Package check result: NOTE

Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: ‘Daniel J. Stekhoven <stekhoven@nexus.ethz.ch>’
  
  New maintainer:
    Daniel J. Stekhoven <stekhoven@nexus.ethz.ch>
  Old maintainer(s):
    Daniel J. Stekhoven <stekhoven@stat.math.ethz.ch>

Changes to worse in reverse depends:

Package: ADAPTS
Check: examples
New result: ERROR
  Running examples in ‘ADAPTS-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: hierarchicalClassify
  > ### Title: Hierarchical Deconvolution
  > ### Aliases: hierarchicalClassify
  > 
  > ### ** Examples
  > 
  > #This toy example 
  > library(ADAPTS)
  > fullLM22 <- ADAPTS::LM22[1:30, 1:4]
  > smallLM22 <- fullLM22[1:25,] 
  > 
  > cellCounts <- hierarchicalClassify(sigMatrix=smallLM22, geneExpr=fullLM22, toPred=fullLM22, 
  +     oneCore=TRUE, nPasses=10, method='DCQ')
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Quantile Normalizing geneExpr to match refExpr
  Setting method to: DCQ
  Error in missForest::missForest(dataMat, parallelize = parallelize) : 
    object 'results' not found
  missForest error
  Quantile Normalizing geneExpr to match refExpr
  Error in preprocessCore::normalize.quantiles.use.target(as.matrix(geneExpr),  : 
    Supplied argument should be a numeric matrix
  Calls: hierarchicalClassify -> estCellPercent -> <Anonymous>
  Execution halted

Package: FuzzyImputationTest
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # This file is part of the standard setup for testthat.
    > # It is recommended that you do not modify it.
    > #
    > # Where should you do additional test configuration?
    > # Learn more about the roles of various files in:
    > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
    > # * https://testthat.r-lib.org/articles/special-files.html
    > 
    > library(testthat)
    > library(FuzzyImputationTest)
    > 
    > test_check("FuzzyImputationTest")
    [ FAIL 1 | WARN 0 | SKIP 15 | PASS 80 ]
    
    ══ Skipped tests (15) ══════════════════════════════════════════════════════════
    • On CRAN (15): 'test-ApplyStatisticalTests.R:152:3',
      'test-CalculateFuzzyMeasures.R:152:3', 'test-ErrorMatrix.R:141:3',
      'test-FuzzifyMatrix.R:7:3', 'test-FuzzyImputation.R:30:3',
      'test-FuzzyNumbersToMatrix.R:16:3', 'test-ImputationDimp.R:30:3',
      'test-ImputationTests.R:152:3', 'test-IntroducingNA.R:7:3',
      'test-MatrixToFuzzyNumbers.R:14:3', 'test-MeasureAHD.R:26:3',
      'test-MeasureEuclidean.R:26:3', 'test-MeasureHSD.R:26:3',
      'test-RemoveNotFuzzy.R:50:3', 'test-StatisticalMeasures.R:152:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-MethodsComparison.R:61:3'): Function returns correct values ────
    Error in `ranger::ranger(x = obsX, y = obsY, num.trees = ntree, mtry = mtry, 
        replace = replace, sample.fraction = sf, min.bucket = if (!is.null(nodesize)) nodesize[1] else 5, 
        write.forest = TRUE, oob.error = TRUE, num.threads = if (!is.null(num.threads)) num.threads else if (parallelize == 
            "forests") foreach::getDoParWorkers() else NULL, verbose = FALSE)`: Error: No covariates found.
    Backtrace:
        ▆
     1. └─testthat::expect_snapshot(...) at test-MethodsComparison.R:61:3
     2.   └─rlang::cnd_signal(state$error)
    
    [ FAIL 1 | WARN 0 | SKIP 15 | PASS 80 ]
    Error: Test failures
    Execution halted

Package: missCompare
Check: tests
New result: ERROR
    Running ‘testthat.R’ [29s/49s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(missCompare)
    
    Attaching package: 'missCompare'
    
    The following object is masked from 'package:stats':
    
        simulate
    
    > 
    > test_check("missCompare")
    [1] "random replacement imputation - in progress"
    [1] "mice mixed imputation - in progress"
    [1] "mi imputation - in progress"
    starting worker pid=4119599 on localhost:11736 at 15:48:09.011
    starting worker pid=4119598 on localhost:11736 at 15:48:09.017
    [1] "missForest imputation - in progress"
    [1] "Hmisc aregImpute imputation - in progress"
    [1] "VIM kNN imputation - in progress"
    [1] "random replacement imputation - in progress"
    [1] "mice mixed imputation - in progress"
    [1] "mi imputation - in progress"
    starting worker pid=4119812 on localhost:11736 at 15:48:13.002
    starting worker pid=4119813 on localhost:11736 at 15:48:13.002
    [1] "missForest imputation - in progress"
    [1] "Hmisc aregImpute imputation - in progress"
    [1] "VIM kNN imputation - in progress"
    [1] "random replacement imputation - in progress"
    [1] "Median imputation - in progress"
    [1] "Mean imputation - in progress"
    [1] "missMDA regularized imputation - in progress"
    [1] "missMDA EM imputation - in progress"
    [1] "pcaMethods PPCA imputation - in progress"
    [1] "pcaMethods svdImpute imputation - in progress"
    [1] "pcaMethods BPCA imputation - in progress"
    [1] "pcaMethods NIPALS imputation - in progress"
    [1] "pcaMethods NLPCA imputation - in progress"
    [1] "mice mixed imputation - in progress"
    [1] "mi imputation - in progress"
    starting worker pid=4120356 on localhost:11736 at 15:48:20.955
    starting worker pid=4120355 on localhost:11736 at 15:48:20.958
    [1] "Amelia II imputation - in progress"
    [1] "missForest imputation - in progress"
    [1] "Hmisc aregImpute imputation - in progress"
    [1] "VIM kNN imputation - in progress"
    [1] "random replacement imputation - in progress"
    [1] "Median imputation - in progress"
    [1] "Mean imputation - in progress"
    [1] "missMDA regularized imputation - in progress"
    [1] "missMDA EM imputation - in progress"
    [1] "pcaMethods PPCA imputation - in progress"
    [1] "pcaMethods svdImpute imputation - in progress"
    [1] "pcaMethods BPCA imputation - in progress"
    [1] "pcaMethods NIPALS imputation - in progress"
    [1] "pcaMethods NLPCA imputation - in progress"
    [1] "mice mixed imputation - in progress"
    [1] "mi imputation - in progress"
    starting worker pid=4121218 on localhost:11736 at 15:48:28.421
    starting worker pid=4121217 on localhost:11736 at 15:48:28.428
    [1] "Amelia II imputation - in progress"
    [1] "missForest imputation - in progress"
    [1] "Hmisc aregImpute imputation - in progress"
    [1] "VIM kNN imputation - in progress"
    [1] "Median imputation - in progress"
    [1] "Mean imputation - in progress"
    [1] "missMDA regularized imputation - in progress"
    [1] "missMDA EM imputation - in progress"
    [1] "pcaMethods svdImpute imputation - in progress"
    [1] "pcaMethods BPCA imputation - in progress"
    [1] "pcaMethods NIPALS imputation - in progress"
    [1] "VIM kNN imputation - in progress"
    [1] "random replacement imputation - in progress"
    [1] "ITERATION 1 OF TOTAL 1 - IN PROGRESS"
    [1] "random replacement imputation - in progress"
    [1] "Median imputation - in progress"
    [1] "Mean imputation - in progress"
    [1] "missMDA regularized imputation - in progress"
    [1] "missMDA EM imputation - in progress"
    [1] "pcaMethods PPCA imputation - in progress"
    [1] "pcaMethods svdImpute imputation - in progress"
    [1] "pcaMethods BPCA imputation - in progress"
    [1] "pcaMethods NIPALS imputation - in progress"
    [1] "pcaMethods NLPCA imputation - in progress"
    [1] "mice mixed imputation - in progress"
    [1] "mi imputation - in progress"
    starting worker pid=4122650 on localhost:11736 at 15:48:44.265
    starting worker pid=4122651 on localhost:11736 at 15:48:44.271
    starting worker pid=4122836 on localhost:11736 at 15:48:46.955
    starting worker pid=4122835 on localhost:11736 at 15:48:46.964
    starting worker pid=4123041 on localhost:11736 at 15:48:49.634
    starting worker pid=4123042 on localhost:11736 at 15:48:49.641
    [1] "Amelia II imputation - in progress"
    [1] "missForest imputation - in progress"
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 35 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test.imp_simulation.R:17:3'): simulation runs without errors ──────
    `impute_simulated(...)` threw an error.
    Message: Error: One or more independent variables not found in data.
    Class:   simpleError/error/condition
    Backtrace:
         ▆
      1. ├─base::suppressWarnings(...) at test.imp_simulation.R:17:3
      2. │ └─base::withCallingHandlers(...)
      3. ├─testthat::expect_error(...)
      4. │ └─testthat:::quasi_capture(...)
      5. │   ├─testthat (local) .capture(...)
      6. │   │ └─base::withCallingHandlers(...)
      7. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      8. └─missCompare::impute_simulated(...)
      9.   ├─base::as.data.frame(test_missForest(sim$Simulated_matrix, list = res))
     10.   └─missCompare::test_missForest(sim$Simulated_matrix, list = res)
     11.     ├─utils::capture.output(results <- lapply(list, missForest_imp))
     12.     │ └─base::withVisible(...elt(i))
     13.     └─base::lapply(list, missForest_imp)
     14.       └─missCompare (local) FUN(X[[i]], ...)
     15.         └─missForest::missForest(X, maxiter = 10, ntree = 100, replace = TRUE)
     16.           ├─stats::predict(RF, data = misX)
     17.           └─ranger:::predict.ranger(RF, data = misX)
     18.             ├─stats::predict(...)
     19.             └─ranger:::predict.ranger.forest(...)
    
