CRAN Package Check Results for Package smartdata

Last updated on 2019-12-12 19:51:09 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.2 10.20 288.32 298.52 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.2 9.48 202.82 212.30 OK
r-devel-linux-x86_64-fedora-clang 1.0.2 353.01 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.2 333.32 NOTE
r-devel-windows-ix86+x86_64 1.0.2 35.00 380.00 415.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0.2 60.00 382.00 442.00 OK
r-patched-linux-x86_64 1.0.2 8.82 246.24 255.06 OK
r-release-linux-x86_64 1.0.2 7.97 243.01 250.98 OK
r-release-windows-ix86+x86_64 1.0.2 29.00 253.00 282.00 OK
r-release-osx-x86_64 1.0.2 NOTE
r-oldrel-windows-ix86+x86_64 1.0.2 13.00 249.00 262.00 OK
r-oldrel-osx-x86_64 1.0.2 NOTE

Check Details

Version: 1.0.2
Check: tests
Result: ERROR
     Running 'testthat.R' [137s/147s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(smartdata)
     Loading required package: mice
     Loading required package: lattice
    
     Attaching package: 'mice'
    
     The following objects are masked from 'package:base':
    
     cbind, rbind
    
     >
     > test_check("smartdata")
     missForest iteration 1 in progress...done!
     missForest iteration 2 in progress...done!
     missForest iteration 3 in progress...done!
     missForest iteration 4 in progress...done!
     [1] "ANS is done"
     [1] "0 samples filtered by NEATER"
     [1] "SLS done"
     finding neighbours
     calculating weights
     computing coordinates
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     smartdata
     --- call from context ---
     checks[[argName]]$check(arg)
     --- call from argument ---
     if (class(x) != "matrix") stop("similarity parameter needs a matrix of similarities of the dataset variabless")
     --- R stacktrace ---
     where 1: checks[[argName]]$check(arg)
     where 2: FUN(X[[i]], ...)
     where 3: lapply(X = X, FUN = FUN, ...)
     where 4: sapply(names(checks), function(argName) {
     arg <- args[[argName]]
     if (is.null(arg) && !is.null(checks[[argName]]$default)) {
     arg <- checks[[argName]]$default
     }
     else {
     checks[[argName]]$check(arg)
     }
     arg
     }, simplify = FALSE)
     where 5: mapArguments(task$args, callArgs)
     where 6: doSpaceTransformation.adaptiveGPCA(task)
     where 7: doSpaceTransformation(task)
     where 8: preprocess.spaceTransformation(task)
     where 9: preprocess(task)
     where 10: space_transformation(antibiotics, "adaptative_gpca", similarity = AntibioticSmall$Q,
     num_features = 2)
     where 11: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     where 12: withCallingHandlers({
     code
     NULL
     }, error = function(cnd) {
     if (can_entrace(cnd)) {
     cnd <- cnd_entrace(cnd)
     }
     return_from(env, cnd)
     })
     where 13: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),
     ...)
     where 14: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
     where 15 at testthat/testSpaceTransformation.R#11: expect_error(space_transformation(antibiotics, "adaptative_gpca",
     similarity = AntibioticSmall$Q, num_features = 2), NA)
     where 16: eval(code, test_env)
     where 17: eval(code, test_env)
     where 18: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 19: doTryCatch(return(expr), name, parentenv, handler)
     where 20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 22: doTryCatch(return(expr), name, parentenv, handler)
     where 23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 24: tryCatchList(expr, classes, parentenv, handlers)
     where 25: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 26: test_code(desc, code, env = parent.frame())
     where 27 at testthat/testSpaceTransformation.R#8: test_that("Correct space transformation", {
     expect_error(space_transformation(ecoli1, "lle_knn", regularization = 3,
     k = 3, num_features = 2, exclude = c("Mcg", "Alm1")),
     NA)
     expect_error(space_transformation(antibiotics, "adaptative_gpca",
     similarity = AntibioticSmall$Q, num_features = 2), NA)
     })
     where 28: eval(code, test_env)
     where 29: eval(code, test_env)
     where 30: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 31: doTryCatch(return(expr), name, parentenv, handler)
     where 32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 33: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 34: doTryCatch(return(expr), name, parentenv, handler)
     where 35: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 36: tryCatchList(expr, classes, parentenv, handlers)
     where 37: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 38: test_code(NULL, exprs, env)
     where 39: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 40: force(code)
     where 41: doWithOneRestart(return(expr), restart)
     where 42: withOneRestart(expr, restarts[[1L]])
     where 43: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 44: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
     {
     reporter$start_file(basename(path))
     lister$start_file(basename(path))
     source_file(path, new.env(parent = env), chdir = TRUE,
     wrap = wrap)
     reporter$.end_context()
     reporter$end_file()
     })
     where 45: FUN(X[[i]], ...)
     where 46: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 47: force(code)
     where 48: doWithOneRestart(return(expr), restart)
     where 49: withOneRestart(expr, restarts[[1L]])
     where 50: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 51: with_reporter(reporter = current_reporter, results <- lapply(paths,
     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
     load_helpers = FALSE, wrap = wrap))
     where 52: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 53: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
     wrap = wrap)
     where 54: test_package_dir(package = package, test_path = test_path, filter = filter,
     reporter = reporter, ..., stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 55: test_check("smartdata")
    
     --- value of length: 2 type: logical ---
     [1] FALSE TRUE
     --- function from context ---
     function (x)
     {
     if (class(x) != "matrix")
     stop("similarity parameter needs a matrix of similarities of the dataset variabless")
     }
     <bytecode: 0xc6125d0>
     <environment: namespace:smartdata>
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
     -- 1. Failure: Correct space transformation (@testSpaceTransformation.R#11) ---
     `space_transformation(...)` threw an error.
     Message: the condition has length > 1
     Class: simpleError/error/condition
     Backtrace:
     1. testthat::expect_error(...)
     6. smartdata::space_transformation(...)
     8. smartdata:::preprocess.spaceTransformation(task)
     10. smartdata:::doSpaceTransformation.adaptiveGPCA(task)
     11. smartdata:::mapArguments(task$args, callArgs)
     12. base::sapply(...)
     13. base::lapply(X = X, FUN = FUN, ...)
     14. smartdata:::FUN(X[[i]], ...)
     15. checks[[argName]]$check(arg)
    
     Possible methods are: 'multivariate', 'univariate'
     For more information do: ?NoiseFiltersR::AENN
     Parameters for AENN are:
     * k: Number of nearest neighbors for KNN
     Default value: 5
     For more information do: ?NoiseFiltersR::hybridRepairFilter
     Parameters for hybrid are:
     * consensus: Use consensus vote if TRUE. Else, use majority vote
     Default value: FALSE
     * action: Strategy to treat noisy instances: 'remove', 'repair', 'hybrid'
     Default value: remove
     Possible methods are: 'AENN', 'ENN', 'BBNR', 'DROP1', 'DROP2', 'DROP3', 'EF', 'ENG', 'HARF', 'GE', 'INFFC', 'IPF', 'Mode', 'PF', 'PRISM', 'RNN', 'ORBoost', 'edgeBoost', 'edgeWeight', 'TomekLinks', 'dynamic', 'hybrid', 'saturation', 'consensusSF', 'classificationSF', 'C45robust', 'C45voting', 'C45iteratedVoting', 'CVCF'
     Possible methods are: 'gibbs_sampling', 'expect_maximization', 'central_imputation', 'knn_imputation', 'rf_imputation', 'PCA_imputation', 'MCA_imputation', 'FAMD_imputation', 'hotdeck', 'iterative_robust', 'regression_imputation', 'ATN'
     For more information do: ?FSelector::chi.squared
     Parameters for chi_squared are:
     * num_features: Number of attributes to pick (apart from class_attr, if supplied).
     Should be lower than number of features in the
     dataset
     Default value: 1
     Possible methods are: 'CNN', 'ENN', 'multiedit', 'FRIS'
     Possible methods are: 'chi2', 'chi_merge', 'extended_chi2', 'mod_chi2', 'CAIM', 'CACC', 'ameva', 'mdlp', 'equalfreq', 'equalwidth', 'globalequalwidth'
     Possible methods are: 'z_score', 'pos_standardization', 'unitization', 'pos_unitization', 'min_max', 'rnorm', 'rpnorm', 'sd_quotient', 'mad_quotient', 'range_quotient', 'max_quotient', 'mean_quotient', 'median_quotient', 'sum_quotient', 'ssq_quotient', 'norm', 'pnorm', 'znorm'
     Possible methods are: 'RACOG', 'wRACOG', 'PDFOS', 'RWO', 'ADASYN', 'ANSMOTE', 'SMOTE', 'MWMOTE', 'BLSMOTE', 'DBSMOTE', 'SLMOTE', 'RSLSMOTE'
     Possible methods are: 'lle_knn', 'lle_epsilon', 'adaptative_gpca'
     == testthat results ===========================================================
     [ OK: 235 | SKIPPED: 0 | WARNINGS: 92 | FAILED: 1 ]
     1. Failure: Correct space transformation (@testSpaceTransformation.R#11)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.2
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘Amelia’ ‘Boruta’ ‘DMwR’ ‘MVN’ ‘NoiseFiltersR’ ‘VIM’ ‘adaptiveGPCA’
     ‘class’ ‘clusterSim’ ‘denoiseR’ ‘discretization’ ‘imbalance’ ‘lle’
     ‘missForest’ ‘missMDA’ ‘outliers’ ‘unbalanced’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64, r-oldrel-osx-x86_64