Running ‘run-base.R’ [391s/393s]
Running the tests in ‘tests/run-base.R’ failed.
Complete output:
  > library(testthat)
  > test_check("mlr", filter = "base_")
  Loading required package: mlr
  Loading required package: ParamHelpers
  
  Attaching package: 'rex'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  ── 1. Error: MulticlassWrapper (@test_base_MulticlassWrapper.R#23)  ────────────
  For learner classif.lqa please install the following packages: lqa
  1: makeLearner("classif.lqa") at testthat/test_base_MulticlassWrapper.R:23
  2: do.call(constructor, list())
  3: (function () 
     {
         makeRLearnerClassif(cl = "classif.lqa", package = "lqa", par.set = makeParamSet(makeDiscreteLearnerParam(id = "penalty", 
             values = c("adaptive.lasso", "ao", "bridge", "enet", "fused.lasso", "genet", 
                 "icb", "lasso", "licb", "oscar", "penalreg", "ridge", "scad", "weighted.fusion")), 
             makeNumericLearnerParam(id = "lambda", lower = 0, requires = quote(penalty %in% 
                 c("adaptive.lasso", "ao", "bridge", "genet", "lasso", "oscar", "penalreg", 
                     "ridge", "scad"))), makeNumericLearnerParam(id = "gamma", lower = 1 + 
                 .Machine$double.eps, requires = quote(penalty %in% c("ao", "bridge", 
                 "genet", "weighted.fusion"))), makeNumericLearnerParam(id = "alpha", 
                 lower = 0, upper = 1, requires = quote(penalty == "genet")), makeNumericLearnerParam(id = "oscar.c", 
                 lower = 0, requires = quote(penalty == "oscar")), makeNumericLearnerParam(id = "a", 
                 lower = 2 + .Machine$double.eps, requires = quote(penalty == "scad")), 
             makeNumericLearnerParam(id = "lambda1", lower = 0, requires = quote(penalty %in% 
                 c("enet", "fused.lasso", "icb", "licb", "weighted.fusion"))), makeNumericLearnerParam(id = "lambda2", 
                 lower = 0, requires = quote(penalty %in% c("enet", "fused.lasso", "icb", 
                     "licb", "weighted.fusion"))), makeDiscreteLearnerParam(id = "method", 
                 default = "lqa.update2", values = c("lqa.update2", "ForwardBoost", "GBlockBoost")), 
             makeNumericLearnerParam(id = "var.eps", default = .Machine$double.eps, lower = 0), 
             makeIntegerLearnerParam(id = "max.steps", lower = 1L, default = 5000L), makeNumericLearnerParam(id = "conv.eps", 
                 default = 0.001, lower = 0), makeLogicalLearnerParam(id = "conv.stop", 
                 default = TRUE), makeNumericLearnerParam(id = "c1", default = 1e-08, 
                 lower = 0), makeIntegerLearnerParam(id = "digits", default = 5L, lower = 1L)), 
             properties = c("numerics", "prob", "twoclass"), par.vals = list(penalty = "lasso", 
                 lambda = 0.1), name = "Fitting penalized Generalized Linear Models with the LQA algorithm", 
             short.name = "lqa", note = "`penalty` has been set to `\"lasso\"` and `lambda` to `0.1` by default. The parameters `lambda`, `gamma`, `alpha`, `oscar.c`, `a`, `lambda1` and `lambda2` are the tuning parameters of the `penalty` function being used, and correspond to the parameters as named in the respective help files. Parameter `c` for penalty method `oscar` has been named `oscar.c`. Parameters `lambda1` and `lambda2` correspond to the parameters named 'lambda_1' and 'lambda_2' of the penalty functions `enet`, `fused.lasso`, `icb`, `licb`, as well as `weighted.fusion`.", 
             callees = c("lqa", "lqa.control", "adaptive.lasso", "ao", "bridge", "enet", 
                 "fused.lasso", "genet", "icb", "lasso", "licb", "oscar", "penalreg", 
                 "ridge", "scad", "weighted.fusion"))
     })()
  4: makeRLearnerClassif(cl = "classif.lqa", package = "lqa", par.set = makeParamSet(makeDiscreteLearnerParam(id = "penalty", 
         values = c("adaptive.lasso", "ao", "bridge", "enet", "fused.lasso", "genet", 
             "icb", "lasso", "licb", "oscar", "penalreg", "ridge", "scad", "weighted.fusion")), 
         makeNumericLearnerParam(id = "lambda", lower = 0, requires = quote(penalty %in% 
             c("adaptive.lasso", "ao", "bridge", "genet", "lasso", "oscar", "penalreg", 
                 "ridge", "scad"))), makeNumericLearnerParam(id = "gamma", lower = 1 + 
             .Machine$double.eps, requires = quote(penalty %in% c("ao", "bridge", "genet", 
             "weighted.fusion"))), makeNumericLearnerParam(id = "alpha", lower = 0, upper = 1, 
             requires = quote(penalty == "genet")), makeNumericLearnerParam(id = "oscar.c", 
             lower = 0, requires = quote(penalty == "oscar")), makeNumericLearnerParam(id = "a", 
             lower = 2 + .Machine$double.eps, requires = quote(penalty == "scad")), makeNumericLearnerParam(id = "lambda1", 
             lower = 0, requires = quote(penalty %in% c("enet", "fused.lasso", "icb", 
                 "licb", "weighted.fusion"))), makeNumericLearnerParam(id = "lambda2", 
             lower = 0, requires = quote(penalty %in% c("enet", "fused.lasso", "icb", 
                 "licb", "weighted.fusion"))), makeDiscreteLearnerParam(id = "method", 
             default = "lqa.update2", values = c("lqa.update2", "ForwardBoost", "GBlockBoost")), 
         makeNumericLearnerParam(id = "var.eps", default = .Machine$double.eps, lower = 0), 
         makeIntegerLearnerParam(id = "max.steps", lower = 1L, default = 5000L), makeNumericLearnerParam(id = "conv.eps", 
             default = 0.001, lower = 0), makeLogicalLearnerParam(id = "conv.stop", default = TRUE), 
         makeNumericLearnerParam(id = "c1", default = 1e-08, lower = 0), makeIntegerLearnerParam(id = "digits", 
             default = 5L, lower = 1L)), properties = c("numerics", "prob", "twoclass"), 
         par.vals = list(penalty = "lasso", lambda = 0.1), name = "Fitting penalized Generalized Linear Models with the LQA algorithm", 
         short.name = "lqa", note = "`penalty` has been set to `\"lasso\"` and `lambda` to `0.1` by default. The parameters `lambda`, `gamma`, `alpha`, `oscar.c`, `a`, `lambda1` and `lambda2` are the tuning parameters of the `penalty` function being used, and correspond to the parameters as named in the respective help files. Parameter `c` for penalty method `oscar` has been named `oscar.c`. Parameters `lambda1` and `lambda2` correspond to the parameters named 'lambda_1' and 'lambda_2' of the penalty functions `enet`, `fused.lasso`, `icb`, `licb`, as well as `weighted.fusion`.", 
         callees = c("lqa", "lqa.control", "adaptive.lasso", "ao", "bridge", "enet", "fused.lasso", 
             "genet", "icb", "lasso", "licb", "oscar", "penalreg", "ridge", "scad", "weighted.fusion"))
  5: addClasses(makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, 
         name, short.name, note, callees), c(cl, "RLearnerClassif"))
  6: makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, name, 
         short.name, note, callees)
  7: requirePackages(package, why = stri_paste("learner", id, sep = " "), default.method = "load")
  8: stopf("For %s please install the following packages: %s", why, ps)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 998 SKIPPED: 0 FAILED: 1
  1. Error: MulticlassWrapper (@test_base_MulticlassWrapper.R#23) 
  
