Running ‘testthat-active_snw.R’ [38s/219s]
  Running ‘testthat-clustering.R’ [5s/23s]
  Running ‘testthat-comparison.R’ [4s/14s]
  Running ‘testthat-core.R’ [40s/204s]
  Running ‘testthat-data_generation.R’ [4s/20s]
  Running ‘testthat-enrichment.R’ [43s/210s]
  Running ‘testthat-scoring.R’ [4s/22s]
  Running ‘testthat-visualization.R’ [4s/20s]
  Running ‘testthat-zzz.R’ [4s/20s]
Running the tests in ‘tests/testthat-active_snw.R’ failed.
Complete output:
  > ##################################################
  > ## Project: pathfindR
  > ## Script purpose: Main "test_check" script for
  > ## "active_snw_functions" functions
  > ## Date: Jan 12, 2020
  > ## Author: Ege Ulgen
  > ##################################################
  > 
  > 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 = "active_snw_functions")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-active_snw_functions.R:10:1'): (code run outside of `test_that()`) ──
  Error in `eval(code, test_env)`: object 'RA_input' not found
  Backtrace:
      ▆
   1. ├─base::suppressMessages(...) at test-active_snw_functions.R:10:0
   2. │ └─base::withCallingHandlers(...)
   3. └─pathfindR::input_processing(...)
   4.   └─base::ncol(input)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Running the tests in ‘tests/testthat-clustering.R’ failed.
Complete output:
  > ##################################################
  > ## Project: pathfindR
  > ## Script purpose: Main "test_check" script for
  > ## "clustering_functions" functions
  > ## Date: Jan 12, 2020
  > ## Author: Ege Ulgen
  > ##################################################
  > 
  > 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 = "clustering_functions")
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 16 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-clustering_functions.R:11:3'): `create_kappa_matrix()` reates kappa matrix ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Failure ('test-clustering_functions.R:33:3'): `create_kappa_matrix()` arg checks works ──
  `create_kappa_matrix(RA_output[1, ])` threw an error with unexpected message.
  Expected match: "`enrichment_res` should contain at least 2 rows"
  Actual message: "object 'RA_output' not found"
  Backtrace:
      ▆
   1. ├─testthat::expect_error(create_kappa_matrix(RA_output[1, ]), "`enrichment_res` should contain at least 2 rows") at test-clustering_functions.R:33:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─pathfindR::create_kappa_matrix(RA_output[1, ])
   7.   └─base::is.data.frame(enrichment_res)
  ── Error ('test-clustering_functions.R:51:3'): `create_kappa_matrix()` arg checks works ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-clustering_functions.R:81:3'): `hierarchical_term_clustering()` returns integer vector ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-clustering_functions.R:93:3'): For `hierarchical_term_clustering()`, `num_clusters` works ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-clustering_functions.R:107:3'): Consistent `hierarchical_term_clustering()` results ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-clustering_functions.R:155:3'): `fuzzy_term_clustering()` returns matrix of cluster memberships ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  Backtrace:
      ▆
   1. └─pathfindR::create_kappa_matrix(RA_output) at test-clustering_functions.R:155:2
   2.   └─base::is.data.frame(enrichment_res)
  ── Error ('test-clustering_functions.R:191:3'): Consistent fuzzy term clustering results ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  Backtrace:
      ▆
   1. └─pathfindR::create_kappa_matrix(RA_output, use_description = TRUE) at test-clustering_functions.R:191:2
   2.   └─base::is.data.frame(enrichment_res)
  ── Error ('test-clustering_functions.R:212:3'): Graph visualization of clusters via `cluster_graph_vis()` works OK ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-clustering_functions.R:242:3'): `cluster_graph_vis()` coloring of 'extra' clusters work ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-clustering_functions.R:262:3'): Check errors of `cluster_graph_vis()` ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-clustering_functions.R:285:3'): `cluster_enriched_terms()` returns the input data frame
            with the additional columns `Cluster` and `Status` ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  Backtrace:
      ▆
   1. └─pathfindR::cluster_enriched_terms(RA_output[1:5, ]) at test-clustering_functions.R:285:2
   2.   └─pathfindR::create_kappa_matrix(...)
   3.     └─base::is.data.frame(enrichment_res)
  
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
Running the tests in ‘tests/testthat-comparison.R’ failed.
Complete output:
  > ##################################################
  > ## Project: pathfindR
  > ## Script purpose: Main "test_check" script for
  > ## "comparison_functions" functions
  > ## Date: Feb 9, 2020
  > ## Author: Ege Ulgen
  > ##################################################
  > 
  > 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 = "comparison_functions")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-comparison_functions.R:9:1'): (code run outside of `test_that()`) ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Running the tests in ‘tests/testthat-core.R’ failed.
Complete output:
  > ##################################################
  > ## Project: pathfindR
  > ## Script purpose: Main "test_check" script for
  > ## "core_functions" functions
  > ## Date: Jan 12, 2020
  > ## Author: Ege Ulgen
  > ##################################################
  > 
  > 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 = "core_functions")
  [ FAIL 4 | WARN 0 | SKIP 5 | PASS 19 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-core_functions.R:87:3'): Expect warning with empty result from `run_pathfindR()` ──
  Error in `eval(code, test_env)`: object 'RA_input' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_warning(...) at test-core_functions.R:87:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─pathfindR::run_pathfindR(...)
   7.   └─pathfindR::input_testing(input, p_val_threshold)
   8.     └─base::is.data.frame(input)
  ── Error ('test-core_functions.R:358:3'): `input_testing()` works ──────────────
  Error in `eval(code, test_env)`: object 'RA_input' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_message(...) at test-core_functions.R:358:2
   2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─pathfindR::input_testing(input = RA_input, p_val_threshold = 0.05)
   7.   └─base::is.data.frame(input)
  ── Error ('test-core_functions.R:441:3'): `input_processing()` errors and warnings work ──
  Error in `eval(code, test_env)`: object 'RA_input' not found
  ── Error ('test-core_functions.R:491:1'): (code run outside of `test_that()`) ──
  Error in `eval(code, test_env)`: object 'RA_input' not found
  
  [ FAIL 4 | WARN 0 | SKIP 5 | PASS 19 ]
  Error: Test failures
  Execution halted
Running the tests in ‘tests/testthat-enrichment.R’ failed.
Complete output:
  > ##################################################
  > ## Project: pathfindR
  > ## Script purpose: Main "test_check" script for
  > ## "enrichment_functions" functions
  > ## Date: Jan 12, 2020
  > ## Author: Ege Ulgen
  > ##################################################
  > 
  > 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_functions")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 26 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-enrichment_functions.R:167:3'): `enrichment_analyses()` returns a data frame ──
  Error in `eval(code, test_env)`: object 'RA_input' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_is(...) at test-enrichment_functions.R:167:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─pathfindR::enrichment_analyses(...)
   5.   └─base::toupper(sig_genes_vec)
  ── Error ('test-enrichment_functions.R:197:1'): (code run outside of `test_that()`) ──
  Error in `eval(code, test_env)`: object 'RA_input' not found
  Backtrace:
      ▆
   1. └─pathfindR::enrichment_analyses(...) at test-enrichment_functions.R:197:0
   2.   └─base::toupper(sig_genes_vec)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 26 ]
  Error: Test failures
  Execution halted
Running the tests in ‘tests/testthat-scoring.R’ failed.
Complete output:
  > ##################################################
  > ## Project: pathfindR
  > ## Script purpose: Main "test_check" script for
  > ## "scoring" functions
  > ## Date: Jan 12, 2020
  > ## Author: Ege Ulgen
  > ##################################################
  > 
  > 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 = "scoring")
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-scoring.R:11:3'): `score_terms()` returns score matrix ─────────
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-scoring.R:42:3'): `score_terms()` arg checks work ──────────────
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-scoring.R:70:3'): duplicated term descriptions test ────────────
  Error in `eval(code, test_env)`: object 'RA_output' not found
  ── Error ('test-scoring.R:81:3'): `plot_scores()` creates term score heatmap ggplot object with correct labels ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  Backtrace:
      ▆
   1. └─pathfindR::score_terms(RA_output[1:3, ], RA_exp_mat, plot_hmap = FALSE) at test-scoring.R:81:2
   2.   └─base::is.data.frame(enrichment_table)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 11 ]
  Error: Test failures
  Execution halted
Running the tests in ‘tests/testthat-visualization.R’ failed.
Complete output:
  > ##################################################
  > ## Project: pathfindR
  > ## Script purpose: Main "test_check" script for
  > ## "visualization_functions" functions
  > ## Date: Jan 12, 2020
  > ## Author: Ege Ulgen
  > ##################################################
  > 
  > 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 = "visualization_functions")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-visualization_functions.R:10:1'): (code run outside of `test_that()`) ──
  Error in `eval(code, test_env)`: object 'RA_output' not found
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted