* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/inlabru.Rcheck’
* using R Under development (unstable) (2026-04-22 r89950)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-04-24 00:55:44 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘inlabru/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘inlabru’ version ‘2.14.0’
* 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 ‘inlabru’ can be installed ... [57s/63s] OK
* used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
* 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 whether startup messages can be suppressed ... 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 ... [74s/90s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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 ... [66s/83s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [174s/154s]
 [175s/155s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (require(testthat, quietly = TRUE)) {
  +   test_check("inlabru")
  + }
  Loading required package: inlabru
  Loading required package: fmesher
  Starting 2 test processes.
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  Saving _problems/test-component-407.R
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  Saving _problems/test-data-76.R
  > test-environment.R: Test message 1
  > test-environment.R: Test message 2
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_
  > test-aggregate.R: ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_
  > test-aggregate.R: ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-aggregate.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-aggregate.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  Saving _problems/test-aggregate-309.R
  > test-mdata.R: OMP: Warning #96: Cannot form a team with 4 threads, using 2 instead.
  > test-mdata.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-mdata.R: OMP: Warning #96: Cannot form a team with 4 threads, using 2 instead.
  > test-mdata.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-mdata.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-mdata.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-mdata.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-mdata.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-mdata.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-mdata.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  > test-mdata.R: OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
  > test-mdata.R: OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  [ FAIL 3 | WARN 0 | SKIP 55 | PASS 182 ]
  
  ══ Skipped tests (55) ══════════════════════════════════════════════════════════
  • On CRAN (55): 'test-01_lgcp_2d.R:2:3', 'test-01_lgcp_2d.R:140:3',
    'test-additive.R:2:3', 'test-02_predict.R:2:3', 'test-02_predict.R:128:3',
    'test-bru_sf.R:4:3', 'test-component.R:226:3', 'test-component.R:294:3',
    'test-component.R:322:3', 'test-component.R:361:3', 'test-component.R:417:3',
    'test-copy.R:2:3', 'test-copy.R:126:3', 'test-copy.R:188:3',
    'test-data.R:5:3', 'test-data.R:87:3', 'test-fmesher_pixels.R:2:3',
    'test-globe_mesh.R:2:3', 'test-globe_mesh.R:62:3', 'test-latent_ar1.R:75:3',
    'test-latent_clinear.R:2:3', 'test-latent_factor.R:2:3',
    'test-latent_factor.R:103:3', 'test-latent_fixed_effects.R:2:3',
    'test-latent_fixed_effects.R:24:3', 'test-latent_fixed_effects.R:50:3',
    'test-latent_fixed_effects.R:71:3', 'test-latent_fixed_effects.R:98:3',
    'test-latent_linear.R:2:3', 'test-latent_linear.R:34:3',
    'test-latent_rw2.R:2:3', 'test-latent_rw2.R:32:3',
    'test-latent_spde_1d.R:31:3', 'test-latent_spde_2d.R:2:3',
    'test-latent_spde_2d.R:97:3', 'test-lgcp_1d.R:28:3', 'test-lgcp_1d.R:105:3',
    'test-lgcp_1d.R:156:3', 'test-lgcp_1d_nonlinear.R:2:3',
    'test-lgcp_1d_nonlinear.R:169:3', 'test-lgcp_2d_covars.R:2:3',
    'test-lgcp_2d_plotsample.R:2:3', 'test-linearisation.R:2:3',
    'test-mapper.R:435:3', 'test-mapper.R:449:3', 'test-mapper.R:505:3',
    'test-mapper.R:611:3', 'test-mapper.R:753:3', 'test-mapper.R:781:3',
    'test-multi_like.R:2:3', 'test-multi_like.R:55:3', 'test-offset.R:2:3',
    'test-response_size.R:2:3', 'test-response_size.R:82:3', 'test-utils.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-component.R:407:7'): Component construction: unsafe intercepts ──
  Error in `sort.int(x, na.last = na.last, decreasing = decreasing, ...)`: 'x' must be atomic
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-component.R:405:3
    2. │ └─testthat:::expect_condition_matching_(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─inlabru::bru_model(cmp, bru_obs_list(list(lik))) at test-component.R:407:7
    8.   ├─inlabru::bru_comp_list(...)