  Execution halted
  ── 2. Error: plotFilterValues (@test_base_generateFilterValuesData.R#79)  ──────
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generateFilterValuesData.R:79
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 3. Error: 1 numeric hyperparam (@test_base_generateHyperParsEffect.R#48)  ───
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generateHyperParsEffect.R:48
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 4. Error: 1 discrete hyperparam (@test_base_generateHyperParsEffect.R#77)  ──
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generateHyperParsEffect.R:77
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 5. Error: 1 numeric hyperparam with optimizer failure (@test_base_generateHyp
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generateHyperParsEffect.R:106
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 6. Error: 1 numeric hyperparam with nested cv (@test_base_generateHyperParsEf
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generateHyperParsEffect.R:137
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 7. Error: 2 hyperparams (@test_base_generateHyperParsEffect.R#167)  ─────────
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generateHyperParsEffect.R:167
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 8. Error: 2 hyperparams nested (@test_base_generateHyperParsEffect.R#236)  ──
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: expect_warning(ggsave(path)) at testthat/test_base_generateHyperParsEffect.R:236
  2: quasi_capture(enquo(object), capture_warnings, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, warning = function(condition) {
         out$push(condition)
         invokeRestart("muffleWarning")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: ggsave(path)
  7: dev(filename = filename, width = dim[1], height = dim[2], ...)
  8: svglite::svglite(file = filename, ...)
  9: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 9. Error: 2+ hyperparams (@test_base_generateHyperParsEffect.R#290)  ────────
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generateHyperParsEffect.R:290
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 10. Error: generateLearningCurve (@test_base_generateLearningCurve.R#11)  ───
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generateLearningCurve.R:11
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 11. Error: generatePartialDependenceData (@test_base_generatePartialDependenc
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_generatePartialDependence.R:19
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 12. Error: generateThreshVsPerfData (@test_base_generateThreshVsPerf.R#12)  ─
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggplot2::ggsave(path) at testthat/test_base_generateThreshVsPerf.R:12
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 13. Error: getHyperPars (@test_base_getHyperPars.R#27)  ─────────────────────
  cannot open the connection
  1: expect_output(print(lrn), "missing=NA") at testthat/test_base_getHyperPars.R:27
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 14. Error: helpLearner of learner with multiple help pages (@test_base_helpLe
  cannot open the connection
  1: expect_output(testfn("classif.qda"), "Choose help page:(\\n[0-9]+ : [0-9a-zA-Z._]+)+\\n\\.\\.\\.: *$") at testthat/test_base_helpLearner.R:19
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 15. Error: helpLearner of wrapped learner (@test_base_helpLearner.R#56)  ────
  cannot open the connection
  1: expect_output(testfn(makeBaggingWrapper(makeLearner("classif.qda"), 2)), "No information about learner") at testthat/test_base_helpLearner.R:56
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 16. Error: helpLearnerParam (@test_base_helpLearner.R#61)  ──────────────────
  cannot open the connection
  1: expect_output(helpLearnerParam("classif.qda"), "method") at testthat/test_base_helpLearner.R:61
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 17. Error: helpLearnerParam of wrapped learner (@test_base_helpLearner.R#101)
  cannot open the connection
  1: expect_output(helpLearnerParam(w1, "nu"), "Value: +4") at testthat/test_base_helpLearner.R:101
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 18. Error: fuzzy matching works for mistyped hyperpars (@test_base_hyperpars.
  cannot open the connection
  1: expect_silent(makeLearner("classif.ksvm", config = cq, sigm = 1)) at testthat/test_base_hyperpars.R:73
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: file()
  
