* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/aPEAR.Rcheck’
* using R Under development (unstable) (2025-01-08 r87545)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘aPEAR/DESCRIPTION’ ... OK
* this is package ‘aPEAR’ version ‘1.0.0’
* 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 ‘aPEAR’ can be installed ... [21s/50s] 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 ... [6s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/13s] OK
* checking whether the package can be unloaded cleanly ... [5s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/15s] 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 ... [27s/31s] 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [19s/20s]
 [19s/20s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(aPEAR)
  > 
  > test_check("aPEAR")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 3 | WARN 4 | SKIP 1 | PASS 101 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-prepareEnrichment.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cluster.R:5:3'): spectral clustering returns correct data format ──
  Error in `spectral(sim, verbose = FALSE)`: Package Spectrum is required to use "spectral" clustering method.
  Backtrace:
      ▆
   1. └─aPEAR:::spectral(sim, verbose = FALSE) at test-cluster.R:5:3
  ── Error ('test-cluster.R:55:3'): pathwayClusters returns something for all implemented methods ──
  Error in `spectral(sim, verbose)`: Package Spectrum is required to use "spectral" clustering method.
  Backtrace:
      ▆
   1. └─aPEAR:::pathwayClusters(sim, method = "s") at test-cluster.R:55:3
   2.   └─aPEAR:::spectral(sim, verbose)
  ── Error ('test-cluster.R:63:3'): pathwayClusters filters out by cluster size ──
  Error in `spectral(sim, verbose)`: Package Spectrum is required to use "spectral" clustering method.
  Backtrace:
      ▆
   1. └─aPEAR:::pathwayClusters(sim, method = "s", minClusterSize = 13) at test-cluster.R:63:3
   2.   └─aPEAR:::spectral(sim, verbose)
  
  [ FAIL 3 | WARN 4 | SKIP 1 | PASS 101 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... NOTE
Note: skipping ‘aPEAR-vignette.Rmd’ due to unavailable dependencies:
  'clusterProfiler'
* 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, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/aPEAR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 4:51.03, 166.71 + 17.32