CRAN Package Check Results for Package xgboost

Last updated on 2020-03-31 21:48:03 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0.2 169.25 219.24 388.49 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.0.2 168.69 167.60 336.29 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.0.2 531.44 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.0.2 494.50 NOTE
r-devel-windows-ix86+x86_64 0.90.0.2 205.00 257.00 462.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 1.0.0.2 257.00 278.00 535.00 NOTE
r-patched-linux-x86_64 1.0.0.2 161.42 195.25 356.67 NOTE
r-patched-solaris-x86 1.0.0.2 546.00 NOTE
r-release-linux-x86_64 1.0.0.2 154.10 186.54 340.64 NOTE
r-release-windows-ix86+x86_64 1.0.0.2 250.00 241.00 491.00 NOTE
r-release-osx-x86_64 1.0.0.2 ERROR
r-oldrel-windows-ix86+x86_64 1.0.0.2 327.00 287.00 614.00 ERROR
r-oldrel-osx-x86_64 0.90.0.2 NOTE

Check Details

Version: 1.0.0.2
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.0.2
Check: installed package size
Result: NOTE
     installed size is 36.5Mb
     sub-directories of 1Mb or more:
     libs 35.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64-gcc8, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.90.0.2
Check: installed package size
Result: NOTE
     installed size is 5.4Mb
     sub-directories of 1Mb or more:
     libs 4.6Mb
Flavors: r-devel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.90.0.2
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0.0.2
Check: examples
Result: ERROR
    Running examples in ‘xgboost-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: cb.gblinear.history
    > ### Title: Callback closure for collecting the model coefficients history
    > ### of a gblinear booster during its training.
    > ### Aliases: cb.gblinear.history
    >
    > ### ** Examples
    >
    > #### Binary classification:
    > #
    > # In the iris dataset, it is hard to linearly separate Versicolor class from the rest
    > # without considering the 2nd order interactions:
    > require(magrittr)
    Loading required package: magrittr
    > x <- model.matrix(Species ~ .^2, iris)[,-1]
    > colnames(x)
     [1] "Sepal.Length" "Sepal.Width"
     [3] "Petal.Length" "Petal.Width"
     [5] "Sepal.Length:Sepal.Width" "Sepal.Length:Petal.Length"
     [7] "Sepal.Length:Petal.Width" "Sepal.Width:Petal.Length"
     [9] "Sepal.Width:Petal.Width" "Petal.Length:Petal.Width"
    > dtrain <- xgb.DMatrix(scale(x), label = 1*(iris$Species == "versicolor"))
    OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
    OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
Flavor: r-release-osx-x86_64

Version: 1.0.0.2
Check: tests
Result: ERROR
     Running ‘testthat.R’ [3s/3s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(xgboost)
     >
     > test_check("xgboost")
     OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
     OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
Flavor: r-release-osx-x86_64

