• using R Under development (unstable) (2025-07-14 r88410)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘epidatr/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘epidatr’ version ‘1.2.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• 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 ‘epidatr’ can be installed ... OK See the install log for details.
• 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 ... [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/1s] 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 ... [6s/9s] OK
• checking Rd files ... [0s/1s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [5s/8s] OK   Running ‘testthat.R’ [5s/8s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [9s/18s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘epidatr.Rmd’ using rmarkdown --- finished re-building ‘epidatr.Rmd’ --- re-building ‘signal-discovery.Rmd’ using rmarkdown Quitting from signal-discovery.Rmd:113-122 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'signal-discovery.Rmd' failed with diagnostics: epidata error: `database error: (builtins.AttributeError) 'NoneType' object has no attribute 'cursor' [SQL: SELECT t.geo_value, t.signal, t.source, t.geo_type, t.time_type, t.time_value, t.direction, t.issue, t.lag, t.missing_value, t.missing_stderr, t.missing_sample_size, t.value, t.stderr, t.sample_size FROM epimetric_latest_v t WHERE ((t.source = %s AND (t.signal = %s))) AND ((t.geo_type = %s AND (t.geo_value = %s))) AND ((t.time_type = %s AND (t.time_value BETWEEN %s AND %s))) ORDER BY t.source ASC, t.signal ASC, t.time_type ASC, t.time_value ASC, t.geo_type ASC, t.geo_value ASC, t.issue ASC LIMIT 10000001] [parameters: [{'source_0t': 'fb-survey', 'source_0t_0': 'smoothed_accept_covid_vaccine', 'geo_type_0t': 'county', 'geo_type_0t_0': '06059', 'time_type_0t': 'day', 'time_type_0t_0': 20201221, 'time_type_0t_0_2': 20201225}]]` --- failed re-building ‘signal-discovery.Rmd’ --- re-building ‘versioned-data.Rmd’ using rmarkdown --- finished re-building ‘versioned-data.Rmd’ SUMMARY: processing the following file failed:   ‘signal-discovery.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR