- using R version 4.6.0 alpha (2026-04-02 r89781)
- using platform: aarch64-apple-darwin23
- R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
- running under: macOS Sequoia 15.7.1
- using session charset: UTF-8
* current time: 2026-04-03 02:13:53 UTC
- 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 ... [2s/2s] OK
See the install log for details.
- 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 ... [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 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 ... [2s/2s] OK
- checking Rd files ... [0s/0s] 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 ... [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 ... [3s/3s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [7s/7s] ERROR
Running ‘testthat.R’ [6s/7s]
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
<chr> <dbl> <dbl> <dbl> <dbl>
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
<chr> <dbl>
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
<chr> <dbl> <dbl>
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
<chr> <int> <dbl>
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
<chr> <chr> <dbl> <dbl> <lgl>
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
<chr> <chr> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
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 <dbl>
-- 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 ... [11s/28s] OK
- checking PDF version of manual ... [2s/3s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '