• using R Under development (unstable) (2025-12-24 r89227)
• 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 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 ... [4s/5s] OK
• checking whether the package can be unloaded cleanly ... [4s/5s] 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 ... [3s/6s] 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/26s] 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 ... [128s/134s] ERROR   Running ‘testthat.R’ [128s/134s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(GPCERF)   >   > test_check("GPCERF")   2025-12-25 17:37:30.81575 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   Loading required package: nnls   Saving _problems/test-compute_deriv_nn-21.R   2025-12-25 17:37:35.348998 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_deriv_weights_gp-17.R   2025-12-25 17:37:39.136248 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_m_sigma-32.R   2025-12-25 17:37:47.305633 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:37:51.225448 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:37:55.018407 gimli2 1097491 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1105294 on localhost:11994 at 17:37:55.353   2025-12-25 17:37:59.42045 gimli2 1097491 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.402 s.   2025-12-25 17:37:59.46593 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:38:03.149663 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:38:06.744652 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_weight_gp-49.R   2025-12-25 17:38:10.925557 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:38:14.636906 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:18.48831 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:38:21.008209 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:21.050573 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:38:24.689993 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:24.709002 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:24.730425 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:24.76524 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:24.804397 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:24.845599 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:24.885033 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:25.037045 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:38:28.647655 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   starting worker pid=1112947 on localhost:11994 at 17:38:29.093   starting worker pid=1112946 on localhost:11994 at 17:38:29.124   2025-12-25 17:38:37.866322 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:38:42.285972 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:42.299581 gimli2 1097491 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-25 17:38:42.308606 gimli2 1097491 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=1116805 on localhost:11994 at 17:38:42.829   2025-12-25 17:38:47.277465 gimli2 1097491 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.96300000000001 s.} ...   2025-12-25 17:38:47.280491 gimli2 1097491 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1118157 on localhost:11994 at 17:38:47.723   2025-12-25 17:38:51.522121 gimli2 1097491 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.242 s.   2025-12-25 17:38:51.52898 gimli2 1097491 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=1119207 on localhost:11994 at 17:38:51.957   2025-12-25 17:38:58.013857 gimli2 1097491 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 6.48899999999999 s.   2025-12-25 17:38:58.016311 gimli2 1097491 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 15.717 s.   2025-12-25 17:38:58.026569 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:58.03619 gimli2 1097491 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-25 17:38:58.074757 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:58.087438 gimli2 1097491 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-25 17:38:58.16663 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:38:58.17647 gimli2 1097491 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-25 17:38:58.203394 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:39:00.527213 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:39:00.541071 gimli2 1097491 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-25 17:39:00.568949 gimli2 1097491 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 32   2025-12-25 17:39:00.581659 gimli2 1097491 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2025-12-25 17:39:00.617618 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-estimate_gps-15.R   2025-12-25 17:39:04.542085 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:39:08.104996 gimli2 1097491 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1123457 on localhost:11994 at 17:39:08.488   2025-12-25 17:39:12.66418 gimli2 1097491 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.559 s.   2025-12-25 17:39:12.666591 gimli2 1097491 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=1124807 on localhost:11994 at 17:39:13.014   2025-12-25 17:39:17.290832 gimli2 1097491 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 4.624 s.   Saving _problems/test-estimate_mean_sd_nn-37.R   2025-12-25 17:39:17.354932 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:39:19.672784 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:39:23.535813 gimli2 1097491 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=1127817 on localhost:11994 at 17:39:23.972   2025-12-25 17:39:27.645303 gimli2 1097491 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.10899999999999 s.   2025-12-25 17:39:27.706303 gimli2 1097491 GPCERF estimate_gps INFO: Started estimating GPS values ...   2025-12-25 17:39:31.727827 gimli2 1097491 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=1130628 on localhost:11994 at 17:39:32.132   2025-12-25 17:39:38.391339 gimli2 1097491 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 6.66200000000001 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 ... [97s/152s] 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