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---> Testing R-mlr3mbo
Executing: cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-mlr3mbo/R-mlr3mbo/work/mlr3mbo" && /opt/local/bin/R CMD check ./mlr3mbo_0.2.4.tar.gz --no-manual --no-build-vignettes
* using log directory ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-mlr3mbo/R-mlr3mbo/work/mlr3mbo/mlr3mbo.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
gcc-mp-13 (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
GNU Fortran (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘mlr3mbo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mlr3mbo’ version ‘0.2.4’
* 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 ‘mlr3mbo’ can be installed ... OK
* used C compiler: ‘gcc-mp-13 (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0’
* used SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
* checking installed package size ... 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ...
‘mlr3mbo.Rmd’ using ‘UTF-8’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘mlr3mbo.Rmd’
...
INFO [21:05:20.609] [bbotk] 1 1
> optimizer$surrogate$param_set$values$catch_errors = FALSE
> optimizer$optimize(instance)
INFO [21:05:20.635] [bbotk] Starting to optimize 1 parameter(s) with '<OptimizerMbo>' and '<TerminatorEvals> [n_evals=10, k=0]'
When sourcing ‘mlr3mbo.R’:
Error: missing value where TRUE/FALSE needed
Execution halted
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR
See
‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-mlr3mbo/R-mlr3mbo/work/mlr3mbo/mlr3mbo.Rcheck/00check.log’
for details.
Command failed: cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-mlr3mbo/R-mlr3mbo/work/mlr3mbo" && /opt/local/bin/R CMD check ./mlr3mbo_0.2.4.tar.gz --no-manual --no-build-vignettes
Exit code: 1
> library(knitr)
> opts_chunk$set(collapse = TRUE, comment = "#>")
> update_db = function() {
+ if (is.null(db$base) || is.null(db$aliases)) {
+ hdb = hsearch_db(package = unique(c(db$index, db$hosted)),
.... [TRUNCATED]
> ref = function(topic, text = topic, format = "markdown") {
+ strip_parenthesis = function(x) sub("\\(\\)$", "", x)
+ checkmate::assert_strin .... [TRUNCATED]
> ref_pkg = function(pkg, format = "markdown") {
+ checkmate::assert_string(pkg, pattern = "^[[:alnum:]._-]+$")
+ checkmate::assert_choice(for .... [TRUNCATED]
> cran_pkg = function(pkg, format = "markdown") {
+ checkmate::assert_string(pkg, pattern = "^[[:alnum:]._-]+$")
+ checkmate::assert_choice(fo .... [TRUNCATED]
> mlr_pkg = function(pkg, format = "markdown") {
+ checkmate::assert_string(pkg, pattern = "^[[:alnum:]._-]+$")
+ checkmate::assert_choice(for .... [TRUNCATED]
> gh_pkg = function(pkg, format = "markdown") {
+ checkmate::assert_string(pkg, pattern = "^[[:alnum:]_-]+/[[:alnum:]._-]+$")
+ checkmate::ass .... [TRUNCATED]
> db = new.env()
> db$index = c("base", "utils", "datasets", "data.table",
+ "stats")
> db$hosted = c("paradox", "mlr3misc", "mlr3", "mlr3data",
+ "mlr3db", "mlr3proba", "mlr3pipelines", "mlr3learners", "mlr3filters",
+ "bbotk ..." ... [TRUNCATED]
> lgr = NULL
> library(mlr3mbo)
> library(data.table)
> as.data.table(mlr_loop_functions)
Key: <key>
key label instance
<char> <char> <char>
