Error when running vignettes code: When sourcing ‘ipums-api-nhgis.R’: Error: Invalid ds_spec specification: geog_levels must not contain missing values

[barracuda156]

--->  Testing R-ipumsr
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-ipumsr/R-ipumsr/work/ipumsr-0.8.0" && /opt/local/bin/R CMD check ./ipumsr_0.8.0.tar.gz --no-manual --no-build-vignettes 
* using log directory ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-ipumsr/R-ipumsr/work/ipumsr-0.8.0/ipumsr.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
    gcc-mp-13 (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
    GNU Fortran (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘ipumsr/DESCRIPTION’ ... OK
* this is package ‘ipumsr’ version ‘0.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘rmapshaper’
* 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 ‘ipumsr’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘cps_select_data.jpg’ ‘fixtures/check-extract-history.yml’
  ‘fixtures/check-extract-info.yml’ ‘fixtures/extract-ready.yml’
  ‘fixtures/micro-sample-ids.yml’
  ‘fixtures/nhgis-metadata-detailed.yml’
  ‘fixtures/nhgis-metadata-summary.yml’ ‘fixtures/submit-extract.yml’
  ‘fixtures/submit-placeholder-extract-usa.yml’
  ‘fixtures/wait-for-extract.yml’ ‘ipums-api-micro.Rmd’
  ‘ipums-api-nhgis.Rmd’ ‘ipums-api.Rmd’ ‘ipums-bigdata.Rmd’
  ‘ipums-read.Rmd’ ‘ipums.Rmd’ ‘microdata_annotated_screenshot.png’
  ‘value-labels.Rmd’
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  ‘ipums-api-micro.Rmd’
  ‘ipums-api-nhgis.Rmd’
  ‘ipums-api.Rmd’
  ‘ipums-bigdata.Rmd’
  ‘ipums-read.Rmd’
  ‘ipums.Rmd’
  ‘value-labels.Rmd’
* checking running R code from vignettes ...
  ‘ipums-api-micro.Rmd’ using ‘UTF-8’... OK
  ‘ipums-api-nhgis.Rmd’ using ‘UTF-8’... failed
  ‘ipums-api.Rmd’ using ‘UTF-8’... OK
  ‘ipums-bigdata.Rmd’ using ‘UTF-8’... OK
  ‘ipums-read.Rmd’ using ‘UTF-8’... OK
  ‘ipums.Rmd’ using ‘UTF-8’... OK
  ‘value-labels.Rmd’ using ‘UTF-8’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘ipums-api-nhgis.Rmd’
  ...

Shapefiles: us_county_2021_tl2021, us_county_2020_tl2020

> define_extract_nhgis(description = "Invalid extract", 
+     datasets = ds_spec("1900_STF1", data_tables = "NP1"))

  When sourcing ‘ipums-api-nhgis.R’:
Error: Invalid `ds_spec` specification:
✖ `geog_levels` must not contain missing values.
Execution halted

* checking re-building of vignette outputs ... SKIPPED
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE

[dtburk]

If you look at the vignette source of ipums-api-nhgis.Rmd, you'll see that the code throwing an error is an example of an invalid extract specification, so the error is expected. The code is in a chunk with option error = TRUE, which signals that knitr should continue building even in the case of an error. Is there a way to modify your checking routine to recognize knitr chunk options?

[barracuda156]

If you look at the vignette source of ipums-api-nhgis.Rmd, you'll see that the code throwing an error is an example of an invalid extract specification, so the error is expected. The code is in a chunk with option error = TRUE, which signals that knitr should continue building even in the case of an error. Is there a way to modify your checking routine to recognize knitr chunk options?

Ah, okay, so this is a known issue. Apparently there is a fix: tidyverse/tibble#1575 (comment)

[dtburk]

Oh, interesting, I will try the purl option out locally and see if it fixes the issue. Thanks!