* using log directory ‘/srv/hornik/tmp/CRAN_pretest/healthiar.Rcheck’ * using R Under development (unstable) (2025-09-18 r88857) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘healthiar/DESCRIPTION’ ... OK * this is package ‘healthiar’ version ‘0.1.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/7s] NOTE Maintainer: ‘Alberto Castro ’ New submission Possibly misspelled words in DESCRIPTION: healthiar (2:18, 21:28) Authors@R field should be a call to person(), or combine such calls. Reading CITATION file fails with $ operator is invalid for atomic vectors when package is not installed. Found the following (possibly) invalid URLs: URL: https://cran.r-project.org/web/packages/tidyr/vignettes/tidy-data.html From: inst/doc/intro_to_healthiar.html Status: 200 Message: OK CRAN URL not in canonical form URL: https://github.com/best-cost/best-cost_WPs/issues (moved to https://github.com/SwissTPH/healthiar/issues) From: inst/doc/intro_to_healthiar.html Status: 301 Message: Moved Permanently URL: https://github.com/best-cost/best-cost_WPs?tab=readme-ov-file#readme (moved to https://github.com/SwissTPH/healthiar?tab=readme-ov-file#readme) From: inst/doc/intro_to_healthiar.html Status: 301 Message: Moved Permanently The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Title field should be in title case. Current version is: ‘R package healthiar to quantify and monetize the burden of disease attributable to exposures’ In title case that is: ‘R Package Healthiar to Quantify and Monetize the Burden of Disease Attributable to Exposures’ Size of tarball: 23913744 bytes * 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 ‘healthiar’ 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 whether startup messages can be suppressed ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘add_info’ ‘attribute_master’ ‘check_if_args_identical’ ‘collapse_df_by_group’ ‘compile_input’ ‘find_joining_columns’ ‘find_multi_value_col_names’ ‘get_discount_factor’ ‘get_impact’ ‘get_impact_with_lifetable’ ‘get_inflation_factor’ ‘get_input_args’ ‘get_output’ ‘get_pop_fraction’ ‘get_ref_prop_pop’ ‘get_risk_and_pop_fraction’ ‘validate_input_attribute’ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [8s/8s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [68s/68s] ERROR Running ‘testthat.R’ [68s/68s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(healthiar) ***** DISCLAIMER ***** The developers are not liable for any calculation errors or inaccuracies resulting from the use of the R package healthiar. It is work in progress and the functions of this R package can change at any moment. ***** HAPPY CODING ***** Attaching package: 'healthiar' The following object is masked from 'package:testthat': compare > > test_check("healthiar") [ FAIL 5 | WARN 5 | SKIP 0 | PASS 243 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-attribute_health.R:1065:3'): results correct |pathway_ar|erf_formula|exp_dist|iteration_FALSE| ── Error in `readChar(con, 5L, useBytes = TRUE)`: cannot open the connection Backtrace: ▆ 1. └─base::load(testthat::test_path("data", "input_data_for_testing_Rpackage.Rdata")) at test-attribute_health.R:1065:3 2. └─base::readChar(con, 5L, useBytes = TRUE) ── Error ('test-attribute_health.R:1282:3'): results correct prevalence-based YLD |pathway_ar|erf_formula|exp_dist|iteration_FALSE| ── Error in `readChar(con, 5L, useBytes = TRUE)`: cannot open the connection Backtrace: ▆ 1. └─base::load(testthat::test_path("data", "input_data_for_testing_Rpackage.Rdata")) at test-attribute_health.R:1282:3 2. └─base::readChar(con, 5L, useBytes = TRUE) ── Error ('test-attribute_health.R:1312:3'): results correct prevalence-based YLD |pathway_ar|erf_formula|exp_dist|iteration_FALSE| ── Error in `readChar(con, 5L, useBytes = TRUE)`: cannot open the connection Backtrace: ▆ 1. └─base::load(testthat::test_path("data", "input_data_for_testing_Rpackage.Rdata")) at test-attribute_health.R:1312:3 2. └─base::readChar(con, 5L, useBytes = TRUE) ── Error ('test-attribute_health.R:1625:5'): error if prop_pop_exp and ar |pathway_rr|erf_log_lin|exp_dist|iteration_FALSE| ── Error in `readChar(con, 5L, useBytes = TRUE)`: cannot open the connection Backtrace: ▆ 1. └─base::load(testthat::test_path("data", "input_data_for_testing_Rpackage.Rdata")) at test-attribute_health.R:1625:5 2. └─base::readChar(con, 5L, useBytes = TRUE) ── Error ('test-attribute_health.R:1746:3'): warning if absolute risk and cutoff ── Error in `readChar(con, 5L, useBytes = TRUE)`: cannot open the connection Backtrace: ▆ 1. └─base::load(testthat::test_path("data", "input_data_for_testing_Rpackage.Rdata")) at test-attribute_health.R:1746:3 2. └─base::readChar(con, 5L, useBytes = TRUE) [ FAIL 5 | WARN 5 | SKIP 0 | PASS 243 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [8s/8s] OK * checking PDF version of manual ... [6s/6s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≥ (U+2265) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≥ (U+2265) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≥ (U+2265) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≤ (U+2264) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≥ (U+2265) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘healthiar-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 3 NOTEs