1: bayesopt_ego Efficient Global Optimization single-crit
2: bayesopt_emo Multi-Objective EGO multi-crit
3: bayesopt_mpcl Multipoint Constant Liar single-crit
4: bayesopt_parego ParEGO multi-crit
5: bayesopt_smsego SMS-EGO multi-crit
man
<char>
1: mlr3mbo::mlr_loop_functions_ego
2: mlr3mbo::mlr_loop_functions_emo
3: mlr3mbo::mlr_loop_functions_mpcl
4: mlr3mbo::mlr_loop_functions_parego
5: mlr3mbo::mlr_loop_functions_smsego
> library(mlr3learners)
Loading required package: mlr3
> surrogate = SurrogateLearner$new(lrn("regr.km"))
> surrogate = srlrn(lrn("regr.km"))
> surrogate$learner
<LearnerRegrKM:regr.km>: Kriging
* Model: -
* Parameters: list()
* Packages: mlr3, mlr3learners, DiceKriging
* Predict Types: response, [se]
* Feature Types: logical, integer, numeric
* Properties: -
> surrogate$param_set
<ParamSet(4)>
Key: <id>
id class lower upper nlevels default
<char> <char> <num> <num> <num> <list>
1: assert_insample_perf ParamLgl NA NA 2 <NoDefault[0]>
2: catch_errors ParamLgl NA NA 2 <NoDefault[0]>
3: perf_measure ParamUty NA NA Inf <NoDefault[0]>
4: perf_threshold ParamDbl -Inf Inf Inf <NoDefault[0]>
parents value
<list> <list>
1: [NULL] FALSE
2: [NULL] TRUE
3: assert_insample_perf [NULL]
4: assert_insample_perf [NULL]
> as.data.table(mlr_acqfunctions)
Key: <key>
key label
<char> <char>
1: aei Augmented Expected Improvement
2: cb Lower / Upper Confidence Bound
3: ehvi Expected Hypervolume Improvement
4: ehvigh Expected Hypervolume Improvement via GH Quadrature
5: ei Expected Improvement
6: eips Expected Improvement Per Second
7: mean Posterior Mean
8: pi Probability Of Improvement
9: sd Posterior Standard Deviation
10: smsego SMS-EGO
man
<char>
1: mlr3mbo::mlr_acqfunctions_aei
2: mlr3mbo::mlr_acqfunctions_cb
3: mlr3mbo::mlr_acqfunctions_ehvi
4: mlr3mbo::mlr_acqfunctions_ehvigh
5: mlr3mbo::mlr_acqfunctions_ei
6: mlr3mbo::mlr_acqfunctions_eips
7: mlr3mbo::mlr_acqfunctions_mean
8: mlr3mbo::mlr_acqfunctions_pi
9: mlr3mbo::mlr_acqfunctions_sd
10: mlr3mbo::mlr_acqfunctions_smsego
> acq_function = AcqFunctionEI$new()
> acq_function = acqf("ei")
> acqf("cb")
<AcqFunctionCB:acq_cb>
Domain:
<ParamSet(0)>
Empty.
Codomain:
<Codomain(0)>
Empty.
Constants:
<ParamSet(1)>
id class lower upper nlevels default value
<char> <char> <num> <num> <num> <list> <list>
1: lambda ParamDbl 0 Inf Inf 2 2
> library(bbotk)
Loading required package: paradox
> acq_optimizer = AcqOptimizer$new(opt("random_search"),
+ terminator = trm("evals"))
> acq_optimizer = acqo(opt("random_search"), terminator = trm("evals"))
> acq_optimizer$optimizer
<OptimizerBatchRandomSearch>: Random Search
* Parameters: batch_size=1
* Parameter classes: ParamLgl, ParamInt, ParamDbl, ParamFct
* Properties: dependencies, single-crit, multi-crit
* Packages: bbotk
> acq_optimizer$terminator
<TerminatorEvals>: Number of Evaluation
* Parameters: n_evals=100, k=0
> acq_optimizer$param_set
<ParamSet(6)>
Key: <id>
id class lower upper nlevels default parents
<char> <char> <num> <num> <num> <list> <list>
1: catch_errors ParamLgl NA NA 2 TRUE [NULL]
2: logging_level ParamFct NA NA 6 warn [NULL]
3: n_candidates ParamInt 1 Inf Inf 1 [NULL]
4: skip_already_evaluated ParamLgl NA NA 2 TRUE [NULL]