  ── 19. Error: ImputeWrapper (@test_base_impute.R#160)  ─────────────────────────
  cannot open the connection
  1: expect_output(print(mm), "root") at testthat/test_base_impute.R:160
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 20. Error: check measure calculations (@test_base_measures.R#262)  ──────────
  cannot open the connection
  1: expect_silent(measureRSQ(c(1, 1, 1, 0), c(2, 2, 2, 2))) at testthat/test_base_measures.R:262
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: file()
  
  ── 21. Error: BenchmarkResult (@test_base_plotBMRBoxplots.R#12)  ───────────────
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_plotBMRBoxplots.R:12
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 22. Error: BenchmarkResult allows spaces (@test_base_plotBMRBoxplots.R#69)  ─
  could not open file '/tmp/RtmpnY4O6c/file56987a31a23b.png'
  1: ggsave(tempfile(fileext = ".png")) at testthat/test_base_plotBMRBoxplots.R:69
  2: grid.draw(plot)
  3: grid.draw.ggplot(plot)
  4: print(x)
  5: print.ggplot(x)
  6: grid.newpage()
  
  ── 23. Error: plotBMRRanksAsBarChart (@test_base_plotBMRRanksAsBarChart.R#19)  ─
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_plotBMRRanksAsBarChart.R:19
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 24. Error: BenchmarkSummary (@test_base_plotBMRSummary.R#18)  ───────────────
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_plotBMRSummary.R:18
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 25. Error: test_CritDifferences (@test_base_plotCritDifferences.R#32)  ──────
  could not open file '/tmp/RtmpnY4O6c/file56987bedb5c1.png'
  1: ggsave(tempfile(fileext = ".png")) at testthat/test_base_plotCritDifferences.R:32
  2: grid.draw(plot)
  3: grid.draw.ggplot(plot)
  4: print(x)
  5: print.ggplot(x)
  6: grid.newpage()
  