Version: 1.0.0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    sh: line 1: 3671 Abort trap: 6 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --slave > '/tmp/RtmpBdHUoK/filee527d3a7a1b' 2>&1 < '/tmp/RtmpBdHUoK/filee52a26c2d8'
    --- re-building ‘discoverYourData.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Loading required package: xgboost
    Loading required package: Matrix
    Loading required package: data.table
    Loading required package: vcd
    Loading required package: grid
    OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
    OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
    sh: line 1: 3678 Abort trap: 6 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --slave > '/tmp/RtmpBdHUoK/filee523888332d' 2>&1 < '/tmp/RtmpBdHUoK/filee5275d7ec59'
    --- re-building ‘xgboostPresentation.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Loading required package: xgboost
    OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
    OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
    sh: line 1: 3685 Abort trap: 6 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --slave > '/tmp/RtmpBdHUoK/filee52db7e297' 2>&1 < '/tmp/RtmpBdHUoK/filee52237d2e8a'
    --- re-building ‘xgboostfromJSON.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
    OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
    sh: line 1: 3694 Abort trap: 6 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --slave > '/tmp/RtmpBdHUoK/filee52516b1f5c' 2>&1 < '/tmp/RtmpBdHUoK/filee524fd7fac6'
    --- re-building ‘xgboost.Rnw’ using knitr
    Loading required package: knitr
    OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
    OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
    SUMMARY: processing the following files failed:
     ‘discoverYourData.Rmd’ ‘xgboostPresentation.Rmd’
     ‘xgboostfromJSON.Rmd’ ‘xgboost.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 1.0.0.2
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'xgboost-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: xgb.ggplot.deepness
    > ### Title: Plot model trees deepness
    > ### Aliases: xgb.ggplot.deepness xgb.plot.deepness
    >
    > ### ** Examples
    >
    >
    > data(agaricus.train, package='xgboost')
    >
    > # Change max_depth to a higher number to get a more significant result
    > bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_depth = 6,
    + eta = 0.1, nthread = 2, nrounds = 50, objective = "binary:logistic",
    + subsample = 0.5, min_child_weight = 2)
    [1] train-error:0.003838
    [2] train-error:0.001996
    [3] train-error:0.001228
    [4] train-error:0.001228
    [5] train-error:0.001228
    [6] train-error:0.001228
    [7] train-error:0.001228
    [8] train-error:0.001228
    [9] train-error:0.001228
    [10] train-error:0.001228
    [11] train-error:0.001228
    [12] train-error:0.001228
    [13] train-error:0.001228
    [14] train-error:0.001228
    [15] train-error:0.001228
    [16] train-error:0.001228
    [17] train-error:0.001228
    [18] train-error:0.001228
    [19] train-error:0.001228
    [20] train-error:0.001228
    [21] train-error:0.001228
    [22] train-error:0.001228
    [23] train-error:0.001228
    [24] train-error:0.001228
    [25] train-error:0.001228
    [26] train-error:0.001228
    [27] train-error:0.001228
    [28] train-error:0.001228
    [29] train-error:0.001228
    [30] train-error:0.001228
    [31] train-error:0.001228
    [32] train-error:0.001228
    [33] train-error:0.001228
    [34] train-error:0.001228
    [35] train-error:0.001228
    [36] train-error:0.001228
    [37] train-error:0.001228
    [38] train-error:0.001228
    [39] train-error:0.001228
    [40] train-error:0.000000
    [41] train-error:0.000000
    [42] train-error:0.000000
    [43] train-error:0.000000
    [44] train-error:0.000000
    [45] train-error:0.000000
    [46] train-error:0.000000
    [47] train-error:0.000000
    [48] train-error:0.000000
    [49] train-error:0.000000
    [50] train-error:0.000000
    >
    > xgb.plot.deepness(bst)
    > xgb.ggplot.deepness(bst)
    Error in update_tibble_attrs(x, ...) :
     object 'tibble_update_attrs' not found
    Calls: xgb.ggplot.deepness ... recycle_columns -> new_tibble -> update_tibble_attrs
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.0.0.2
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [45s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(xgboost)
     >
     > test_check("xgboost")
     [1] train-rmse:1.678965
     [2] train-rmse:1.678965
     [3] train-rmse:1.524624
     [4] train-rmse:1.441523
     [5] train-rmse:1.437758
     [6] train-rmse:1.377895
     [7] train-rmse:1.305894
     [8] train-rmse:1.336120
     [9] train-rmse:1.316072
     [10] train-rmse:1.316031
     [11] train-rmse:1.319404
     [12] train-rmse:1.235097
     [13] train-rmse:1.225430
     [14] train-rmse:1.221079
     [15] train-rmse:1.235220
     [16] train-rmse:1.219153
     [17] train-rmse:1.226439
     [18] train-rmse:1.235026
     [19] train-rmse:1.244651
     [20] train-rmse:1.253197
     [21] train-rmse:1.262494
     [22] train-rmse:1.272865
     [23] train-rmse:1.276073
     [24] train-rmse:1.277041
     [25] train-rmse:1.287974
     [26] train-rmse:1.289816
     [27] train-rmse:1.292365
     [28] train-rmse:1.282785
     [29] train-rmse:1.283805
     [30] train-rmse:1.290661
     [31] train-rmse:1.289439
     [32] train-rmse:1.281995
     [1] train-error:0.047136
     [1] train-error:0.046523+0.000910 test-error:0.046524+0.003641
     [2] train-error:0.022263+0.000720 test-error:0.022264+0.002881
     [1] train-error:0.046522+0.001311 test-error:0.046523+0.005246
     [2] train-error:0.022263+0.000485 test-error:0.022263+0.001943
     [1] train-logloss:0.380601
     [2] train-logloss:0.247327
     [3] train-logloss:0.175046
     [4] train-logloss:0.122303
     [5] train-logloss:0.089890
     [1] train-logloss:0.497351
     [2] train-logloss:0.357289
     [3] train-logloss:0.257217
     [4] train-logloss:0.184524
     [5] train-logloss:0.132112
     [1] train-auc:0.900000 test-auc:0.800000
     [1] eval-error:0.042831 train-error:0.046522
     [2] eval-error:0.021726 train-error:0.022263
     [1] eval-error:0.042831 train-error:0.046522
     [2] eval-error:0.021726 train-error:0.022263
     [1] train-error:0.046522
     [2] train-error:0.022263
     [1] train-error:0.333333
     [1] train-rmse:1.940066
     [2] train-rmse:1.560864
     [3] train-rmse:1.277414
     [4] train-rmse:1.068562
     [5] train-rmse:0.903897
     [6] train-rmse:0.763228
     [7] train-rmse:0.664924
     [8] train-rmse:0.570358
     [9] train-rmse:0.507416
     [10] train-rmse:0.458599
     [11] train-rmse:0.394349
     [12] train-rmse:0.355794
     [13] train-rmse:0.305484
     [14] train-rmse:0.271176
     [15] train-rmse:0.259943
     [16] train-rmse:0.238429
     [17] train-rmse:0.228003
     [18] train-rmse:0.212117
     [19] train-rmse:0.187830
     [20] train-rmse:0.173381
     [21] train-rmse:0.164001
     [22] train-rmse:0.156113
     [23] train-rmse:0.143242
     [24] train-rmse:0.130215
     [25] train-rmse:0.120160
     [26] train-rmse:0.112119
     [27] train-rmse:0.104753
     [28] train-rmse:0.096786
     [29] train-rmse:0.089361
     [30] train-rmse:0.083706
     [1] train-rmse:1.940066
     [2] train-rmse:1.675038
     [3] train-rmse:1.462383
     [4] train-rmse:1.283198
     [5] train-rmse:1.155542
     [6] train-rmse:1.049559
     [7] train-rmse:0.942910
     [8] train-rmse:0.859371
     [9] train-rmse:0.774970
     [10] train-rmse:0.725452
     [11] train-rmse:0.679127
     [12] train-rmse:0.628614
     [13] train-rmse:0.594549
     [14] train-rmse:0.535545
     [15] train-rmse:0.485623
     [16] train-rmse:0.460187
     [17] train-rmse:0.413632
     [18] train-rmse:0.403692
     [19] train-rmse:0.385314
     [20] train-rmse:0.366654
     [21] train-rmse:0.354532
     [22] train-rmse:0.326526
     [23] train-rmse:0.316875
     [24] train-rmse:0.301910
     [25] train-rmse:0.285458
     [26] train-rmse:0.275437
     [27] train-rmse:0.267556
     [28] train-rmse:0.263727
     [29] train-rmse:0.253460
     [30] train-rmse:0.235433
     -- 1. Error: xgb.plot.tree works with and without feature names (@test_helpers.R
     object 'tibble_update_attrs' not found
     Backtrace:
     1. xgboost::xgb.plot.tree(feature_names = feature.names, model = bst.Tree)
     5. DiagrammeR::create_graph(...)
     9. dplyr::tibble(node = as.integer(NA))
     10. tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
     11. tibble::new_tibble(output, nrow = first_size %||% 0L)
     12. tibble:::update_tibble_attrs(x, ...)
    
     -- 2. Error: xgb.plot.multi.trees works with and without feature names (@test_he
     object 'tibble_update_attrs' not found
     Backtrace:
     1. xgboost::xgb.plot.multi.trees(...)
     5. DiagrammeR::create_graph(...)
     9. dplyr::tibble(node = as.integer(NA))
     10. tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
     11. tibble::new_tibble(output, nrow = first_size %||% 0L)
     12. tibble:::update_tibble_attrs(x, ...)
    
     -- 3. Error: xgb.plot.deepness works (@test_helpers.R#351) --------------------
     object 'tibble_update_attrs' not found
     Backtrace:
     1. xgboost::xgb.ggplot.deepness(model = bst.Tree)
     2. xgboost:::multiplot(p1, p2, cols = 1)
     4. ggplot2:::print.ggplot(...)
     6. ggplot2:::ggplot_build.ggplot(x)
     7. ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
     8. ggplot2:::f(l = layers[[i]], d = data[[i]])
     9. l$compute_aesthetics(d, plot)
     10. ggplot2:::f(..., self = self)
     11. ggplot2:::as_gg_data_frame(evaled)
     14. tibble:::as_tibble.list(x)
     15. tibble:::lst_to_tibble(x, .rows, .name_repair, col_lengths(x))
     16. tibble:::recycle_columns(x, .rows, lengths)
     17. tibble::new_tibble(x, nrow = nrow, subclass = NULL)
     18. tibble:::update_tibble_attrs(x, ...)
    
     == testthat results ===========================================================
     [ OK: 972 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
     1. Error: xgb.plot.tree works with and without feature names (@test_helpers.R#338)
     2. Error: xgb.plot.multi.trees works with and without feature names (@test_helpers.R#343)
     3. Error: xgb.plot.deepness works (@test_helpers.R#351)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64