5: warmstart ParamLgl NA NA 2 FALSE [NULL]
6: warmstart_size ParamInt 1 Inf Inf <NoDefault[0]> warmstart
value
<list>
1: TRUE
2: warn
3: 1
4: TRUE
5: FALSE
6: [NULL]
> optimizer = OptimizerMbo$new(bayesopt_ego, surrogate = surrogate,
+ acq_function = acq_function, acq_optimizer = acq_optimizer)
> optimizer = opt("mbo", loop_function = bayesopt_ego,
+ surrogate = surrogate, acq_function = acq_function, acq_optimizer = acq_optimizer)
> optimizer
<OptimizerMbo>: Model Based Optimization
* Parameter classes: ParamLgl, ParamInt, ParamDbl
* Properties: single-crit
* Packages: mlr3mbo, mlr3, mlr3learners, DiceKriging, bbotk
* Loop function: bayesopt_ego
* Surrogate: LearnerRegrKM
* Acquisition Function: AcqFunctionEI
* Acquisition Function Optimizer: (OptimizerBatchRandomSearch |
TerminatorEvals)
> as.data.table(mlr_result_assigners)
Key: <key>
key label man
<char> <char> <char>
1: archive Archive mlr3mbo::mlr_result_assigners_archive
2: surrogate Mean Surrogate Prediction mlr3mbo::mlr_result_assigners_surrogate
> result_assigner = ResultAssignerArchive$new()
> result_assigner = ras("archive")
> tuner = TunerMbo$new(bayesopt_ego, surrogate = surrogate,
+ acq_function = acq_function, acq_optimizer = acq_optimizer)
> mlr3misc::get_private(tuner)[[".optimizer"]]
<OptimizerMbo>: Model Based Optimization
* Parameter classes: ParamLgl, ParamInt, ParamDbl
* Properties: single-crit
* Packages: mlr3mbo, mlr3, mlr3learners, DiceKriging, bbotk
* Loop function: bayesopt_ego
* Surrogate: LearnerRegrKM
* Acquisition Function: AcqFunctionEI
* Acquisition Function Optimizer: (OptimizerBatchRandomSearch |
TerminatorEvals)
> set.seed(2906)
> domain = ps(x = p_dbl(lower = -1, upper = 1))
> codomain = ps(y = p_dbl(tags = "minimize"))
> objective_function = function(xs) {
+ list(y = xs$x^2)
+ }
> objective = ObjectiveRFun$new(fun = objective_function,
+ domain = domain, codomain = codomain)
> instance = OptimInstanceBatchSingleCrit$new(objective = objective,
+ terminator = trm("evals", n_evals = 10))
> initial_design = data.table(x = rep(1, 4))
> instance$eval_batch(initial_design)
INFO [21:05:14.351] [bbotk] Evaluating 4 configuration(s)
INFO [21:05:14.755] [bbotk] Result of batch 1:
INFO [21:05:14.802] [bbotk] x y
INFO [21:05:14.802] [bbotk] 1 1
INFO [21:05:14.802] [bbotk] 1 1
INFO [21:05:14.802] [bbotk] 1 1
INFO [21:05:14.802] [bbotk] 1 1
> surrogate = srlrn(default_gp())
> acq_function = acqf("ei")
> acq_optimizer = acqo(opt("random_search", batch_size = 1000),
+ terminator = trm("evals", n_evals = 1000))
> optimizer = opt("mbo", loop_function = bayesopt_ego,
+ surrogate = surrogate, acq_function = acq_function, acq_optimizer = acq_optimizer)
> optimizer$optimize(instance)
INFO [21:05:15.700] [bbotk] Starting to optimize 1 parameter(s) with '<OptimizerMbo>' and '<TerminatorEvals> [n_evals=10, k=0]'
WARN [21:05:16.084] [bbotk] missing value where TRUE/FALSE needed
INFO [21:05:16.088] [bbotk] surrogate_update_error / mbo_error / error / condition
INFO [21:05:16.092] [bbotk] Proposing a randomly sampled point
INFO [21:05:16.170] [bbotk] Evaluating 1 configuration(s)
INFO [21:05:16.224] [bbotk] Result of batch 2:
INFO [21:05:16.231] [bbotk] x y
INFO [21:05:16.231] [bbotk] 0.6742299 0.4545859
INFO [21:05:17.004] [bbotk] Evaluating 1 configuration(s)
INFO [21:05:17.051] [bbotk] Result of batch 3:
INFO [21:05:17.060] [bbotk] x x_domain acq_ei .already_evaluated y
INFO [21:05:17.060] [bbotk] 0.6686506 <list[1]> 0.04358144 FALSE 0.4470936
INFO [21:05:17.911] [bbotk] Evaluating 1 configuration(s)
INFO [21:05:17.955] [bbotk] Result of batch 4:
INFO [21:05:17.963] [bbotk] x x_domain acq_ei .already_evaluated y
INFO [21:05:17.963] [bbotk] 0.3883431 <list[1]> 0.1264502 FALSE 0.1508104
INFO [21:05:18.653] [bbotk] Evaluating 1 configuration(s)
INFO [21:05:18.698] [bbotk] Result of batch 5:
INFO [21:05:18.706] [bbotk] x x_domain acq_ei .already_evaluated y
INFO [21:05:18.706] [bbotk] -0.5325387 <list[1]> 0.2231679 FALSE 0.2835975
INFO [21:05:19.436] [bbotk] Evaluating 1 configuration(s)
INFO [21:05:19.482] [bbotk] Result of batch 6:
INFO [21:05:19.490] [bbotk] x x_domain acq_ei .already_evaluated y
INFO [21:05:19.490] [bbotk] 0.04818857 <list[1]> 0.1256543 FALSE 0.002322138
INFO [21:05:20.156] [bbotk] Evaluating 1 configuration(s)
INFO [21:05:20.201] [bbotk] Result of batch 7:
INFO [21:05:20.225] [bbotk] x x_domain acq_ei .already_evaluated y
INFO [21:05:20.225] [bbotk] -0.01951836 <list[1]> 0.002040261 FALSE 0.0003809664
INFO [21:05:20.458] [bbotk] Finished optimizing after 10 evaluation(s)
INFO [21:05:20.461] [bbotk] Result:
INFO [21:05:20.467] [bbotk] x x_domain y
INFO [21:05:20.467] [bbotk] <num> <list> <num>
INFO [21:05:20.467] [bbotk] -0.01951836 <list[1]> 0.0003809664
x x_domain y
<num> <list> <num>
1: -0.01951836 <list[1]> 0.0003809664
> instance$archive$data
x y x_domain timestamp batch_nr acq_ei
<num> <num> <list> <POSc> <int> <num>
1: 1.00000000 1.0000000000 <list[1]> 2024-09-15 21:05:14 1 NA
2: 1.00000000 1.0000000000 <list[1]> 2024-09-15 21:05:14 1 NA
3: 1.00000000 1.0000000000 <list[1]> 2024-09-15 21:05:14 1 NA
4: 1.00000000 1.0000000000 <list[1]> 2024-09-15 21:05:14 1 NA
5: 0.67422986 0.4545859064 <list[1]> 2024-09-15 21:05:16 2 NA
6: 0.66865060 0.4470936288 <list[1]> 2024-09-15 21:05:17 3 0.043581438
7: 0.38834314 0.1508103944 <list[1]> 2024-09-15 21:05:17 4 0.126450231
8: -0.53253872 0.2835974922 <list[1]> 2024-09-15 21:05:18 5 0.223167948
9: 0.04818857 0.0023221379 <list[1]> 2024-09-15 21:05:19 6 0.125654255
10: -0.01951836 0.0003809664 <list[1]> 2024-09-15 21:05:20 7 0.002040261
.already_evaluated
<lgcl>
1: NA
2: NA
3: NA
4: NA
5: NA
6: FALSE
7: FALSE
8: FALSE
9: FALSE
10: FALSE
> instance$archive$clear()
> instance$eval_batch(initial_design)
INFO [21:05:20.486] [bbotk] Evaluating 4 configuration(s)
INFO [21:05:20.603] [bbotk] Result of batch 1:
INFO [21:05:20.609] [bbotk] x y
INFO [21:05:20.609] [bbotk] 1 1
INFO [21:05:20.609] [bbotk] 1 1
INFO [21:05:20.609] [bbotk] 1 1
INFO [21:05:20.609] [bbotk] 1 1
> optimizer$surrogate$param_set$values$catch_errors = FALSE
> optimizer$optimize(instance)
INFO [21:05:20.635] [bbotk] Starting to optimize 1 parameter(s) with '<OptimizerMbo>' and '<TerminatorEvals> [n_evals=10, k=0]'
When sourcing ‘mlr3mbo.R’:
Error: missing value where TRUE/FALSE needed
Execution halted
The text was updated successfully, but these errors were encountered:
The text was updated successfully, but these errors were encountered: