* using log directory 'd:/Rcompile/CRANpkg/local/4.5/pathfindR.Rcheck'
* using R version 4.5.3 (2026-03-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'pathfindR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathfindR' version '3.0.1'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'pathfindR' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
* checking installed package size ... 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 ... [5s] OK
* checking whether the package can be loaded with stated dependencies ... [4s] OK
* checking whether the package can be unloaded cleanly ... [4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s] OK
* checking whether the namespace can be unloaded cleanly ... [5s] OK
* checking loading without being on the library search path ... [5s] 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] OK
* checking Rd files ... [2s] OK
* checking Rd metadata ... 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 ... [1s] 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 compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [44s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [183s] ERROR
  Running 'testthat-active-snw.R' [12s]
  Running 'testthat-clustering.R' [8s]
  Running 'testthat-comparison.R' [4s]
  Running 'testthat-cpp.R' [4s]
  Running 'testthat-data_generation.R' [4s]
  Running 'testthat-enrichment.R' [35s]
  Running 'testthat-run-pathfindr.R' [4s]
  Running 'testthat-scoring.R' [5s]
  Running 'testthat-search-and-enrichment-wrapper.R' [8s]
  Running 'testthat-utility.R' [13s]
  Running 'testthat-visualization.R' [86s]
Running the tests in 'tests/testthat-enrichment.R' failed.
Complete output:
  > library(testthat)
  > library(pathfindR)
  Loading required package: pathfindR.data
  > 
  > test_check("pathfindR", filter = "enrichment")
  Saving _problems/test-enrichment-177.R
  Saving _problems/test-enrichment-182.R
  Saving _problems/test-enrichment-188.R
  Saving _problems/test-enrichment-189.R
  Saving _problems/test-enrichment-204.R
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 119 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-enrichment.R:174:3'): `enrichment_analyses()` -- returns a data frame ──
  Expected `enr_res1 <- ...` to inherit from "character".
  Actual inheritance: "NULL"
  ── Failure ('test-enrichment.R:182:3'): `enrichment_analyses()` -- returns a data frame ──
  Expected `nrow(enr_res1) <= total` to be TRUE.
  Differences:
  `actual`:       
  `expected`: TRUE
  
  ── Failure ('test-enrichment.R:185:3'): `enrichment_analyses()` -- returns a data frame ──
  Expected `enr_res2 <- ...` to inherit from "character".
  Actual inheritance: "NULL"
  ── Failure ('test-enrichment.R:189:3'): `enrichment_analyses()` -- returns a data frame ──
  Expected `ncol(enr_res2) == ncol(enr_res1) + 1` to be TRUE.
  Differences:
  `actual`:       
  `expected`: TRUE
  
  ── Error ('test-enrichment.R:201:3'): `summarize_enrichment_results()` -- returns summarized enrichment results ──
  Error in `summarize_enrichment_results(enrichment_res = combined_res[, -6])`: `enrichment_res` should be a data frame
  Backtrace:
      ▆
   1. ├─testthat::expect_is(...) at test-enrichment.R:201:3
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─pathfindR::summarize_enrichment_results(...)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 119 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [39s] OK
* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... [12s] OK
* DONE
Status: 1 ERROR