    9.   └─inlabru:::bru_comp_list.bru_comp_list(...)
   10.     ├─inlabru::bru_comp_list(list(object), .envir = .envir, ...)
   11.     └─inlabru:::bru_comp_list.list(list(object), .envir = .envir, ...)
   12.       ├─inlabru::add_mappers(object, lhoods = lhoods, inputs = inputs)
   13.       └─inlabru:::add_mappers.bru_comp_list(...)
   14.         ├─inlabru::add_mappers(...)
   15.         └─inlabru:::add_mappers.bru_comp(...)
   16.           └─inlabru:::add_mapper(...)
   17.             └─inlabru:::make_unique_inputs(inp_, allow_list = TRUE)
   18.               └─inlabru:::make_unique_inputs(inp_, allow_list = FALSE)
   19.                 ├─base::sort(unique(unlist(inp)), na.last = NA)
   20.                 └─base::sort.default(unique(unlist(inp)), na.last = NA)
   21.                   └─base::sort.int(...)
  ── Error ('test-data.R:76:7'): Component construction: unsafe intercepts, data is list ──
  Error in `sort.int(x, na.last = na.last, decreasing = decreasing, ...)`: 'x' must be atomic
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-data.R:74:3
    2. │ └─testthat:::expect_condition_matching_(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─inlabru::bru_model(cmp, bru_obs_list(list(lik))) at test-data.R:76:7
    8.   ├─inlabru::bru_comp_list(...)
    9.   └─inlabru:::bru_comp_list.bru_comp_list(...)
   10.     ├─inlabru::bru_comp_list(list(object), .envir = .envir, ...)
   11.     └─inlabru:::bru_comp_list.list(list(object), .envir = .envir, ...)
   12.       ├─inlabru::add_mappers(object, lhoods = lhoods, inputs = inputs)
   13.       └─inlabru:::add_mappers.bru_comp_list(...)
   14.         ├─inlabru::add_mappers(...)
   15.         └─inlabru:::add_mappers.bru_comp(...)
   16.           └─inlabru:::add_mapper(...)
   17.             └─inlabru:::make_unique_inputs(inp_, allow_list = TRUE)
   18.               └─inlabru:::make_unique_inputs(inp_, allow_list = FALSE)
   19.                 ├─base::sort(unique(unlist(inp)), na.last = NA)
   20.                 └─base::sort.default(unique(unlist(inp)), na.last = NA)
   21.                   └─base::sort.int(...)
  ── Error ('test-aggregate.R:290:7'): Aggregated Gaussian observations, using domain/samplers feature ──
  Error in `sort.int(x, na.last = na.last, decreasing = decreasing, ...)`: 'x' must be atomic
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-aggregate.R:288:3
    2. │ └─testthat:::expect_condition_matching_(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─inlabru::bru_model(...) at test-aggregate.R:290:7
    8.   ├─inlabru::bru_comp_list(...)
    9.   └─inlabru:::bru_comp_list.bru_comp_list(...)
   10.     ├─inlabru::bru_comp_list(list(object), .envir = .envir, ...)
   11.     └─inlabru:::bru_comp_list.list(list(object), .envir = .envir, ...)
   12.       ├─inlabru::add_mappers(object, lhoods = lhoods, inputs = inputs)
   13.       └─inlabru:::add_mappers.bru_comp_list(...)
   14.         ├─inlabru::add_mappers(...)
   15.         └─inlabru:::add_mappers.bru_comp(...)
   16.           └─inlabru:::add_mapper(...)
   17.             └─inlabru:::make_unique_inputs(inp_, allow_list = TRUE)
   18.               └─inlabru:::make_unique_inputs(inp_, allow_list = FALSE)
   19.                 ├─base::sort(unique(unlist(inp)), na.last = NA)
   20.                 └─base::sort.default(unique(unlist(inp)), na.last = NA)
   21.                   └─base::sort.int(...)
  
  [ FAIL 3 | WARN 0 | SKIP 55 | PASS 182 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [195s/291s] OK
* checking PDF version of manual ... [24s/36s] OK
* checking HTML version of manual ... [33s/49s] 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/gannet/ripley/R/packages/tests-MKL/inlabru.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 16:17.18, 701.80 + 79.31