* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/spartan.Rcheck’ * using R Under development (unstable) (2019-12-29 r77627) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘spartan/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spartan’ version ‘3.0.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘spartan’ can be installed ... [14s/20s] 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 use of S3 registration ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘gplots’ 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 ... [22s/26s] 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 ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [46s/52s] [47s/53s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > Sys.setenv("R_TESTS"="") > library(testthat) > library(spartan) Loading required package: randomForest randomForest 4.6-14 Type rfNews() to see new features/changes/bug fixes. Loading required package: e1071 > options(warn = 2) > test_check("spartan", report="summary") Test of Spartan Consistency Analysis: ..S......................................................................................... Test of A-Test calculation utilities: .......... Test of Spartan eFAST Analysis: .........................................................................................................................................trying URL 'http://www.kieranalden.info/spartan/test_data/netlogo_efast.zip' Content type 'application/zip' length 505212 bytes (493 KB) ================================================== downloaded 493 KB ...... Test of Spartan eFAST Sampling: ...... Test of Spartan Netlogo eFAST Sampling: S Test of Spartan Emulation Sensitivity Analysis: SS Testing Spartan Utilities Class: . Test of Spartan Evolution Utilities: SS....... Test of Error Checking of Spartan Function Arguments: ............................................................................................................................. Test of Spartan LHC Analysis: ....................................................................................1................ Testing Spartan LHC Plotting Utilities Class: ................................................................ Test of Spartan Latin-Hypercube Sampling: .....S............ Test of Spartan Netlogo Latin-Hypercube Sampling: SS Test Neural Network Utilities: SSSSSSSSSS Test of Spartan Robustness Analysis: .........................................23....................................... Test of Spartan Robustness Sampling: ........S Testing Spartan Utilities Class: .................................... ══ Skipped ═════════════════════════════════════════════════════════════════════ 1. read_simulation_results (@test_aleatory_analysis.R#19) - Reason: On CRAN 2. efast_generate_sample_netlogo (@test_efast_sampling_netlogo.R#7) - Reason: On CRAN 3. emulate_efast_sampled_parameters (@test_emulation_sensitivity_analysis.R#6) - Reason: On CRAN 4. emulate_lhc_sampled_parameters (@test_emulation_sensitivity_analysis.R#42) - Reason: On CRAN 5. emulator_parameter_evolution (@test_evolution.R#6) - Reason: On CRAN 6. nsga2_set_user_params (@test_evolution.R#40) - Reason: On CRAN 7. sample_parameter_space (@test_lhc_sampling.R#17) - Reason: On CRAN 8. process_netlogo_parameter_range_info (@test_lhc_sampling_netlogo.R#6) - Reason: On CRAN 9. lhc_generate_lhc_sample_netlogo (@test_lhc_sampling_netlogo.R#21) - Reason: On CRAN 10. determine_optimal_neural_network_structure (@test_neural_network_utilities.R#7) - Reason: On CRAN 11. kfoldCrossValidation (@test_neural_network_utilities.R#32) - Reason: On CRAN 12. analysenetwork_structures (@test_neural_network_utilities.R#55) - Reason: On CRAN 13. createAndEvaluateFolds (@test_neural_network_utilities.R#81) - Reason: On CRAN 14. updateErrorForStructure (@test_neural_network_utilities.R#107) - Reason: On CRAN 15. select_suitable_structure (@test_neural_network_utilities.R#137) - Reason: On CRAN 16. calculate_fold_MSE (@test_neural_network_utilities.R#154) - Reason: On CRAN 17. createTrainingFold (@test_neural_network_utilities.R#190) - Reason: On CRAN 18. createTestFold (@test_neural_network_utilities.R#213) - Reason: On CRAN 19. create_neural_network (@test_neural_network_utilities.R#236) - Reason: On CRAN 20. oat_generate_netlogo_behaviour_space_XML (@test_robustness_sampling.R#56) - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure: lhc_generateLHCSummary_overTime (@test_lhc_analysis.R#342) ───── toString(result[1, ]) not equal to "63.8870291068684, 0.738687975020334, 0.150462160198018, 0.0299383036779426, 0.866686868487718, 0.569160230072564, 1.91462180475669, 28.5928070217056". 1/1 mismatches x[1]: "63.8870291068684, 0.738687975020334, 0.150462160198018, 0.029938303677942 x[1]: 6, 0.866686868487718, 0.569160230072564, 1.9146218047567, 28.5928070217056 x[1]: " y[1]: "63.8870291068684, 0.738687975020334, 0.150462160198018, 0.029938303677942 y[1]: 6, 0.866686868487718, 0.569160230072564, 1.91462180475669, 28.592807021705 y[1]: 6" ── 2. Failure: compare_all_values_of_parameter_to_baseline (@test_robustness_ana toString(parameter_results[, 5]) not equal to "0.0102491184165624, 0.0251285044106754, 0.0999416399182959, 0.231847664519616, 0.375974968256848, 0.630726093419215, 0.748333446320024, 0.816536104689008, 0.867025964341401, 0.898266219239374, 0.908655249040426, 0.926498881431767, 0.942322417909103". 1/1 mismatches x[1]: "0.0102491184165624, 0.0251285044106754, 0.0999416399182959, 0.23184766451 x[1]: 9616, 0.375974968256848, 0.630726093419215, 0.748333446320024, 0.816536104 x[1]: 689008, 0.8670259643414, 0.898266219239374, 0.908655249040426, 0.926498881 x[1]: 431767, 0.942322417909103" y[1]: "0.0102491184165624, 0.0251285044106754, 0.0999416399182959, 0.23184766451 y[1]: 9616, 0.375974968256848, 0.630726093419215, 0.748333446320024, 0.816536104 y[1]: 689008, 0.867025964341401, 0.898266219239374, 0.908655249040426, 0.9264988 y[1]: 81431767, 0.942322417909103" ── 3. Failure: compare_all_values_of_parameter_to_baseline (@test_robustness_ana toString(parameter_results[, 6]) not equal to "0.989750881583438, 0.974871495589325, 0.900058360081704, 0.768152335480384, 0.624025031743152, 0.630726093419215, 0.748333446320024, 0.816536104689008, 0.867025964341401, 0.898266219239374, 0.908655249040426, 0.926498881431767, 0.942322417909103". 1/1 mismatches x[1]: "0.989750881583438, 0.974871495589325, 0.900058360081704, 0.76815233548038 x[1]: 4, 0.624025031743152, 0.630726093419215, 0.748333446320024, 0.816536104689 x[1]: 008, 0.8670259643414, 0.898266219239374, 0.908655249040426, 0.926498881431 x[1]: 767, 0.942322417909103" y[1]: "0.989750881583438, 0.974871495589325, 0.900058360081704, 0.76815233548038 y[1]: 4, 0.624025031743152, 0.630726093419215, 0.748333446320024, 0.816536104689 y[1]: 008, 0.867025964341401, 0.898266219239374, 0.908655249040426, 0.9264988814 y[1]: 31767, 0.942322417909103" ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [7s/10s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘Built_Emulation_RF_GLM.Rda’ ‘Ensemble_Testing_Velocity.pdf’ ‘GLM_TestSet_Velocity.pdf’ ‘GLM_TrainingSet_Velocity.pdf’ ‘RF_TestSet_Velocity.pdf’ ‘RF_TrainingSet_Velocity.pdf’ ‘built_ensemble.Rda’ ‘partitioned_data.Rda’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/data/gannet/ripley/R/packages/tests-noLD/spartan.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:21.91, 145.43 + 8.61