  ── 26. Error: plotLearnerPrediction (@test_base_plotLearnerPrediction.R#6)  ────
  could not open file '/tmp/RtmpnY4O6c/file569876bd2b8b.png'
  1: ggsave(tempfile(fileext = ".png")) at testthat/test_base_plotLearnerPrediction.R:6
  2: grid.draw(plot)
  3: grid.draw.ggplot(plot)
  4: print(x)
  5: print.ggplot(x)
  6: grid.newpage()
  
  ── 27. Error: plotResiduals with prediction object (@test_base_plotResiduals.R#1
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_plotResiduals.R:11
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 28. Error: plotResiduals with BenchmarkResult (@test_base_plotResiduals.R#46)
  cannot open stream /tmp/RtmpnY4O6c/test.svg
  1: ggsave(path) at testthat/test_base_plotResiduals.R:46
  2: dev(filename = filename, width = dim[1], height = dim[2], ...)
  3: svglite::svglite(file = filename, ...)
  4: svglite_(file, bg, width, height, pointsize, standalone, aliases)
  
  ── 29. Error: resample (@test_base_resample.R#30)  ─────────────────────────────
  cannot open the connection
  1: expect_output(print(r1), "Resample Result") at testthat/test_base_resample.R:30
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 30. Error: resample printer respects show.info (@test_base_resample.R#192)  ─
  cannot open the connection
  1: expect_silent(resample(lrn, bh.task, cv10, list(mape, medae, mse))) at testthat/test_base_resample.R:192
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: file()
  
  ── 31. Error: selectFeatures (@test_base_selectFeatures.R#15)  ─────────────────
  cannot open the connection
  1: expect_output(print(ctrl), "Imputation value: <worst>") at testthat/test_base_selectFeatures.R:15
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 32. Error: tune (@test_base_tuning.R#30)  ───────────────────────────────────
  cannot open the connection
  1: expect_output(print(ctrl), "Imputation value: <worst>") at testthat/test_base_tuning.R:30
  2: quasi_capture(enquo(object), capture_output, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: capture_output_lines(code, print, width = width)
  5: eval_with_output(code, print = print, width = width)
  6: file()
  
  ── 33. Error: tuning allows usage of budget (@test_base_tuning.R#120)  ─────────
  Assertion on 'discrete.names' failed: Must be of type 'logical flag', not 'NULL'.
  1: tuneParams(lrn, binaryclass.task, resampling = rdesc, par.set = ps, control = ctrl) at testthat/test_base_tuning.R:120
  2: sel.func(learner, task, resampling, measures, par.set, control, opt.path, show.info, 
         resample.fun)
  3: sampleValue(par.set, start, trafo = FALSE)
  4: sampleValue.ParamSet(par.set, start, trafo = FALSE)
  5: lapply(par$pars, sampleValue, discrete.names = discrete.names, trafo = trafo)
  6: FUN(X[[i]], ...)
  7: sampleValue.Param(X[[i]], ...)
  8: assertFlag(discrete.names)
  9: makeAssertion(x, res, .var.name, add)
  10: mstop("Assertion on '%s' failed: %s.", var.name, res)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3178 SKIPPED: 0 FAILED: 33
  1. Error: MulticlassWrapper (@test_base_MulticlassWrapper.R#23) 
  2. Error: plotFilterValues (@test_base_generateFilterValuesData.R#79) 
  3. Error: 1 numeric hyperparam (@test_base_generateHyperParsEffect.R#48) 
  4. Error: 1 discrete hyperparam (@test_base_generateHyperParsEffect.R#77) 
  5. Error: 1 numeric hyperparam with optimizer failure (@test_base_generateHyperParsEffect.R#106) 
  6. Error: 1 numeric hyperparam with nested cv (@test_base_generateHyperParsEffect.R#137) 
  7. Error: 2 hyperparams (@test_base_generateHyperParsEffect.R#167) 
  8. Error: 2 hyperparams nested (@test_base_generateHyperParsEffect.R#236) 
  9. Error: 2+ hyperparams (@test_base_generateHyperParsEffect.R#290) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted