* using log directory ‘/Users/ripley/R/packages/tests-devel/survinger.Rcheck’ * using R Under development (unstable) (2026-04-01 r89773) * using platform: aarch64-apple-darwin25.4.0 * R was compiled by Apple clang version 21.0.0 (clang-2100.0.123.102) GNU Fortran (GCC) 14.2.0 * running under: macOS Tahoe 26.4 * using session charset: UTF-8 * current time: 2026-04-03 08:17:28 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘survinger/DESCRIPTION’ ... OK * this is package ‘survinger’ version ‘0.1.0’ * 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 ‘survinger’ can be installed ... OK * 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 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... 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 ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR 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(survinger) > > test_check("survinger") -- Lineage Prevalence Estimate ------------------------------------------------- Lineage: "BA.2.86" Method: "hajek" Confidence level: 0.95 Time periods: 1 # A tibble: 1 x 5 time prevalence se ci_lower ci_upper 1 2024-W01 0.3 0.05 0.2 0.4 -- Optimal Sequencing Allocation ----------------------------------------------- Objective: min_mse Total capacity: 100 sequences Strata: 1 # A tibble: 1 x 2 stratum n_allocated 1 A 100 -- Reporting Delay Distribution ------------------------------------------------ Distribution: "negbin" Strata: none (pooled) Observations: 100 Mean delay: 10 days # A tibble: 1 x 3 stratum mu size 1 all 10 3 -- Genomic Surveillance Design ------------------------------------------------- Observations: 421 Strata: 3 (region) Date range: 2024-01-01 to 2024-01-28 Lineages: 4 Sources: clinical, sentinel, wastewater Weight range: [5.354, 20.231] -- Surveillance Design Summary ------------------------------------------------- Sequences: 421 Strata: 3 (region) Period: 2024-01-01 to 2024-01-28 -- Top lineages BA.5: 252 XBB.1.5: 121 Other: 34 BA.2.86: 14 -- Sampling weights Min. 1st Qu. Median Mean 3rd Qu. Max. 5.354 8.813 12.273 12.619 16.252 20.231 -- Optimal Sequencing Allocation ----------------------------------------------- Objective: min_mse Total capacity: 100 sequences Strata: 3 # A tibble: 3 x 3 region n_allocated proportion 1 Region_A 24 0.24 2 Region_B 8 0.08 3 Region_C 68 0.68 Saving _problems/test-03-prevalence-63.R -- Reporting Delay Distribution ------------------------------------------------ Distribution: "negbin" Strata: none (pooled) Observations: 768 Mean delay: 10 days # A tibble: 1 x 5 stratum distribution mu size converged 1 all negbin 10.1 2.96 TRUE -- Design-Weighted Delay-Adjusted Prevalence ----------------------------------- Correction: "design:hajek+delay:direct" # A tibble: 10 x 9 time lineage n_obs_raw n_obs_adjusted prevalence se ci_lower ci_upper 1 2024-W01 BA.2.86 56 56.0 0.0147 0.0256 0 0.0649 2 2024-W02 BA.2.86 58 58.0 0.117 0.0726 0 0.260 3 2024-W03 BA.2.86 52 52.0 0 0 0 0 4 2024-W04 BA.2.86 53 53.0 0.0361 0.0257 0 0.0863 5 2024-W05 BA.2.86 52 52.0 0.0135 0.0256 0 0.0638 6 2024-W06 BA.2.86 68 68.0 0.0444 0.0409 0 0.125 7 2024-W07 BA.2.86 46 46.0 0 0 0 0 8 2024-W08 BA.2.86 51 51.0 0.0693 0.0518 0 0.171 9 2024-W09 BA.2.86 48 48.0 0.0659 0.0610 0 0.185 10 2024-W10 BA.2.86 66 66.2 0.0549 0.0465 0 0.146 # i 1 more variable: mean_report_prob -- Surveillance System Report -------------------------------------------------- -- Design Structure -- Total sequences: 3,031 Strata: 3 Period: 2024-01-01 to 2024-02-25 -- Sequencing Inequality -- Rate range: 3.29% to 45.56% Rate ratio: 13.8x Gini coefficient: 0.365 i Moderate inequality. Weighting recommended. -- Estimation Impact -- Effective sample size: 1501 (49.5% of total) Mean |weighted - naive| bias: 2.07 percentage points -- Detection Power -- Target: detect BA.5 at 1% prevalence Weekly detection probability: 97.8% Sequences needed for 95% detection: 299 -- Detection Power Curve ------------------------------------------------------- Prevalence range: 0.1% to 5% -- Thresholds 50% detection requires 0.2% prevalence 80% detection requires 0.5% prevalence 95% detection requires 0.8% prevalence [ FAIL 1 | WARN 1 | SKIP 0 | PASS 159 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-03-prevalence.R:63:3'): CI contains point estimate ─────────── Expected `all(est$prevalence >= est$ci_lower)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 1 | SKIP 0 | PASS 159 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [10s/10s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/Users/ripley/R/packages/tests-devel/survinger.Rcheck/00check.log’ for details. 48.75 real 39.72 user 7.89 sys