error with renv::dependencies

[jkylearmstrong]

When I go to render a file I recently started getting this error:

grateful::cite_packages(output = "paragraph",
                         out.dir = getwd(),
                         omit = NULL,
                         dependencies = F,
                         include.RStudio = F,
                         passive.voice = T)

updating existing packages
ERROR: 
compilation failed- error
Text line contains an invalid character.
l.5119 Please see `^^[
                      ]8;;ide:help:renv::dependencies^^G?renv::dependencies^... 

I have added a .renvignore file and I have suppressed everything except the list of .qmd files I plan on rendering and the DESCRIPTION file. When I run

grateful::cite_packages(output = "paragraph",
                         out.dir = getwd(),
                         omit = NULL,
                         dependencies = F,
                         include.RStudio = F,
                         passive.voice = T)

interactively I am not seeing any issues.

The result of

X <- capture.output(renv::dependencies(), "message")

is 2498 lines,

Any idea what might be causing this?

To be clear renv has been experiencing some issues since the last update (rstudio/renv#2089 , rstudio/renv#2091), but I have reverted back to version

> packageVersion('renv')
[1] ‘1.0.11’

[jkylearmstrong]

I was able to get the document to render when I switched to:

grateful::cite_packages(output = "paragraph",
                        out.dir = getwd(),
                        pkgs = "Session",
                        omit = NULL,
                        dependencies = F,
                        include.RStudio = F,
                        passive.voice = T)

not sure why I'm getting the error with pkgs = "All" option when

> unique(renv::dependencies(progress = FALSE)$Package)
 [1] "knitr"          "dplyr"          "tidyr"          "tidyverse"     
 [5] "here"           "readr"          "labelled"       "datasci"       
 [9] "furrr"          "missForest"     "grateful"       "rmarkdown"     
[13] "purrr"          "ggplot2"        "pacman"         "cowplot"       
[17] "broom.helpers"  "gt"             "gtsummary"      "survival"      
[21] "caret"          "tibble"         "patchwork"      "ggpubr"        
[25] "lmerTest"       "broom"          "broom.mixed"    "stringr"       
[29] "ggridges"       "officer"        "quarto"         "arsenal"       
[33] "data.table"     "distributional" "ggdist"         "tidymodels"    
[37] "readxl"         "janitor"        "forcats"        "scales"        
[41] "ggfortify"      "plotly"         "ggmice"         "mice"          
[45] "doFuture"       "future"         "parallel"       "censored"      
[49] "workflowsets"   "vip"            "magick"         "ranger"        
[53] "lme4"           "yardstick"      "kableExtra"     "equatiomatic"  
[57] "writexl"        "glmnet"         "stats"          "kknn"          
[61] "finetune"       "survminer"      "futuremice"     "ggrepel"       
[65] "glue"           "partykit"       "tools"          "multilevelmod" 
[69] "rsample"        "DALEX"          "DALEXtra"       "doParallel"    
[73] "openxlsx"       "nnet"           "Amelia"         "AMR"           
[77] "corrplot"       "embed"          "fs"             "ggforce"       
[81] "ingredients"    "renv"           "shiny"          "tune"          
[85] "xgboost"  

[Pakillo]

Hi @jkylearmstrong

Thanks for the report. Is your repository public so that I can have a look to investigate what might be going on? It looks like {renv} or {grateful} are finding too many packages to cite? Or some weird interaction with Quarto? (since you mentioned it works fine when running interactively)

What is the output of grateful::scan_packages() in your repo? Does it coincide with the output of unique(renv::dependencies(progress = FALSE)$Package) you posted above?

Also, what is the output of

grateful::cite_packages(output = "paragraph",
                         out.dir = getwd(),
                         omit = NULL,
                         dependencies = F,
                         include.RStudio = F,
                         passive.voice = T)

Thanks

[jkylearmstrong]

I will try and test with updates to renv and see what comes out at this point.

Right now I rolled back renv to the prior version and applied "session" to account for errors to keep my project functional.