Running 'testthat.R' [163s]
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. Error: (unknown) (@test-active_snw_functions.R#91)  ----------------------
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. base::suppressMessages(...)
    3. pathfindR::input_processing(...)
    4. org.Hs.eg.db::org.Hs.eg_dbconn
    5. base::getExportedValue(pkg, name)
    6. base::asNamespace(ns)
    7. base::getNamespace(ns)
    8. base::loadNamespace(name)
   10. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -sif=D:\temp\RtmpgvpXhL\Biogrid.sif
  -sig=d:\RCompile\CRANpkg\local\4.0\pathfindR.Rcheck\tests\testthat\pathfindR_Results\active_snw_searches\Iteration_1\active_snw_search\input_for_search.txt
  -method=GR
  -saTemp0=1
  -saTemp1=0.01
  -saIter=10000
  -geneInitProb=0.01
  -gaPop=400
  -gaIter=200
  -gaThread=5
  -gaCrossover=1
  -gaMut=0
  -grMaxDepth=1
  -grSearchDepth=1
  -grOverlap=0.5
  -grSubNum=1000
  >
  D:\temp\RtmpEf9di7/console_out_active_snws_1.txt
  Unknown argument: -gaCrossover
  Unknown argument: >
  Unknown argument: D:\temp\RtmpEf9di7/console_out_active_snws_1.txt
  {FAM110A=3.40869878715016E-6, RNASE2=1.00849945745823E-5}
  1% of seeds checked
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  98% of seeds checked
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  100%
  Filtering
  Subnetwork number17778
  Subnetwork number65
  Subnetwork number65
  1% of subnetworks checked, 2 filtered subnetworks in the list
  3% of subnetworks checked, 3 filtered subnetworks in the list
  4% of subnetworks checked, 4 filtered subnetworks in the list
  6% of subnetworks checked, 5 filtered subnetworks in the list
  7% of subnetworks checked, 6 filtered subnetworks in the list
  9% of subnetworks checked, 7 filtered subnetworks in the list
  10% of subnetworks checked, 8 filtered subnetworks in the list
  12% of subnetworks checked, 9 filtered subnetworks in the list
  13% of subnetworks checked, 10 filtered subnetworks in the list
  15% of subnetworks checked, 11 filtered subnetworks in the list
  16% of subnetworks checked, 12 filtered subnetworks in the list
  18% of subnetworks checked, 13 filtered subnetworks in the list
  20% of subnetworks checked, 14 filtered subnetworks in the list
  21% of subnetworks checked, 15 filtered subnetworks in the list
  23% of subnetworks checked, 16 filtered subnetworks in the list
  24% of subnetworks checked, 17 filtered subnetworks in the list
  26% of subnetworks checked, 18 filtered subnetworks in the list
  27% of subnetworks checked, 18 filtered subnetworks in the list
  29% of subnetworks checked, 19 filtered subnetworks in the list
  30% of subnetworks checked, 20 filtered subnetworks in the list
  32% of subnetworks checked, 21 filtered subnetworks in the list
  33% of subnetworks checked, 22 filtered subnetworks in the list
  35% of subnetworks checked, 23 filtered subnetworks in the list
  36% of subnetworks checked, 24 filtered subnetworks in the list
  38% of subnetworks checked, 25 filtered subnetworks in the list
  40% of subnetworks checked, 26 filtered subnetworks in the list
  41% of subnetworks checked, 27 filtered subnetworks in the list
  43% of subnetworks checked, 28 filtered subnetworks in the list
  44% of subnetworks checked, 29 filtered subnetworks in the list
  46% of subnetworks checked, 30 filtered subnetworks in the list
  47% of subnetworks checked, 31 filtered subnetworks in the list
  49% of subnetworks checked, 32 filtered subnetworks in the list
  50% of subnetworks checked, 33 filtered subnetworks in the list
  52% of subnetworks checked, 34 filtered subnetworks in the list
  53% of subnetworks checked, 35 filtered subnetworks in the list
  55% of subnetworks checked, 36 filtered subnetworks in the list
  56% of subnetworks checked, 37 filtered subnetworks in the list
  58% of subnetworks checked, 38 filtered subnetworks in the list
  60% of subnetworks checked, 39 filtered subnetworks in the list
  61% of subnetworks checked, 40 filtered subnetworks in the list
  63% of subnetworks checked, 41 filtered subnetworks in the list
  64% of subnetworks checked, 42 filtered subnetworks in the list
  66% of subnetworks checked, 43 filtered subnetworks in the list
  67% of subnetworks checked, 44 filtered subnetworks in the list
  69% of subnetworks checked, 45 filtered subnetworks in the list
  70% of subnetworks checked, 46 filtered subnetworks in the list
  72% of subnetworks checked, 47 filtered subnetworks in the list
  73% of subnetworks checked, 48 filtered subnetworks in the list
  75% of subnetworks checked, 49 filtered subnetworks in the list
  76% of subnetworks checked, 50 filtered subnetworks in the list
  78% of subnetworks checked, 51 filtered subnetworks in the list
  80% of subnetworks checked, 52 filtered subnetworks in the list
  81% of subnetworks checked, 53 filtered subnetworks in the list
  83% of subnetworks checked, 54 filtered subnetworks in the list
  84% of subnetworks checked, 55 filtered subnetworks in the list
  86% of subnetworks checked, 56 filtered subnetworks in the list
  87% of subnetworks checked, 57 filtered subnetworks in the list
  89% of subnetworks checked, 58 filtered subnetworks in the list
  90% of subnetworks checked, 59 filtered subnetworks in the list
  92% of subnetworks checked, 60 filtered subnetworks in the list
  93% of subnetworks checked, 61 filtered subnetworks in the list
  95% of subnetworks checked, 62 filtered subnetworks in the list
  96% of subnetworks checked, 63 filtered subnetworks in the list
  100%
  -- 2. Error: `input_processing()` works (@test-core_functions.R#379)  ----------
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. testthat::expect_is(...)
    4. pathfindR::input_processing(...)
    5. org.Hs.eg.db::org.Hs.eg_dbconn
    6. base::getExportedValue(pkg, name)
    7. base::asNamespace(ns)
    8. base::getNamespace(ns)
    9. base::loadNamespace(name)
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   14. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 3. Failure: `input_processing()` errors and warnings work (@test-core_functio
  `input_processing(tmp_input, p_val_threshold = 0.05, pin_name_path = "Biogrid")` threw an error with unexpected message.
  Expected match: "None of the genes were in the PIN\nPlease check your gene symbols"
  Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. pathfindR::input_processing(...)
    7. org.Hs.eg.db::org.Hs.eg_dbconn
    8. base::getExportedValue(pkg, name)
    9. base::asNamespace(ns)
   10. base::getNamespace(ns)
   11. base::loadNamespace(name)
   13. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   16. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 4. Failure: `input_processing()` errors and warnings work (@test-core_functio
  `input_processing(tmp_input, p_val_threshold = 0.05, pin_name_path = "Biogrid")` threw an error with unexpected message.
  Expected match: "After processing, 1 gene \\(or no genes\\) could be mapped to the PIN"
  Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. pathfindR::input_processing(...)
    7. org.Hs.eg.db::org.Hs.eg_dbconn
    8. base::getExportedValue(pkg, name)
    9. base::asNamespace(ns)
   10. base::getNamespace(ns)
   11. base::loadNamespace(name)
   13. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   16. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 5. Error: (unknown) (@test-visualization_functions.R#14)  -------------------
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. base::suppressMessages(input_processing(RA_input, 0.05, "Biogrid"))
    3. pathfindR::input_processing(RA_input, 0.05, "Biogrid")
    4. org.Hs.eg.db::org.Hs.eg_dbconn
    5. base::getExportedValue(pkg, name)
    6. base::asNamespace(ns)
    7. base::getNamespace(ns)
    8. base::loadNamespace(name)
   10. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  == testthat results  ===========================================================
  [ OK: 269 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: (unknown) (@test-active_snw_functions.R#91) 
  2. Error: `input_processing()` works (@test-core_functions.R#379) 
  3. Failure: `input_processing()` errors and warnings work (@test-core_functions.R#444) 
  4. Failure: `input_processing()` errors and warnings work (@test-core_functions.R#451) 
  5. Error: (unknown) (@test-visualization_functions.R#14) 
  
  Error: testthat unit tests failed
  Execution halted