• using R Under development (unstable) (2026-01-08 r89292)
• 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 ... [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 15.2.0-12) 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/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
• checking loading without being on the library search path ... [2s/2s] 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/17s] 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 ... [71s/100s] ERROR   Running ‘testthat.R’ [71s/100s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(GPCERF)   >   > test_check("GPCERF")   2026-01-09 13:21:58.633809 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   Loading required package: nnls   Saving _problems/test-compute_deriv_nn-21.R   2026-01-09 13:22:02.677136 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_deriv_weights_gp-17.R   2026-01-09 13:22:06.516339 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_m_sigma-32.R   2026-01-09 13:22:13.227728 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:16.686011 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:19.684185 gimli1 1992919 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=2009235 on localhost:11876 at 13:22:20.179   2026-01-09 13:22:22.596642 gimli1 1992919 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.913 s.   2026-01-09 13:22:22.622535 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:26.146939 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:29.441829 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_weight_gp-49.R   2026-01-09 13:22:32.610205 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:35.511554 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:37.436759 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:39.63869 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:39.671938 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:42.817019 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:42.849796 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:42.878499 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:42.909822 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:42.933355 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:42.970699 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:43.002213 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:43.026428 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:46.53713 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   starting worker pid=2033937 on localhost:11876 at 13:22:46.894   starting worker pid=2033936 on localhost:11876 at 13:22:46.905   2026-01-09 13:22:52.341269 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:22:55.29241 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:22:55.308621 gimli1 1992919 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-09 13:22:55.311779 gimli1 1992919 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=2042095 on localhost:11876 at 13:22:55.571   2026-01-09 13:22:58.571279 gimli1 1992919 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 3.255 s.} ...   2026-01-09 13:22:58.573112 gimli1 1992919 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=2045276 on localhost:11876 at 13:22:58.951   2026-01-09 13:23:01.307357 gimli1 1992919 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.734 s.   2026-01-09 13:23:01.313661 gimli1 1992919 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=2047572 on localhost:11876 at 13:23:01.685   2026-01-09 13:23:04.95719 gimli1 1992919 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.643 s.   2026-01-09 13:23:04.958771 gimli1 1992919 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 9.65 s.   2026-01-09 13:23:04.967399 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:23:04.986637 gimli1 1992919 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-09 13:23:05.00441 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:23:05.02255 gimli1 1992919 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-09 13:23:05.064654 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:23:05.086404 gimli1 1992919 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-09 13:23:05.099283 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:23:07.330179 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:23:07.345287 gimli1 1992919 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-09 13:23:07.35404 gimli1 1992919 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-08 r89292), detected cores: 64   2026-01-09 13:23:07.36075 gimli1 1992919 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-09 13:23:07.380022 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-estimate_gps-15.R   2026-01-09 13:23:10.89304 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:23:14.055415 gimli1 1992919 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=2059558 on localhost:11876 at 13:23:14.387   2026-01-09 13:23:16.756986 gimli1 1992919 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.702 s.   2026-01-09 13:23:16.758866 gimli1 1992919 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=2061080 on localhost:11876 at 13:23:17.014   2026-01-09 13:23:19.73319 gimli1 1992919 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 2.974 s.   Saving _problems/test-estimate_mean_sd_nn-37.R   2026-01-09 13:23:19.800642 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:23:22.104346 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:23:25.157755 gimli1 1992919 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=2066894 on localhost:11876 at 13:23:25.526   2026-01-09 13:23:27.799338 gimli1 1992919 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.64100000000001 s.   2026-01-09 13:23:27.822166 gimli1 1992919 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-09 13:23:31.103778 gimli1 1992919 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=2070662 on localhost:11876 at 13:23:31.406   2026-01-09 13:23:35.34944 gimli1 1992919 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.244 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/101s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [2s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE