* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/ebrahim.gof.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: 2026-10-29 22:32:42 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘ebrahim.gof/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ebrahim.gof’ version ‘2.10.0’
* 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 ‘ebrahim.gof’ can be installed ... [8s/12s] 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 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 ... [16s/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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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’ [25s/28s]
 [26s/29s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ebrahim.gof)
  > 
  > test_check("ebrahim.gof") 
  Saving _problems/test-bagoft-fast-30.R
  Saving _problems/test-bagoft-fast-30.R
  Saving _problems/test-bagoft-fast-30.R
  Saving _problems/test-bagoft-fast-44.R
  Saving _problems/test-bagoft-fast-44.R
  Saving _problems/test-bagoft-fast-60.R
  Saving _problems/test-bagoft-fast-60.R
  Saving _problems/test-bagoft-fast-60.R
  Saving _problems/test-bagoft-fast-60.R
  Saving _problems/test-bagoft-fast-60.R
  Saving _problems/test-deepgof1-108.R
  Saving _problems/test-deepgof1-230.R
  Saving _problems/test-def-external-62.R
  Saving _problems/test-def-external-129.R
  Saving _problems/test-def-external-130.R
  Saving _problems/test-def-external-131.R
  [ FAIL 16 | WARN 31 | SKIP 14 | PASS 1032 ]
  
  ══ Skipped tests (14) ══════════════════════════════════════════════════════════
  • On CRAN (14): 'test-battery-input.R:138:3', 'test-deepgof1.R:11:3',
    'test-deepgof1.R:25:3', 'test-deepgof1.R:56:3', 'test-deepgof1.R:152:3',
    'test-gof_certificate.R:31:3', 'test-gof_certificate.R:43:3',
    'test-gof_certificate.R:58:3', 'test-na-exclude.R:33:3',
    'test-parallel.R:5:3', 'test-parallel.R:31:3', 'test-proj-gof.R:75:3',
    'test-run-all-gof.R:158:3', 'test-run-all-gof.R:193:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-bagoft-fast.R:30:3'): bagoft.fast reproduces BAGofT exactly: two covariates ──
  Expected pmean to be identical to `unname(pkg[[k]])`.
  Differences:
  Objects equal but not identical
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:30:3
   2.   └─testthat::expect_identical(...) at test-bagoft-fast.R:13:3
  ── Failure ('test-bagoft-fast.R:30:3'): bagoft.fast reproduces BAGofT exactly: two covariates ──
  Expected pmedian to be identical to `unname(pkg[[k]])`.
  Differences:
  Objects equal but not identical
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:30:3
   2.   └─testthat::expect_identical(...) at test-bagoft-fast.R:13:3
  ── Failure ('test-bagoft-fast.R:30:3'): bagoft.fast reproduces BAGofT exactly: two covariates ──
  Expected `unname(fast$simRes)` to be identical to `unname(pkg$simRes)`.
  Differences:
  Objects equal but not identical
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:30:3
   2.   └─testthat::expect_identical(unname(fast$simRes), unname(pkg$simRes)) at test-bagoft-fast.R:15:3
  ── Failure ('test-bagoft-fast.R:44:3'): bagoft.fast reproduces BAGofT exactly: a factor and a column the model omits ──
  Expected pmedian to be identical to `unname(pkg[[k]])`.
  Differences:
  Objects equal but not identical
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:44:3
   2.   └─testthat::expect_identical(...) at test-bagoft-fast.R:13:3
  ── Failure ('test-bagoft-fast.R:44:3'): bagoft.fast reproduces BAGofT exactly: a factor and a column the model omits ──
  Expected `unname(fast$simRes)` to be identical to `unname(pkg$simRes)`.
  Differences:
  Objects equal but not identical
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:44:3
   2.   └─testthat::expect_identical(unname(fast$simRes), unname(pkg$simRes)) at test-bagoft-fast.R:15:3
  ── Failure ('test-bagoft-fast.R:60:3'): bagoft.fast reproduces BAGofT exactly: seven covariates (dcPre pre-selection) ──
  Expected p.value to be identical to `unname(pkg[[k]])`.
  Differences:
  1/1 mismatches
  [1] 0 - 0.75 == -0.75
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:60:3
   2.   └─testthat::expect_identical(...) at test-bagoft-fast.R:13:3
  ── Failure ('test-bagoft-fast.R:60:3'): bagoft.fast reproduces BAGofT exactly: seven covariates (dcPre pre-selection) ──
  Expected p.value2 to be identical to `unname(pkg[[k]])`.
  Differences:
  1/1 mismatches
  [1] 0 - 0.75 == -0.75
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:60:3
   2.   └─testthat::expect_identical(...) at test-bagoft-fast.R:13:3
  ── Failure ('test-bagoft-fast.R:60:3'): bagoft.fast reproduces BAGofT exactly: seven covariates (dcPre pre-selection) ──
  Expected pmean to be identical to `unname(pkg[[k]])`.
  Differences:
  1/1 mismatches
  [1] 0.0488 - 0.406 == -0.357
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:60:3
   2.   └─testthat::expect_identical(...) at test-bagoft-fast.R:13:3
  ── Failure ('test-bagoft-fast.R:60:3'): bagoft.fast reproduces BAGofT exactly: seven covariates (dcPre pre-selection) ──
  Expected pmedian to be identical to `unname(pkg[[k]])`.
  Differences:
  1/1 mismatches
  [1] 0.0277 - 0.351 == -0.323
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:60:3
   2.   └─testthat::expect_identical(...) at test-bagoft-fast.R:13:3
  ── Failure ('test-bagoft-fast.R:60:3'): bagoft.fast reproduces BAGofT exactly: seven covariates (dcPre pre-selection) ──
  Expected `unname(fast$simRes)` to be identical to `unname(pkg$simRes)`.
  Differences:
  Component 1: Mean relative difference: 0.5700543
  Component 2: Mean relative difference: 0.8845834
  Component 3: Mean relative difference: 0.8808741
  Backtrace:
      ▆
   1. └─ebrahim.gof (local) expect_same_bagoft(f, p) at test-bagoft-fast.R:60:3
   2.   └─testthat::expect_identical(unname(fast$simRes), unname(pkg$simRes)) at test-bagoft-fast.R:15:3
  ── Failure ('test-deepgof1.R:108:3'): with two covariates the all-pairs reading is the default rule, bit for bit ──
  Expected `a$boot` to be identical to `b$boot`.
  Differences:
  Objects equal but not identical
  ── Failure ('test-deepgof1.R:230:3'): the axis rule reads covariates, not spline or dummy columns ──
  Expected `a$boot` to be identical to `b$boot`.
  Differences:
  Objects equal but not identical
  ── Failure ('test-def-external.R:61:3'): external mode on a glm uses its y and fitted probabilities as frozen predictions ──
  Expected `edge.gof(fit, external = TRUE)` to be identical to `edge.gof(as.numeric(fit$y), predicted_probs = fitted(fit), external = TRUE)`.
  Differences:
  Objects equal but not identical
  ── Failure ('test-def-external.R:129:3'): G = 'auto' is max(10, ceiling(n / 25)) ──
  Expected `def.gof(fit, G = "auto")` to be identical to `def.gof(fit, G = 25)`.
  Differences:
  Objects equal but not identical
  ── Failure ('test-def-external.R:130:3'): G = 'auto' is max(10, ceiling(n / 25)) ──
  Expected `edge.gof(fit, G = "auto", external = TRUE)[, -2]` to be identical to `edge.gof(fit, G = 25, external = TRUE)[, -2]`.
  Differences:
  Objects equal but not identical
  ── Failure ('test-def-external.R:131:3'): G = 'auto' is max(10, ceiling(n / 25)) ──
  Expected `def.ensemble.gof(fit, G = "auto")` to be identical to `def.ensemble.gof(fit, G = 25)`.
  Differences:
  Objects equal but not identical
  
  [ FAIL 16 | WARN 31 | SKIP 14 | PASS 1032 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [30s/36s] 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/ebrahim.gof.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:37.89, 113.18 + 9.35