:37.730375 gimli2 1827049 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 5.931 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 ... [98s/153s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE