• using R version 4.6.1 Patched (2026-06-28 r90199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.3.0-1) 15.3.0     GNU Fortran (Debian 15.3.0-1) 15.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-07-01 17:09:11 UTC
• 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 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 ‘pathfindR’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-15 (Debian 15.3.0-1) 15.3.0’
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [4s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/4s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/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 ... [27s/37s] OK
• checking Rd files ... [1s/1s] 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 ... [0s/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 compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [29s/39s] OK Examples with CPU (user + system) or elapsed time > 5s                      user system elapsed input_processing 6.636 0.287 9.300 enrichment_analyses 4.347 0.011 6.154
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [196s/262s] ERROR   Running ‘testthat-active-snw.R’ [11s/14s]   Running ‘testthat-clustering.R’ [7s/9s]   Running ‘testthat-comparison.R’ [5s/6s]   Running ‘testthat-cpp.R’ [4s/5s]   Running ‘testthat-data_generation.R’ [5s/6s]   Running ‘testthat-enrichment.R’ [34s/48s]   Running ‘testthat-run-pathfindr.R’ [4s/6s]   Running ‘testthat-scoring.R’ [6s/7s]   Running ‘testthat-search-and-enrichment-wrapper.R’ [6s/12s]   Running ‘testthat-utility.R’ [19s/25s]   Running ‘testthat-visualization.R’ [95s/123s] 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 ... [47s/58s] OK
• checking PDF version of manual ... [7s/10s] OK
• checking HTML version of manual ... [5s/9s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR