• using R Under development (unstable) (2026-01-09 r89293)
• 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 ... [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: ‘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/2s] 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 ... [14s/16s] 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/101s] ERROR   Running ‘testthat.R’ [71s/101s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(GPCERF)   >   > test_check("GPCERF")   2026-01-10 13:22:55.104365 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   Loading required package: nnls   Saving _problems/test-compute_deriv_nn-21.R   2026-01-10 13:22:58.6179 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_deriv_weights_gp-17.R   2026-01-10 13:23:02.397976 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_m_sigma-32.R   2026-01-10 13:23:08.403501 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:11.636886 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:15.234818 gimli1 2547300 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=2561984 on localhost:11061 at 13:23:15.656   2026-01-10 13:23:17.907624 gimli1 2547300 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.673 s.   2026-01-10 13:23:17.934452 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:21.203703 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:24.539283 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-compute_weight_gp-49.R   2026-01-10 13:23:28.03404 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:30.947861 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:32.935643 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:35.163002 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:35.195322 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:38.487269 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:38.51488 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:38.544865 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:38.578834 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:38.614371 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:38.647658 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:38.683067 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:38.708339 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:42.349575 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   starting worker pid=2583700 on localhost:11061 at 13:23:42.770   starting worker pid=2583701 on localhost:11061 at 13:23:42.776   2026-01-10 13:23:49.002845 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:23:52.256453 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:23:52.276733 gimli1 2547300 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-10 13:23:52.279533 gimli1 2547300 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=2593936 on localhost:11061 at 13:23:52.710   2026-01-10 13:23:55.772854 gimli1 2547300 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 3.492 s.} ...   2026-01-10 13:23:55.774879 gimli1 2547300 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=2597247 on localhost:11061 at 13:23:56.221   2026-01-10 13:23:58.77358 gimli1 2547300 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.999 s.   2026-01-10 13:23:58.775284 gimli1 2547300 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=2600424 on localhost:11061 at 13:23:59.151   2026-01-10 13:24:02.273313 gimli1 2547300 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.498 s.   2026-01-10 13:24:02.275183 gimli1 2547300 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 9.999 s.   2026-01-10 13:24:02.278996 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:24:02.291863 gimli1 2547300 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-10 13:24:02.308978 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:24:02.323962 gimli1 2547300 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-10 13:24:02.369038 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:24:02.384603 gimli1 2547300 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-10 13:24:02.399422 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:24:04.722643 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:24:04.742684 gimli1 2547300 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-10 13:24:04.756038 gimli1 2547300 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2026-01-09 r89293), detected cores: 64   2026-01-10 13:24:04.774428 gimli1 2547300 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...   2026-01-10 13:24:04.79379 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   Saving _problems/test-estimate_gps-15.R   2026-01-10 13:24:08.062146 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:24:10.892735 gimli1 2547300 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=2611840 on localhost:11061 at 13:24:11.176   2026-01-10 13:24:13.472127 gimli1 2547300 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.58 s.   2026-01-10 13:24:13.473577 gimli1 2547300 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...   starting worker pid=2613604 on localhost:11061 at 13:24:13.856   2026-01-10 13:24:16.696734 gimli1 2547300 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.223 s.   Saving _problems/test-estimate_mean_sd_nn-37.R   2026-01-10 13:24:16.731977 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:24:19.060709 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:24:22.287717 gimli1 2547300 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...   starting worker pid=2619661 on localhost:11061 at 13:24:22.552   2026-01-10 13:24:24.977628 gimli1 2547300 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.69000000000001 s.   2026-01-10 13:24:25.007556 gimli1 2547300 GPCERF estimate_gps INFO: Started estimating GPS values ...   2026-01-10 13:24:28.517034 gimli1 2547300 GPCERF find_optimal_nn INFO: Started finding optimal values ...   starting worker pid=2625857 on localhost:11061 at 13:24:28.776   2026-01-10 13:24:32.645678 gimli1 2547300 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.127 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/116s] OK
• checking PDF version of manual ... [4s/6s] 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