* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/gaussianprocesses.Rcheck’
* using R Under development (unstable) (2026-10-28 r90786)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
    GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-10-30 00:24:41 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘gaussianprocesses/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gaussianprocesses’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘gaussianprocesses’ can be installed ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [19s/21s] OK
* checking Rd files ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [52s/54s]
 [52s/54s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gaussianprocesses)
  > 
  > test_check("gaussianprocesses")
  Saving _problems/test-mean-coefficients-291.R
  Saving _problems/test-mean-coefficients-291.R
  Timing stopped at: 0.006 0 0.006
  [ FAIL 2 | WARN 0 | SKIP 40 | PASS 6199 ]
  
  ══ Skipped tests (40) ══════════════════════════════════════════════════════════
  • On CRAN (39): 'test-changepoint-kernel.R:311:3',
    'test-gp-simulation-benchmarks.R:114:3', 'test-gp-uncertainty.R:58:3',
    'test-spectral-mixture.R:301:3', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7',
    'test-validation-references.R:69:7', 'test-validation-references.R:69:7'
  • _pkgdown.yml is not in the package (1): 'test-api-stability.R:63:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mean-coefficients.R:291:5'): optimize_gp() maximizes profile and restricted likelihoods ──
  Expected `fit()$optimization` to be identical to `model$optimization`.
  Differences:
      actual$optimized_parameters | expected$optimized_parameters    
  [1] 0.870707639694134           - 0.870707639642575             [1]
  [2] 0.369478976082430           - 0.369478976078105             [2]
  [3] 75701.263445226388285       - 75701.267141279284260         [3]
  [4] 0.002237090974580           - 0.002237090974612             [4]
  
    `actual$objective`: -26.31989089916191
  `expected$objective`: -26.31989089916206
  
  actual$optima vs expected$optima
                         log_marginal_likelihood          gap
    actual$optima[1, ]                  26.31989 0.000000e+00
  - actual$optima[2, ]                  26.31989 2.926275e-08
  + expected$optima[2, ]                26.31989 2.926391e-08
  - actual$optima[3, ]                  26.31989 7.124509e-08
  + expected$optima[3, ]                26.31989 7.124487e-08
  
  actual$optima$log_marginal_likelihood vs expected$optima$log_marginal_likelihood
  - 26.31989089916191
  + 26.31989089916206
  - 26.31989086989916
  + 26.31989086989816
  - 26.31989082791682
  + 26.31989082791720
  
    `actual$optima$gap`: 0.00000000000000 0.00000002926275 0.00000007124509
  `expected$optima$gap`: 0.00000000000000 0.00000002926391 0.00000007124487
  
    `actual$log_marginal_likelihood`: 26.31989089916191
  `expected$log_marginal_likelihood`: 26.31989089916206
  
      actual$mean_coefficients | expected$mean_coefficients    
  [1] 0.69616292162427         - 0.69616292164127           [1]
  [2] 1.64682203488466         - 1.64682203486535           [2]
  [3] -1.02321751279327        - -1.02321751279302          [3]
  
    `actual$start_results[[1]]$objective`: -26.31989089916191
  `expected$start_results[[1]]$objective`: -26.31989089916206
  
  actual$start_results[[1]]$parameters vs expected$start_results[[1]]$parameters
  - 0.870707639694134
  + 0.870707639642575
  - 0.369478976082430
  + 0.369478976078105
  - 75701.263445226388285
  + 75701.267141279284260
  - 0.002237090974580
  + 0.002237090974612
  
    `actual$start_results[[2]]$objective`: -26.31989082791682
  `expected$start_results[[2]]$objective`: -26.31989082791720
  
  actual$start_results[[2]]$parameters vs expected$start_results[[2]]$parameters
  - 0.870573498017276
  + 0.870573497794135
  - 0.369466927018876
  + 0.369466926997790
  - 50620.049788012605859
  + 50620.066291453120357
  - 0.002236998621533
  + 0.002236998621481
  
    `actual$start_results[[3]]$objective`: -26.3198908698992
  `expected$start_results[[3]]$objective`: -26.3198908698982
  
  actual$start_results[[3]]$parameters vs expected$start_results[[3]]$parameters
  - 0.87055651581420
  + 0.87055651604728
  - 0.36946935778782
  + 0.36946935779766
  - 64139.78359064437245
  + 64139.79887801059522
  - 0.00223707199519
  + 0.00223707199533
  
  ml
  ── Failure ('test-mean-coefficients.R:291:5'): optimize_gp() maximizes profile and restricted likelihoods ──
  Expected `fit()$optimization` to be identical to `model$optimization`.
  Differences:
      actual$optimized_parameters | expected$optimized_parameters    
  [1] 2.361934508409              - 2.361934386905                [1]
  [2] 0.428818489705              - 0.428818487091                [2]
  [3] 73392.012289644103          - 73390.041376440859            [3]
  [4] 0.002394657850              - 0.002394657834                [4]
  
    `actual$objective`: -26.0351750282027
  `expected$objective`: -26.0351750282086
  
  actual$optima vs expected$optima
                         log_marginal_likelihood          gap
    actual$optima[1, ]                  26.03518 0.000000e+00
  - actual$optima[2, ]                  26.03517 5.481977e-08
  + expected$optima[2, ]                26.03517 5.482543e-08
  - actual$optima[3, ]                  26.03517 1.117659e-07
  + expected$optima[3, ]                26.03517 1.117719e-07
  
  actual$optima$log_marginal_likelihood vs expected$optima$log_marginal_likelihood
  - 26.03517502820274
  + 26.03517502820856
  - 26.03517497338297
  + 26.03517497338313
  - 26.03517491643682
  + 26.03517491643668
  
    `actual$optima$gap`: 0.0000000000000 0.0000000548198 0.0000001117659
  `expected$optima$gap`: 0.0000000000000 0.0000000548254 0.0000001117719
  
    `actual$log_marginal_likelihood`: 26.0351750282027
  `expected$log_marginal_likelihood`: 26.0351750282086
  
    `actual$mean_coefficients`: 0.495975184062 1.916224163474 -1.025829562665
  `expected$mean_coefficients`: 0.495975191136 1.916224152758 -1.025829562569
  
    `actual$start_results[[1]]$objective`: -26.03517497338297
  `expected$start_results[[1]]$objective`: -26.03517497338313
  
  actual$start_results[[1]]$parameters vs expected$start_results[[1]]$parameters
  - 2.36129270544276
  + 2.36129270490637
  - 0.42880782465344
  + 0.42880782462133
  - 36235.96164339475945
  + 36235.96948292988964
  - 0.00239460020304
  + 0.00239460020334
  
    `actual$start_results[[2]]$objective`: -26.0351750282027
  `expected$start_results[[2]]$objective`: -26.0351750282086
  
  actual$start_results[[2]]$parameters vs expected$start_results[[2]]$parameters
  - 2.361934508409
  + 2.361934386905
  - 0.428818489705
  + 0.428818487091
  - 73392.012289644103
  + 73390.041376440859
  - 0.002394657850
  + 0.002394657834
  
    `actual$start_results[[3]]$objective`: -26.03517491643682
  `expected$start_results[[3]]$objective`: -26.03517491643668
  
  actual$start_results[[3]]$parameters vs expected$start_results[[3]]$parameters
  - 2.36168181131775
  + 2.36168181188419
  - 0.42883032396365
  + 0.42883032393820
  - 35869.46563117404003
  + 35869.39851319808804
  - 0.00239450900526
  + 0.00239450900609
  
  reml
  
  [ FAIL 2 | WARN 0 | SKIP 40 | PASS 6199 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [37s/41s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-MKL/gaussianprocesses.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:41.77, 138.54 + 8.52