Running ‘testthat.R’ [14s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(assignPOP)
  > 
  > test_check("assignPOP")
  
    Correct assignment rates were estimated!!
    A total of 3 assignment tests for 3 pops.
    Results were also saved in a 'Rate_of_3_tests_3_pops.txt' file in the directory.1. Error: Calculate assignment accuracy for Monte-Carlo results (@test_accuracy.R#8) 
  operator '>' not meaningful for units
  1: expect_output(str(plot), "List of 9") at testthat/test_accuracy.R:8
  2: capture_output(object)
  3: capture_output_as_vector(code, print)
  4: with_sink(temp, withVisible(code))
  5: withVisible(code)
  6: str(plot)
  7: str.default(plot)
  8: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  9: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  10: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(1), indent.str = quote("  .."))
  11: str(obj, ...)
  12: str.default(obj, ...)
  13: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  14: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  15: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(2), indent.str = quote("  .. .."))
  16: str(obj, ...)
  17: str.default(obj, ...)
  18: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  19: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  20: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(3), indent.str = quote("  .. .. .."))
  21: str(obj, ...)
  22: str.default(obj, ...)
  23: Ops.unit(ao, 1e-10)
  24: stop(gettextf("operator '%s' not meaningful for units", .Generic), domain = NA)
  
  
    Correct assignment rates were estimated!!
    A total of 3 assignment tests for 3 pops.
    Results were also saved in a 'Rate_of_3_tests_3_pops.txt' file in the directory.2. Error: Calculate assignment accuracy for K-fold results (@test_accuracy.R#18) 
  operator '>' not meaningful for units
  1: expect_output(str(plot), "List of 9") at testthat/test_accuracy.R:18
  2: capture_output(object)
  3: capture_output_as_vector(code, print)
  4: with_sink(temp, withVisible(code))
  5: withVisible(code)
  6: str(plot)
  7: str.default(plot)
  8: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  9: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  10: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(1), indent.str = quote("  .."))
  11: str(obj, ...)
  12: str.default(obj, ...)
  13: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  14: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  15: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(2), indent.str = quote("  .. .."))
  16: str(obj, ...)
  17: str.default(obj, ...)
  18: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  19: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  20: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(3), indent.str = quote("  .. .. .."))
  21: str(obj, ...)
  22: str.default(obj, ...)
  23: Ops.unit(ao, 1e-10)
  24: stop(gettextf("operator '%s' not meaningful for units", .Generic), domain = NA)
  
  
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    ################ assignPOP v1.1.3 ################
  
    A GENEPOP format file was successfully imported!
  
    Imported Data Info: 24 obs. by 5 loci (diploid)
    Number of pop: 3
    Number of inds (pop.1): 8
    Number of inds (pop.2): 10
    Number of inds (pop.3): 6
    DataMatrix: 24 rows by 20 columns, with 19 allele variables
  
    Data output in a list comprising the following three elements:
    YOUR_LIST_NAME$DataMatrix
    YOUR_LIST_NAME$SampleID
    YOUR_LIST_NAME$LocusName
  
    Multiprocess is off. Only single core will be used for analysis.
  
    Monte-Carlo cross-validation done!!
    3 assignment tests completed!!  Multiprocess is off. Only single core will be used for analysis.
  
    Monte-Carlo cross-validation done!!
    3 assignment tests completed!!  Multiprocess is off. Only single core will be used for analysis.
  
    Monte-Carlo cross-validation done!!
    6 assignment tests completed!!  Multiprocess is off. Only single core will be used for analysis.
  
    Monte-Carlo cross-validation done!!
    12 assignment tests completed!!  Multiprocess is off. Only single core will be used for analysis.
  
    Monte-Carlo cross-validation done!!
    12 assignment tests completed!!  Multiprocess is off. Only single core will be used for analysis.
  
    Monte-Carlo cross-validation done!!
    3 assignment tests completed!!
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    ################ assignPOP v1.1.3 ################
  
    A GENEPOP format file was successfully imported!
  
    Imported Data Info: 24 obs. by 5 loci (diploid)
    Number of pop: 3
    Number of inds (pop.1): 8
    Number of inds (pop.2): 10
    Number of inds (pop.3): 6
    DataMatrix: 24 rows by 20 columns, with 19 allele variables
  
    Data output in a list comprising the following three elements:
    YOUR_LIST_NAME$DataMatrix
    YOUR_LIST_NAME$SampleID
    YOUR_LIST_NAME$LocusName
  
  
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    |======================================================================| 100%
  
    ################ assignPOP v1.1.3 ################
  
    A GENEPOP format file was successfully imported!
  
    Imported Data Info: 24 obs. by 5 loci (diploid)
    Number of pop: 1
    Number of inds (pop.1): 24
    DataMatrix: 24 rows by 20 columns, with 19 allele variables
  
    Data output in a list comprising the following three elements:
    YOUR_LIST_NAME$DataMatrix
    YOUR_LIST_NAME$SampleID
    YOUR_LIST_NAME$LocusName
  
  
    Known and unknown datasets have identical features. 
    Performing PCA on genetic data for dimensionality reduction...
    Assignment test is done! See results in your designated folder.
    Predicted populations and probabilities are saved in [AssignmentResult.txt]
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    |======================================================================| 100%
  
    ################ assignPOP v1.1.3 ################
  
    A GENEPOP format file was successfully imported!
  
    Imported Data Info: 24 obs. by 5 loci (diploid)
    Number of pop: 3
    Number of inds (pop.1): 8
    Number of inds (pop.2): 10
    Number of inds (pop.3): 6
    DataMatrix: 24 rows by 20 columns, with 19 allele variables
  
    Data output in a list comprising the following three elements:
    YOUR_LIST_NAME$DataMatrix
    YOUR_LIST_NAME$SampleID
    YOUR_LIST_NAME$LocusName
  
    Multiprocess is off. Only single core will be used for analysis.
  
    K-fold cross-validation done!!
    3 assignment tests completed!!  Import a .CSV file.
    4 additional variables detected.
    Checking variable data type...
     ng1(integer)   ng2(integer)   ng3(integer)   ng4(integer)
    New data set created!!
    It has 18 observations by 24 variables
    including 4 loci(19 alleles) plus 4 additional variables(4 columns)  Multiprocess is off. Only single core will be used for analysis.
  
    K-fold cross-validation done!!
    3 assignment tests completed!!  ng1(integer)  ng2(integer)  ng3(integer)  ng4(integer)  Multiprocess is off. Only single core will be used for analysis.
  
    K-fold cross-validation done!!
    3 assignment tests completed!!
    Results were saved in a 'High_Fst_Locus_Freq.txt' file in the directory.3. Error: Plot membership probability (@test_membership.R#5) -------------------
  operator '>' not meaningful for units
  1: expect_output(str(plot), "List of 10") at testthat/test_membership.R:5
  2: capture_output(object)
  3: capture_output_as_vector(code, print)
  4: with_sink(temp, withVisible(code))
  5: withVisible(code)
  6: str(plot)
  7: str.default(plot)
  8: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  9: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  10: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(1), indent.str = quote("  .."))
  11: str(obj, ...)
  12: str.default(obj, ...)
  13: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  14: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  15: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(2), indent.str = quote("  .. .."))
  16: str(obj, ...)
  17: str.default(obj, ...)
  18: strSub(object[[i]], give.length = give.length, nest.lev = nest.lev + 1, indent.str = paste(indent.str, 
         ".."))
  19: do.call(function(...) str(obj, ...), c(aList, list(...)), quote = TRUE)
  20: (function (...) 
     str(obj, ...))(max.level = quote(NA), vec.len = quote(4L), digits.d = quote(3L), 
         nchar.max = quote(128), give.attr = quote(TRUE), drop.deparse.attr = quote(TRUE), 
         give.head = quote(TRUE), width = quote(80L), envir = quote(NULL), strict.width = quote("no"), 
         formatNum = quote(function (x, ...) 
         format(x, trim = TRUE, drop0trailing = TRUE, ...)), list.len = quote(99), give.length = quote(TRUE), 
         nest.lev = quote(3), indent.str = quote("  .. .. .."))
  21: str(obj, ...)
  22: str.default(obj, ...)
  23: Ops.unit(ao, 1e-10)
  24: stop(gettextf("operator '%s' not meaningful for units", .Generic), domain = NA)
  
  testthat results ================================================================
  OK: 38 SKIPPED: 0 FAILED: 3
  1. Error: Calculate assignment accuracy for Monte-Carlo results (@test_accuracy.R#8) 
  2. Error: Calculate assignment accuracy for K-fold results (@test_accuracy.R#18) 
  3. Error: Plot membership probability (@test_membership.R#5) 
  
  Error: testthat unit tests failed
  Execution halted