* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/spCF.Rcheck’
* using R Under development (unstable) (2026-10-30 r90795)
* 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 09:41:13 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘spCF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spCF’ version ‘0.2.2.1’
* 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 ‘spCF’ can be installed ... [32s/24s] OK
* used C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
* 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 ... [20s/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 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [24s/26s]
 [24s/26s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spCF)
  > 
  > test_check("spCF")
  Loading required package: shiny
  
  Attaching package: 'bslib'
  
  The following object is masked from 'package:utils':
  
      page
  
  terra 1.9.50
  
  Attaching package: 'terra'
  
  The following objects are masked from 'package:testthat':
  
      compare, describe
  
  Linking to GEOS 3.14.1, GDAL 3.12.4, PROJ 9.8.1; sf_use_s2() is TRUE
  `shiny::dataTableOutput()` is deprecated as of shiny 1.8.1.
  Please use `DT::DTOutput()` instead.
  Since you have a suitable version of DT (>= v0.32.1), shiny::dataTableOutput() will automatically use DT::DTOutput() under-the-hood.
  If this happens to break your app, set `options(shiny.legacy.datatable = TRUE)` to get the legacy datatable implementation (or `FALSE` to squelch this message).
  See <https://rstudio.github.io/DT/shiny.html> for more information.
  Saving _problems/test-stage_bound-47.R
  [ FAIL 1 | WARN 0 | SKIP 11 | PASS 369 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test-add_learn.R:17:3', 'test-mapping.R:17:3',
    'test-mapping.R:38:3', 'test-mapping.R:57:3', 'test-mapping.R:75:3',
    'test-mapping.R:113:3', 'test-mapping.R:143:3', 'test-mapping.R:178:3',
    'test-spCFmap.R:5:3', 'test-spCFmap.R:20:3'
  • lightgbm is installed, so the guard cannot be exercised (1):
    'test-add_learn.R:43:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-stage_bound.R:47:3'): cf_glm uses the bound for poisson and ignores it for binomial ──
  Expected `b1$pred0` to be identical to `b0$pred0`.
  Differences:
      actual$pred         | expected$pred          
  [1] 0.71664271763132570 | 0.71664271763132570 [1]
  [2] 0.71664271763132570 | 0.71664271763132570 [2]
  [3] 0.89639592876067253 | 0.89639592876067253 [3]
  [4] 0.64664302099757587 - 0.64664302099757609 [4]
  [5] 0.64664302099757587 - 0.64664302099757609 [5]
  
      actual$pred_sd       | expected$pred_sd        
  [1] 0.450628375601574482 | 0.450628375601574482 [1]
  [2] 0.450628375601574482 | 0.450628375601574482 [2]
  [3] 0.304746234861013210 | 0.304746234861013210 [3]
  [4] 0.478012368451596170 - 0.478012368451596115 [4]
  [5] 0.478012368451596170 - 0.478012368451596115 [5]
  
  
  [ FAIL 1 | WARN 0 | SKIP 11 | PASS 369 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [33s/35s] 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/spCF.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:38.41, 144.02 + 12.82