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 35 ]
    Error: Test failures
    Execution halted

Package: promor
Check: tests
New result: ERROR
    Running ‘testthat.R’ [8s/8s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(promor)
    > 
    > test_check("promor")
    0 empty row(s) removed.
    2 empty column(s) removed.
    1 protein(s) (rows) only identified by site removed.
    4 protein(s) identified by 2 or fewer unique peptides removed.
    Zeros have been replaced with NAs.
    Data have been log-transformed.
    4 proteins with higher than 33% NAs in at least one group removed.
    0 empty row(s) removed.
    4 empty column(s) removed.
    10 protein contaminant(s) (rows) removed.
    0 protein(s) identified by 2 or fewer unique peptides removed.
    Zeros have been replaced with NAs.
    Data have been log-transformed.
      missForest iteration 1 in progress...done!
        estimated error(s): 1.04084 
        difference(s): 0.0005251996 
        time: 0.014 seconds
    
      missForest iteration 2 in progress...done!
        estimated error(s): 1.067432 
        difference(s): 0.002956259 
        time: 0.007 seconds
    
     b  c  b  c 
    20 22 39 82 
     a  c  a  c 
    11 22 83 82 
     a  b  a  b 
    11 20 83 39 
    change in estimate:  0.02415548 
    change in estimate:  0.02101209 
    change in estimate:  0.01821531 
    change in estimate:  0.0157772 
    change in estimate:  0.01367284 
    change in estimate:  0.01186459 
    change in estimate:  0.01031291 
    change in estimate:  0.008980791 
    1 siginificantly differentially expressed proteins found.
    
    Testing glm...
    
    
    Testing rf...
    
    
    Testing svmRadial...
    
    
    Done!
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-protein_analysis.R:336:3'): impute_na works for rf ───────────
    impute_na(df, method = "RF", seed = 327) (`actual`) not equal to `df_rf` (`expected`).
    
    actual vs expected
                           a        b      c
    - actual[1, ]   12.00000 29.33333 82.000
    + expected[1, ] 12.00000 26.60000 82.000
    - actual[2, ]   34.00000 29.33333 40.000
    + expected[2, ] 34.00000 32.15000 40.000
      actual[3, ]   11.00000 39.00000 22.000
    - actual[4, ]   83.00000 29.00000 50.350
    + expected[4, ] 83.00000 29.00000 53.125
    - actual[5, ]   42.09000 20.00000 50.350
    + expected[5, ] 62.16333 20.00000 66.025
    - actual[6, ]   67.00000 29.33333 70.000
    + expected[6, ] 67.00000 22.30000 70.000
    
      `actual$a[2:6]`: 34.0 11.0 83.0 42.1 67.0
    `expected$a[2:6]`: 34.0 11.0 83.0 62.2 67.0
    
      `actual$b`: 29.3 29.3 39.0 29.0 20.0 29.3
    `expected$b`: 26.6 32.1 39.0 29.0 20.0 22.3
    
      `actual$c`: 82.0 40.0 22.0 50.4 50.4 70.0
    `expected$c`: 82.0 40.0 22.0 53.1 66.0 70.0
    Backtrace:
        ▆
     1. ├─base::suppressWarnings(...) at test-protein_analysis.R:336:3
     2. │ └─base::withCallingHandlers(...)
     3. └─testthat::expect_equal(...)
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
    Error: Test failures
    Execution halted