• using R Under development (unstable) (2023-09-29 r85235)
• using platform: x86_64-pc-linux-gnu
• R was compiled by
      gcc-13 (GCC) 13.2.0
      GNU Fortran (GCC) 13.2.0
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘pathfindR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘pathfindR’ version ‘2.2.0’
• 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 ‘pathfindR’ can be installed ... [16s/19s] OK
  See the install log for details.
• 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 R 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 ... [25s/37s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [53s/61s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [134s/161s] ERROR
    Running ‘testthat-active_snw.R’ [38s/45s]
    Running ‘testthat-clustering.R’
    Running ‘testthat-comparison.R’
    Running ‘testthat-core.R’
    Running ‘testthat-data_generation.R’
    Running ‘testthat-enrichment.R’ [39s/46s]
    Running ‘testthat-scoring.R’
    Running ‘testthat-utility.R’ [23s/27s]
    Running ‘testthat-visualization.R’
    Running ‘testthat-zzz.R’
  Running the tests in ‘tests/testthat-enrichment.R’ failed.
  Complete output:
    > library(testthat)
    > library(pathfindR)
    Loading required package: pathfindR.data
    ##############################################################################
                            Welcome to pathfindR!
    
    Please cite the article below if you use pathfindR in published reseach:
    
    Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive
    Identification of Enriched Pathways in Omics Data Through Active Subnetworks.
    Front. Genet. doi:10.3389/fgene.2019.00858
    
    ##############################################################################
    >
    > test_check("pathfindR", filter = "enrichment")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 44 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-enrichment.R:45:5'): `enrichment()` -- returns a data frame ────
    Error in `enrichment(input_genes = example_pathfindR_input$Gene.symbol,
        sig_genes_vec = c(), background_genes = c(), enrichment_threshold = 1)`: `sig_genes_vec` should be a vector
    Backtrace:
        ▆
     1. ├─testthat::expect_is(...) at test-enrichment.R:45:4
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─pathfindR::enrichment(...)
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 44 ]
    Error: Test failures
    Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [80s/97s] OK
• checking PDF version of manual ... [9s/14s] 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