Better error message for Error knitting README.Rmd

[stefaniebutland]

@seankross I got the following error msg when I tried to knit README.Rmd after create_readme. I'm stumped. Any help appreciated.

Error msg

  |.....................                               |  40% [setup]          

processing file: README.Rmd

Error in `!continue`:
! invalid argument type
Backtrace:
  1. rmarkdown::render("/Users/stefaniebutland/README.Rmd", encoding = "UTF-8")
  2. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  3. knitr:::process_file(text, output)
  6. knitr:::process_group(group)
  7. knitr:::call_block(x)
  8. knitr:::block_exec(params)
  9. knitr:::eng_r(options)
 12. knitr (local) evaluate(...)
 13. evaluate::evaluate(...)

Quitting from lines 9-11 [setup] (README.Rmd)
Execution halted

sessionInfo

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.6.9

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Vancouver
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] fs_1.6.4       tibble_3.2.1   rmarkdown_2.28 kyber_0.1.0   

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.9      dplyr_1.1.4         compiler_4.4.0      gitcreds_0.1.2      tidyselect_1.2.1   
 [6] Rcpp_1.0.13         stringr_1.5.1       credentials_2.0.1   yaml_2.3.10         fastmap_1.2.0      
[11] R6_2.5.1            generics_0.1.3      knitr_1.48          openssl_2.2.2       lubridate_1.9.3    
[16] pillar_1.9.0        rlang_1.1.4         utf8_1.2.4          stringi_1.8.4       xfun_0.47          
[21] sys_3.4.2           timechange_0.3.0    cli_3.6.3           magrittr_2.0.3      digest_0.6.37      
[26] gh_1.4.1            googlesheets4_1.1.1 rstudioapi_0.16.0   askpass_1.2.0       gert_2.1.2         
[31] lifecycle_1.0.4     vctrs_0.6.5         parsermd_0.1.3      evaluate_1.0.0      gargle_1.5.2       
[36] glue_1.7.0          cellranger_1.1.0    googledrive_2.1.1   fansi_1.0.6         purrr_1.0.2        
[41] tools_4.4.0         pkgconfig_2.0.3     htmltools_0.5.8.1  

[stefaniebutland]

I realize this is likely a "me" issue.

[stefaniebutland]

yep. A "me" issue. Cohort name did not match what I had in CohortRegistry

[stefaniebutland]

Sean can you give a helpful error message for this scenario? (pls don't add to Main till I have completed making repos)

My error was CohortRegistry sheet said cohort_name = 2024-noaa-a but I told kyber to look for params: cohort_name: "2024-nmfs-a". Would be ideal if error message indicated a mismatch between these

[seankross]

Hey sorry I am just getting here now! Can do.