• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘miceFast/DESCRIPTION’ ... OK
• this is package ‘miceFast’ version ‘0.8.5’
• package encoding: UTF-8
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• checking whether package ‘miceFast’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’
• checking package directory ... OK
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• checking examples ... [3s/5s] ERROR Running examples in ‘miceFast-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fill_NA > ### Title: 'fill_NA' function for the imputations purpose. > ### Aliases: fill_NA fill_NA.data.frame fill_NA.data.table fill_NA.matrix > > ### ** Examples > > library(miceFast) > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’:     filter, lag The following objects are masked from ‘package:base’:     intersect, setdiff, setequal, union > library(data.table) Attaching package: ‘data.table’ The following objects are masked from ‘package:dplyr’:     between, first, last The following object is masked from ‘package:base’:     %notin% > ### Data > # airquality dataset with additional variables > data(air_miss) > ### Intro: dplyr > # IMPUTATIONS > air_miss <- air_miss %>% + # Imputations with a grouping option (models are separately assessed for each group) + # taking into account provided weights + group_by(groups) %>% + do(mutate(., Solar_R_imp = fill_NA( + x = ., + model = "lm_pred", + posit_y = "Solar.R", + posit_x = c("Wind", "Temp", "Intercept"), + w = .[["weights"]] + ))) %>% + ungroup() %>% + # Imputations - discrete variable + mutate(x_character_imp = fill_NA( + x = ., + model = "lda", + posit_y = "x_character", + posit_x = c("Wind", "Temp") + )) %>% + # logreg was used because almost log-normal distribution of Ozone + # imputations around mean + mutate(Ozone_imp1 = fill_NA( + x = ., + model = "lm_bayes", + posit_y = "Ozone", + posit_x = c("Intercept"), + logreg = TRUE + )) %>% + # imputations using positions - Intercept, Temp + mutate(Ozone_imp2 = fill_NA( + x = ., + model = "lm_bayes", + posit_y = 1, + posit_x = c(4, 6), + logreg = TRUE + )) %>% + # multiple imputations (average of x30 imputations) + # with a factor independent variable, weights and logreg options + mutate(Ozone_imp3 = fill_NA_N( + x = ., + model = "lm_noise", + posit_y = "Ozone", + posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), + w = .[["weights"]], + logreg = TRUE, + k = 30 + )) %>% + mutate(Ozone_imp4 = fill_NA_N( + x = ., + model = "lm_bayes", + posit_y = "Ozone", + posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), + w = .[["weights"]], + logreg = TRUE, + k = 30 + )) %>% + group_by(groups) %>% + do(mutate(., Ozone_imp5 = fill_NA( + x = ., + model = "lm_pred", + posit_y = "Ozone", + posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), + w = .[["weights"]], + logreg = TRUE + ))) %>% + do(mutate(., Ozone_imp6 = fill_NA_N( + x = ., + model = "pmm", + posit_y = "Ozone", + posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), + w = .[["weights"]], + logreg = TRUE, + k = 20 + ))) %>% + ungroup() %>% + # Average of a few methods + mutate(Ozone_imp_mix = rowMeans(select(., starts_with("Ozone_imp")))) %>% + # Protecting against collinearity or low number of observations - across small groups + # Be carful when using a grouping option + # because of lack of protection against collinearity or low number of observations. + # There could be used a tryCatch(fill_NA(...),error=function(e) return(...)) + group_by(groups) %>% + do(mutate(., Ozone_chac_imp = tryCatch( + fill_NA( + x = ., + model = "lda", + posit_y = "Ozone_chac", + posit_x = c( + "Intercept", + "Month", + "Day", + "Temp", + "x_character_imp" + ), + w = .[["weights"]] + ), + error = function(e) .[["Ozone_chac"]] + ))) %>% + ungroup() > > # Sample of results > air_miss[which(is.na(air_miss[, 1]))[1:5], ] # A tibble: 5 × 23   Ozone Solar.R Wind Temp Day Intercept index weights groups x_character   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <fct> <chr> 1 NA NA 14.3 56 5 1 5 0.995 5 <NA> 2 NA 194 8.6 69 10 1 10 0.995 5 (140,210] 3 NA 66 16.6 57 25 1 25 1.01 5 (0,70] 4 NA 266 14.9 58 26 1 26 1.00 5 (210,280] 5 NA NA 8 57 27 1 27 1.000 5 <NA> # ℹ 13 more variables: Ozone_chac <chr>, Ozone_f <fct>, Ozone_high <lgl>, # Solar_R_imp <dbl>, x_character_imp <chr>, Ozone_imp1 <dbl>, # Ozone_imp2 <dbl>, Ozone_imp3 <dbl>, Ozone_imp4 <dbl>, Ozone_imp5 <dbl>, # Ozone_imp6 <dbl>, Ozone_imp_mix <dbl>, Ozone_chac_imp <chr> > > ### Intro: data.table > # IMPUTATIONS > # Imputations with a grouping option (models are separately assessed for each group) > # taking into account provided weights > data(air_miss) > setDT(air_miss) > air_miss[, Solar_R_imp := fill_NA_N( + x = .SD, + model = "lm_bayes", + posit_y = "Solar.R", + posit_x = c("Wind", "Temp", "Intercept"), + w = .SD[["weights"]], + k = 100 + ), by = .(groups)] %>% + # Imputations - discrete variable + .[, x_character_imp := fill_NA( + x = .SD, + model = "lda", + posit_y = "x_character", + posit_x = c("Wind", "Temp", "groups") + )] %>% + # logreg was used because almost log-normal distribution of Ozone + # imputations around mean + .[, Ozone_imp1 := fill_NA( + x = .SD, + model = "lm_bayes", + posit_y = "Ozone", + posit_x = c("Intercept"), + logreg = TRUE + )] %>% + # imputations using positions - Intercept, Temp + .[, Ozone_imp2 := fill_NA( + x = .SD, + model = "lm_bayes", + posit_y = 1, + posit_x = c(4, 6), + logreg = TRUE + )] %>% + # model with a factor independent variable + # multiple imputations (average of x30 imputations) + # with a factor independent variable, weights and logreg options + .[, Ozone_imp3 := fill_NA_N( + x = .SD, + model = "lm_noise", + posit_y = "Ozone", + posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), + w = .SD[["weights"]], + logreg = TRUE, + k = 30 + )] %>% + .[, Ozone_imp4 := fill_NA_N( + x = .SD, + model = "lm_bayes", + posit_y = "Ozone", + posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), + w = .SD[["weights"]], + logreg = TRUE, + k = 30 + )] %>% + .[, Ozone_imp5 := fill_NA( + x = .SD, + model = "lm_pred", + posit_y = "Ozone", + posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), + w = .SD[["weights"]], + logreg = TRUE + ), .(groups)] %>% + .[, Ozone_imp6 := fill_NA_N( + x = .SD, + model = "pmm", + posit_y = "Ozone", + posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), + w = .SD[["weights"]], + logreg = TRUE, + k = 10 + ), .(groups)] %>% + # Average of a few methods + .[, Ozone_imp_mix := apply(.SD, 1, mean), .SDcols = Ozone_imp1:Ozone_imp6] %>% + # Protecting against collinearity or low number of observations - across small groups + # Be carful when using a data.table grouping option + # because of lack of protection against collinearity or low number of observations. + # There could be used a tryCatch(fill_NA(...),error=function(e) return(...)) + + .[, Ozone_chac_imp := tryCatch( + fill_NA( + x = .SD, + model = "lda", + posit_y = "Ozone_chac", + posit_x = c( + "Intercept", + "Month", + "Day", + "Temp", + "x_character_imp" + ), + w = .SD[["weights"]] + ), + error = function(e) .SD[["Ozone_chac"]] + ), .(groups)] Error in `[.data.table`(air_miss, , `:=`(Solar_R_imp, fill_NA_N(x = .SD, :   attempt access index 13/13 in VECTOR_ELT Calls: %>% -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/12s] ERROR   Running ‘testthat.R’ [9s/11s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > Sys.setenv("OMP_THREAD_LIMIT" = 2)   >   > library(testthat)   > library(miceFast)   > library(data.table)      Attaching package: 'data.table'      The following object is masked from 'package:base':          %notin%      > library(dplyr)      Attaching package: 'dplyr'      The following objects are masked from 'package:data.table':          between, first, last      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      > library(magrittr)      Attaching package: 'magrittr'      The following objects are masked from 'package:testthat':          equals, is_less_than, not      >   > test_check("miceFast")   Saving _problems/test-fill_NA_funcs-474.R   Saving _problems/test-fill_NA_funcs-599.R   [ FAIL 2 | WARN 3 | SKIP 0 | PASS 102 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-fill_NA_funcs.R:379:3'): data.table pipeline fill_NA_N, fill_NA accuracy - con ──   Error in ``[.data.table`(data_DT, , `:=`(y_imp, fill_NA(x = .SD, model = "lm_pred", posit_y = "y", posit_x = c("Intercept", "x2", "x3", "x4"), w = .SD[["weights"]])), by = .(group))`: attempt access index 13/13 in VECTOR_ELT   Backtrace:       ▆    1. ├─... %>% ... at test-fill_NA_funcs.R:379:3    2. ├─...[]    3. └─data.table:::`[.data.table`(...)   ── Error ('test-fill_NA_funcs.R:540:3'): data.table pipeline fill_NA/fill_NA_N accuracy - disc ──   Error in ``[.data.table`(data_DT, , `:=`(y_imp, fill_NA(x = .SD, model = "lda", posit_y = "y_fac", posit_x = c("x2", "x3", "x4", "x5"))), by = .(group))`: attempt access index 16/16 in VECTOR_ELT   Backtrace:       ▆    1. ├─... %>% ... at test-fill_NA_funcs.R:540:3    2. ├─...[]    3. └─data.table:::`[.data.table`(...)      [ FAIL 2 | WARN 3 | SKIP 0 | PASS 102 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [10s/13s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘miceFast-intro.Rmd’ using rmarkdown Quitting from miceFast-intro.Rmd:221-299 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 13/13 in VECTOR_ELT --- Backtrace:     ▆  1. ├─... %>% ...  2. ├─...[]  3. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'miceFast-intro.Rmd' failed with diagnostics: attempt access index 13/13 in VECTOR_ELT --- failed re-building ‘miceFast-intro.Rmd’ SUMMARY: processing the following file failed:   ‘miceFast-intro.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/6s] OK
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• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs