* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/infectiousR.Rcheck’
* using R Under development (unstable) (2026-04-22 r89950)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-04-24 00:52:50 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘infectiousR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘infectiousR’ version ‘0.1.1’
* 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 ‘infectiousR’ can be installed ... 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 ... [7s/10s] OK
* checking Rd files ... 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 ... 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’ [12s/16s]
 [13s/16s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [21s/27s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘infectiousR_vignette.Rmd’ using rmarkdown

Quitting from infectiousR_vignette.Rmd:83-105 [covid-stats-simple-plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'filter' applied to an object of class "NULL"
---
Backtrace:
    ▆
 1. ├─... %>% ...
 2. ├─ggplot2::ggplot(...)
 3. ├─dplyr::mutate(., case_rate = (cases/population) * 1e+05)
 4. ├─dplyr::select(., -updated, -starts_with("today"))
 5. └─dplyr::filter(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'infectiousR_vignette.Rmd' failed with diagnostics:
no applicable method for 'filter' applied to an object of class "NULL"
--- failed re-building ‘infectiousR_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘infectiousR_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [8s/10s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-MKL/infectiousR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:47.55, 103.53 + 15.45