• using R Under development (unstable) (2025-01-24 r87627)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8
• checking for file ‘diseasystore/DESCRIPTION’ ... OK
• this is package ‘diseasystore’ version ‘0.3.0’
• 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 ‘diseasystore’ can be installed ... [10s/13s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘0_R6_utils.R’ ‘0_linters.R’ ‘2_FeatureHandler.R’     ‘3_feature_store_helpers.R’ ‘DiseasystoreBase.R’     ‘DiseasystoreEcdcRespiratoryViruses.R’ ‘DiseasystoreGoogleCovid19.R’     ‘DiseasystoreSimulist.R’ ‘drop_diseasystore.R’     ‘source_conn_helpers.R’ ‘test_diseasystore.R’ ‘truncate_interlace.R’
• 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 ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking whether startup messages can be suppressed ... [1s/2s] 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/7s] OK
• checking Rd files ... [0s/1s] 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/1s] 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 ... [2s/6s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [209s/304s] OK   Running ‘spelling.R’ [0s/1s]   Running ‘testthat.R’ [209s/303s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [60s/81s] ERROR Error(s) in re-building vignettes: --- re-building ‘benchmarks.Rmd’ using rmarkdown fatal: not a git repository (or any of the parent directories): .git --- finished re-building ‘benchmarks.Rmd’ --- re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’ using rmarkdown --- finished re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’ --- re-building ‘diseasystore-google-covid-19.Rmd’ using rmarkdown --- finished re-building ‘diseasystore-google-covid-19.Rmd’ --- re-building ‘diseasystore.Rmd’ using rmarkdown --- finished re-building ‘diseasystore.Rmd’ --- re-building ‘extending-diseasystore-example.Rmd’ using rmarkdown Quitting from lines 537-540 [stratifications_positive_sex_age_plot] (extending-diseasystore-example.Rmd) Error: processing vignette 'extending-diseasystore-example.Rmd' failed with diagnostics: Faceting variables must have at least one value. --- failed re-building ‘extending-diseasystore-example.Rmd’ --- re-building ‘extending-diseasystore.Rmd’ using rmarkdown --- finished re-building ‘extending-diseasystore.Rmd’ SUMMARY: processing the following file failed:   ‘extending-diseasystore-example.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [6s/8s] OK
• DONE Status: 1 ERROR, 1 NOTE
• using check arguments '--no-clean-on-error '