* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/AgePopDenom.Rcheck’ * using R Under development (unstable) (2025-07-18 r88431) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-19) 14.2.0 GNU Fortran (Debian 14.2.0-19) 14.2.0 * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘AgePopDenom/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AgePopDenom’ version ‘1.2.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/7s] NOTE Maintainer: ‘Mohamed A. Yusuf ’ New submission Package was archived on CRAN CRAN repository db overrides: X-CRAN-Comment: Archived on 2025-07-11 as issues were not corrected in time. * 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 ‘AgePopDenom’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... 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 ... [4s/4s] OK * checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [2s/2s] ERROR Running ‘testthat.R’ [2s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(AgePopDenom) > > test_check("AgePopDenom") -- Processing DHS data and joining with shapefile ------------------------------ i Processing country: KE v Processed country: KE (1 of 2) i Processing country: TZ v Processed country: TZ (2 of 2) -- Process gamma parameters ---------------------------------------------------- i Aggregating and extracting gamma for: KEN x Aggregating and extracting gamma for: KEN ... failed [ FAIL 1 | WARN 0 | SKIP 1 | PASS 14 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-AgePopDenom.R:199:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-AgePopDenom.R:126:3'): process_dhs_data correctly processes DHS survey data ── Error in `purrr::map(unique(binded_dataset$country_code_iso3), function(country_code) { processed_count <<- processed_count + 1 cli::cli_process_start(msg = glue::glue("Aggregating and extracting gamma for: {country_code}"), msg_done = glue::glue("Aggregated and extracted gamma for: {country_code} ", "({processed_count} of {\n length(unique(binded_dataset$country_code_iso3))})")) processed_data <- aggregate_and_extract_gamma(dplyr::filter(binded_dataset, country_code_iso3 == country_code, !is.na(urban) | !is.na(lat) | !is.na(long))) outlier_free_data <- dplyr::mutate(dplyr::ungroup(dplyr::mutate(dplyr::group_by(dplyr::filter(processed_data$outlier_free_data, long != lat), survey_code), year_of_survey = max(year_of_survey, na.rm = TRUE))), country_year = paste0(country, " - ", year_of_survey, " (", survey_code, ")")) age_param_data <- dplyr::mutate(dplyr::ungroup(dplyr::mutate(dplyr::group_by(dplyr::filter(processed_data$age_param_data, lon != lat), survey_code), year_of_survey = max(year_of_survey, na.rm = TRUE))), country_year = paste0(country, " - ", year_of_survey, " (", survey_code, ")")) list(outlier_free_data = outlier_free_data, age_param_data = age_param_data) })`: i In index: 1. Caused by error in `aggregate_and_extract_gamma()`: ! Package 'numDeriv' is required for this function. Please install it with install.packages('numDeriv') Backtrace: ▆ 1. ├─AgePopDenom::process_dhs_data(...) at test-AgePopDenom.R:126:3 2. │ └─purrr::map(...) 3. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 4. │ ├─purrr:::with_indexed_errors(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ ├─purrr:::call_with_cleanup(...) 7. │ └─AgePopDenom (local) .f(.x[[i]], ...) 8. │ └─AgePopDenom::aggregate_and_extract_gamma(...) 9. │ └─base::stop(...) 10. └─base::.handleSimpleError(...) 11. └─purrr (local) h(simpleError(msg, call)) 12. └─cli::cli_abort(...) 13. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 1 | PASS 14 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [0s/0s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE