Running ‘test.R’ [3s/4s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(corehunter)
  Loading required package: rJava
  > 
  > test_check("corehunter")
  Error in .jcall("java/lang/Class", "Ljava/lang/Class;", "forName", cl,  : 
    RcallMethod: cannot determine object class
  ── 1. Failure: arguments are checked (@testAnalysis.R#11)  ─────────────────────
  `evaluateCore(1:10, testData(), "obj")` threw an error with unexpected message.
  Expected match: "'chobj'"
  Actual message: "java.lang.StackOverflowError"
  
  Error in .jcall("java/lang/Class", "Ljava/lang/Class;", "forName", cl,  : 
    RcallMethod: cannot determine object class
  ── 2. Failure: arguments are checked (@testAnalysis.R#12)  ─────────────────────
  `evaluateCore(123456, testData(), objective("EN", "PD"))` threw an error with unexpected message.
  Expected match: "unable to select"
  Actual message: "java.lang.StackOverflowError"
  
  ── 3. Error: larger cores are more representative but have higher redundancy (@t
  java.lang.StackOverflowError
  
  ── 4. Failure: arguments are checked (@testData.R#10)  ─────────────────────────
  `distances(file = 123)` threw an error with unexpected message.
  Expected match: "should be a file path"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 5. Failure: arguments are checked (@testData.R#11)  ─────────────────────────
  `distances(file = "i/do/not/exist")` threw an error with unexpected message.
  Expected match: "does not exist"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 6. Failure: arguments are checked (@testData.R#12)  ─────────────────────────
  `distances(data = "whoops")` threw an error with unexpected message.
  Expected match: "a matrix or a data frame"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 7. Failure: arguments are checked (@testData.R#13)  ─────────────────────────
  `distances(matrix(letters[1:25], nrow = 5, ncol = 5))` threw an error with unexpected message.
  Expected match: "should be numeric"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 8. Failure: arguments are checked (@testData.R#14)  ─────────────────────────
  `distances(matrix(0, nrow = 5, ncol = 5))` threw an error with unexpected message.
  Expected match: "names are required"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 9. Failure: arguments are checked (@testData.R#17)  ─────────────────────────
  `distances(m)` threw an error with unexpected message.
  Expected match: "matrix should be symmetric"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 10. Error: class (@testData.R#21)  ──────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 11. Error: read distance data from file (@testData.R#27)  ───────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 12. Error: create distance data from matrix (@testData.R#61)  ───────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 13. Error: print (@testData.R#109)  ─────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 14. Failure: arguments are checked (@testData.R#128)  ───────────────────────
  `genotypes(file = 124, format = "default")` threw an error with unexpected message.
  Expected match: "should be a file path"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 15. Failure: arguments are checked (@testData.R#129)  ───────────────────────
  `genotypes(file = "i/do/not/exist", format = "biparental")` threw an error with unexpected message.
  Expected match: "does not exist"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 16. Failure: arguments are checked (@testData.R#131)  ───────────────────────
  `genotypes(data = "123", format = "default")` threw an error with unexpected message.
  Expected match: "data frame"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 17. Failure: arguments are checked (@testData.R#132)  ───────────────────────
  `genotypes(data = "abc", format = "biparental")` threw an error with unexpected message.
  Expected match: "matrix or data frame"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 18. Failure: arguments are checked (@testData.R#133)  ───────────────────────
  `genotypes(data = 1:3, format = "frequency")` threw an error with unexpected message.
  Expected match: "matrix or data frame"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 19. Failure: arguments are checked (@testData.R#135)  ───────────────────────
  `genotypes(data = m, format = "biparental")` threw an error with unexpected message.
  Expected match: "0, 1, 2"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 20. Failure: arguments are checked (@testData.R#137)  ───────────────────────
  `genotypes(data = m, format = "biparental")` threw an error with unexpected message.
  Expected match: "matrix should be numeric"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 21. Failure: arguments are checked (@testData.R#139)  ───────────────────────
  `genotypes(data = m, format = "biparental")` threw an error with unexpected message.
  Expected match: "row names are required"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  Error in .jcall("java/lang/Class", "Ljava/lang/Class;", "forName", cl,  : 
    RcallMethod: cannot determine object class
  ── 22. Error: arguments are checked (@testData.R#141)  ─────────────────────────
  java.lang.StackOverflowError
  
  ── 23. Error: class (@testData.R#159)  ─────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 24. Error: warned when reading frequency or biparental data as default (@test
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 25. Error: read genotype data from file (@testData.R#185)  ──────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 26. Error: create default genotype data from data frame (@testData.R#282)  ──
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 27. Error: create biparental genotype data from matrix or data frame (@testDa
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 28. Error: create frequency data from matrix or data frame (@testData.R#408) 
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 29. Error: print (@testData.R#455)  ─────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 30. Failure: arguments are checked (@testData.R#519)  ───────────────────────
  `phenotypes(file = 124)` threw an error with unexpected message.
  Expected match: "should be a file path"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 31. Failure: arguments are checked (@testData.R#520)  ───────────────────────
  `phenotypes(file = "i/do/not/exist")` threw an error with unexpected message.
  Expected match: "does not exist"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 32. Failure: arguments are checked (@testData.R#522)  ───────────────────────
  `phenotypes(file = "data/phenotypes-no-types.csv")` threw an error with unexpected message.
  Expected match: "types are required"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 33. Failure: arguments are checked (@testData.R#523)  ───────────────────────
  `phenotypes(data = 456)` threw an error with unexpected message.
  Expected match: "should be a data frame"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 34. Failure: arguments are checked (@testData.R#527)  ───────────────────────
  `phenotypes(data = df)` threw an error with unexpected message.
  Expected match: "names are required"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 35. Failure: arguments are checked (@testData.R#530)  ───────────────────────
  `phenotypes(df, types = c("I", "N", "R"))` threw an error with unexpected message.
  Expected match: "does not correspond to number of data columns"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 36. Failure: arguments are checked (@testData.R#531)  ───────────────────────
  `phenotypes(df, types = c("I", "NSS"))` threw an error with unexpected message.
  Expected match: "one or two characters"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 37. Failure: arguments are checked (@testData.R#532)  ───────────────────────
  `phenotypes(df, types = c("X", "Y"))` threw an error with unexpected message.
  Expected match: "unknown scale"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 38. Failure: arguments are checked (@testData.R#533)  ───────────────────────
  `phenotypes(file = "data/phenotypes-unknown-type.csv")` threw an error with unexpected message.
  Expected match: "unsupported variable type"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 39. Failure: arguments are checked (@testData.R#536)  ───────────────────────
  `phenotypes(df)` threw an error with unexpected message.
  Expected match: "infer variable type"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 40. Failure: arguments are checked (@testData.R#539)  ───────────────────────
  `phenotypes(df, min = c("a", NA))` threw an error with unexpected message.
  Expected match: "should be numeric"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 41. Failure: arguments are checked (@testData.R#540)  ───────────────────────
  `phenotypes(df, max = c(F, NA))` threw an error with unexpected message.
  Expected match: "should be numeric"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 42. Failure: arguments are checked (@testData.R#541)  ───────────────────────
  `phenotypes(df, min = c(1, NA, 10))` threw an error with unexpected message.
  Expected match: "number of data columns"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 43. Failure: arguments are checked (@testData.R#542)  ───────────────────────
  `phenotypes(df, max = c(5, NA, 100))` threw an error with unexpected message.
  Expected match: "number of data columns"
  Actual message: "java.lang.NoClassDefFoundError: Could not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder"
  
  ── 44. Error: class (@testData.R#546)  ─────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 45. Error: read phenotype data from file (@testData.R#552)  ─────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 46. Error: phenotype file with single trait (@testData.R#590)  ──────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 47. Error: create phenotype data from data frame (@testData.R#633)  ─────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 48. Error: print (@testData.R#690)  ─────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 49. Error: class (@testData.R#722)  ─────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 50. Error: distance matrix (@testData.R#732)  ───────────────────────────────
  java.lang.StackOverflowError
  
  ── 51. Error: size (@testData.R#736)  ──────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 52. Error: example data (@testData.R#740)  ──────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 53. Error: print (@testData.R#747)  ─────────────────────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 54. Error: arguments are checked (@testExecution.R#10)  ─────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  Error in .jcall("java/lang/Class", "Ljava/lang/Class;", "forName", cl,  : 
    RcallMethod: cannot determine object class
  ── 55. Error: default objectives (@testExecution.R#33)  ────────────────────────
  Java Exception <no description because toString() failed>.jfindClass(as.character(class))new("jobjRef", jobj = <pointer: 0x557891eb9728>, jclass = "java/lang/Throwable")
  Backtrace:
    1. testthat::expect_silent(core <- testSampleCore(genotypeData()))
   14. global::genotypeData()
   15. corehunter::genotypes(file = genotypeFile(size, format), format = format)
   16. corehunter:::ch.api()
   17. rJava::J("org.corehunter.API")
   18. rJava:::jclassName(class)
   19. rJava::.jfindClass(as.character(class))
  
  ── 56. Error: result contains indices or names (@testExecution.R#53)  ──────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  Error in .jcall("java/lang/Class", "Ljava/lang/Class;", "forName", cl,  : 
    RcallMethod: cannot determine object class
  ── 57. Error: multiple objectives (@testExecution.R#63)  ───────────────────────
  Java Exception <no description because toString() failed>.jfindClass(as.character(class))new("jobjRef", jobj = <pointer: 0x557891eb9738>, jclass = "java/lang/Throwable")
  Backtrace:
    1. testthat::expect_silent(...)
   14. global::testData()
   17. global::genotypeData()
   18. corehunter::genotypes(file = genotypeFile(size, format), format = format)
   19. corehunter:::ch.api()
   20. rJava::J("org.corehunter.API")
   21. rJava:::jclassName(class)
   22. rJava::.jfindClass(as.character(class))
  
  ── 58. Error: seed is respected (@testExecution.R#71)  ─────────────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 59. Error: seed is respected (fast mode) (@testExecution.R#80)  ─────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 60. Error: seed is respected (multi-objective, with normalization) (@testExec
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 61. Error: seed is respected (multi-objective, no normalization) (@testExecut
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 62. Error: fixed ids are respected (@testExecution.R#116)  ──────────────────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ── 63. Error: core has expected class and elements (@testExecution.R#182)  ─────
  java.lang.NoClassDefFoundCould not initialize class java.nio.file.FileSystems$DefaultFileSystemHolder
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 44 | SKIPPED: 0 | WARNINGS: 30 | FAILED: 63 ]
  1. Failure: arguments are checked (@testAnalysis.R#11) 
  2. Failure: arguments are checked (@testAnalysis.R#12) 
  3. Error: larger cores are more representative but have higher redundancy (@testAnalysis.R#16) 
  4. Failure: arguments are checked (@testData.R#10) 
  5. Failure: arguments are checked (@testData.R#11) 
  6. Failure: arguments are checked (@testData.R#12) 
  7. Failure: arguments are checked (@testData.R#13) 
  8. Failure: arguments are checked (@testData.R#14) 
  9. Failure: arguments are checked (@testData.R#17) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted