Running ‘testthat.R’ [185s/268s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ##################################################
  > ## Project: pathfindR
  > ## Script purpose: Main test_check script
  > ## Date: Aug 28, 2019
  > ## Author: Ege Ulgen
  > ##################################################
  > 
  > library(testthat)
  > library(pathfindR)
  ##############################################################################
                          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")
  ── 1. Failure: Graph visualization of clusters via `cluster_graph_vis()` works O
  `cluster_graph_vis(clu_obj, kappa_mat, enrichment_res)` produced warnings.
  
  ── 2. Failure: Graph visualization of clusters via `cluster_graph_vis()` works O
  `cluster_graph_vis(clu_obj, kappa_mat, enrichment_res, use_description = TRUE)` produced warnings.
  
  ── 3. Failure: `cluster_graph_vis()` coloring of 'extra' clusters work (@test-cl
  `cluster_graph_vis(clu_obj, kappa_mat, enrichment_res)` produced warnings.
  
  sh: 0: getcwd() failed: No such file or directory
  Visualizing: Spliceosome                                                                                                                                                                                                          
  Visualizing: Spliceosome                                                                                                                                                                                                          
  Visualizing: Spliceosome                                                                                                                                                                                                          
  Visualizing: Spliceosome                                                                                                                                                                                                          
  Visualizing: Spliceosome                                                                                                                                                                                                          
  Downloading pathway diagrams of 1 KEGG pathways
  
  
    |                                                                            
    |                                                                      |   0%Downloading pathway diagrams of 1 KEGG pathways
  
  
    |                                                                            
    |                                                                      |   0%Downloading pathway diagrams of 1 KEGG pathways
  
  
    |                                                                            
    |                                                                      |   0%Downloading pathway diagrams of 1 KEGG pathways
  
  
    |                                                                            
    |                                                                      |   0%══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 376 | SKIPPED: 5 | WARNINGS: 3 | FAILED: 3 ]
  1. Failure: Graph visualization of clusters via `cluster_graph_vis()` works OK (@test-clustering_functions.R#208) 
  2. Failure: Graph visualization of clusters via `cluster_graph_vis()` works OK (@test-clustering_functions.R#222) 
  3. Failure: `cluster_graph_vis()` coloring of 'extra' clusters work (@test-clustering_functions.R#242) 
  
  Error: testthat unit tests failed
  Execution halted