* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/EIX.Rcheck’ * using R Under development (unstable) (2020-10-07 r79311) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘EIX/DESCRIPTION’ ... OK * this is package ‘EIX’ version ‘1.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘lightgbm’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘EIX’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘MASS’ ‘Matrix’ ‘tidyr’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [14s/14s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [16s/16s] OK * checking examples with --run-donttest ... ERROR Running examples in ‘EIX-Ex.R’ failed The error most likely occurred in: > ### Name: importance > ### Title: Importance of variables and interactions in the model > ### Aliases: importance > > ### ** Examples > > library("EIX") > library("Matrix") > sm <- sparse.model.matrix(left ~ . - 1, data = HR_data) > > library("xgboost") > param <- list(objective = "binary:logistic", max_depth = 2) > xgb_model <- xgboost(sm, params = param, label = HR_data[, left] == 1, nrounds = 25, verbose=0) > > imp <- importance(xgb_model, sm, option = "both") > imp Feature sumGain sumCover meanGain meanCover 1: satisfaction_level 9549.00 33480.0 502.60 1762.0 2: time_spend_company 3902.00 16670.0 354.70 1516.0 3: number_project 3645.00 11670.0 331.40 1061.0 4: last_evaluation 993.00 9803.0 141.90 1400.0 5: last_evaluation:average_montly_hours 702.10 697.7 702.10 697.7 6: last_evaluation:time_spend_company 564.30 665.5 564.30 665.5 7: last_evaluation:satisfaction_level 502.90 1374.0 502.90 1374.0 8: average_montly_hours 487.50 6995.0 97.50 1399.0 9: last_evaluation:number_project 390.20 1163.0 390.20 1163.0 10: satisfaction_level:time_spend_company 332.20 753.6 332.20 753.6 11: average_montly_hours:time_spend_company 262.60 549.2 262.60 549.2 12: average_montly_hours:last_evaluation 249.10 837.4 249.10 837.4 13: Work_accident 198.00 2820.0 98.99 1410.0 14: satisfaction_level:average_montly_hours 168.40 496.0 168.40 496.0 15: salarylow 90.24 1444.0 90.24 1444.0 16: satisfaction_level:number_project 87.10 1096.0 87.10 1096.0 17: time_spend_company:last_evaluation 86.27 1242.0 86.27 1242.0 18: salarymedium 45.28 709.2 45.28 709.2 frequency mean5Gain 1: 19 1513.00 2: 11 670.40 3: 11 697.40 4: 7 183.00 5: 1 702.10 6: 1 564.30 7: 1 502.90 8: 5 97.50 9: 1 390.20 10: 1 332.20 11: 1 262.60 12: 1 249.10 13: 2 98.99 14: 1 168.40 15: 1 90.24 16: 1 87.10 17: 1 86.27 18: 1 45.28 > plot(imp, top = 10) > > imp <- importance(xgb_model, sm, option = "variables") > imp Feature numberOfRoots weightedRoot meanDepth sumGain sumCover 1: satisfaction_level 11 8.9340 0.1598 10050.00 34850.0 2: time_spend_company 3 0.1399 0.9042 5061.00 18640.0 3: number_project 0 0.0000 1.0000 4122.00 13930.0 4: average_montly_hours 3 0.0920 0.7652 1358.00 8189.0 5: last_evaluation 5 0.4139 0.3519 1328.00 11880.0 6: Work_accident 2 0.0381 0.0000 198.00 2820.0 7: salarylow 1 0.0087 0.0000 90.24 1444.0 8: salarymedium 0 0.0000 1.0000 45.28 709.2 meanGain meanCover frequency mean5Gain 1: 502.60 1743.0 20 1513.00 2: 361.50 1332.0 14 751.50 3: 317.10 1071.0 13 721.70 4: 194.00 1170.0 7 241.70 5: 147.60 1320.0 9 208.60 6: 98.99 1410.0 2 98.99 7: 90.24 1444.0 1 90.24 8: 45.28 709.2 1 45.28 > plot(imp, top = nrow(imp)) > > imp <- importance(xgb_model, sm, option = "interactions") > imp Feature sumGain sumCover meanGain meanCover 1: last_evaluation:average_montly_hours 702.10 697.7 702.10 697.7 2: last_evaluation:time_spend_company 564.30 665.5 564.30 665.5 3: last_evaluation:satisfaction_level 502.90 1374.0 502.90 1374.0 4: last_evaluation:number_project 390.20 1163.0 390.20 1163.0 5: satisfaction_level:time_spend_company 332.20 753.6 332.20 753.6 6: average_montly_hours:time_spend_company 262.60 549.2 262.60 549.2 7: average_montly_hours:last_evaluation 249.10 837.4 249.10 837.4 8: satisfaction_level:average_montly_hours 168.40 496.0 168.40 496.0 9: satisfaction_level:number_project 87.10 1096.0 87.10 1096.0 10: time_spend_company:last_evaluation 86.27 1242.0 86.27 1242.0 frequency mean5Gain 1: 1 702.10 2: 1 564.30 3: 1 502.90 4: 1 390.20 5: 1 332.20 6: 1 262.60 7: 1 249.10 8: 1 168.40 9: 1 87.10 10: 1 86.27 > plot(imp, top = nrow(imp)) > > imp <- importance(xgb_model, sm, option = "variables") > imp Feature numberOfRoots weightedRoot meanDepth sumGain sumCover 1: satisfaction_level 11 8.9340 0.1598 10050.00 34850.0 2: time_spend_company 3 0.1399 0.9042 5061.00 18640.0 3: number_project 0 0.0000 1.0000 4122.00 13930.0 4: average_montly_hours 3 0.0920 0.7652 1358.00 8189.0 5: last_evaluation 5 0.4139 0.3519 1328.00 11880.0 6: Work_accident 2 0.0381 0.0000 198.00 2820.0 7: salarylow 1 0.0087 0.0000 90.24 1444.0 8: salarymedium 0 0.0000 1.0000 45.28 709.2 meanGain meanCover frequency mean5Gain 1: 502.60 1743.0 20 1513.00 2: 361.50 1332.0 14 751.50 3: 317.10 1071.0 13 721.70 4: 194.00 1170.0 7 241.70 5: 147.60 1320.0 9 208.60 6: 98.99 1410.0 2 98.99 7: 90.24 1444.0 1 90.24 8: 45.28 709.2 1 45.28 > plot(imp, top = NULL, radar = FALSE, xmeasure = "sumCover", ymeasure = "sumGain") > > ## No test: > library(lightgbm) Error in library(lightgbm) : there is no package called ‘lightgbm’ Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [37s/37s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/data/blackswan/ripley/R/packages/tests-devel/EIX.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:06.76, 119.64 + 8.12