thematic_on breaks if another package includes ggplot (maybe?)

[elfatherbrown]

The problem

I have a shiny app built as a package with golem that uses many plotting libraries including ggplot2 and as soon as I tried thematic_on or thematic_shiny I got:

"Error in get(S3[i, 1L], mode = "function", envir = parent.frame()): invalid first argument".

I digged in and discovered that the same problem that happens with my package, happens with others that include ggplot2:

    library(thematic)
#> This version of thematic is designed to work with rmarkdown version 2.7.0 or higher. Consider upgrading via remotes::install_github('rstudio/rmarkdown#1706')
thematic::thematic_on()
thematic::thematic_off()
library(survMisc)
#> Loading required package: survival
thematic::thematic_on()
#> Error in get(S3[i, 1L], mode = "function", envir = parent.frame()): invalid first argument

^{Created on 2021-02-16 by the reprex package (v1.0.0)}

Further digging on thematic's code

On another box I set out to debug thematic. I cloned it and this is what I did.

On this function I put a browser:

ggplot_build_set <- function() {
  browser()
  if (!is_installed("ggplot2")) return(NULL)
  ggplot_build_restore()
  # Note that assignInNamespace() does S3 method registration, but to
  # find the relevant generic, it looks in the parent.frame()...
  # so this line here is prevent that from failing if ggplot2 hasn't been attached
  # https://github.com/wch/r-source/blob/d0ede8/src/library/utils/R/objects.R#L472
  ggplot_build <- getFromNamespace("ggplot_build", "ggplot2")
  .globals$ggplot_build <- getFromNamespace("ggplot_build.ggplot", "ggplot2")
  assign_in_namespace <- assignInNamespace
  assign_in_namespace("ggplot_build.ggplot", ggthematic_build, "ggplot2")
}

Discovered that the aforementioned "get" problem with S3 comes from assign_in_namespace("ggplot_build.ggplot", ggthematic_build, "ggplot2"). So I copied the assign_in_namespace (from assignInNamespace, as it does in the code), but set a browser on that.

What I discovered is that inside the assignInNamespace code, down by the line:

...
genfun <- get(S3[i, 1L], mode = "function", envir = parent.frame())
...

S3[i,1L] returns a list that contains the name of the function, but get wants a string. So, as you can see:

This goes away if one rewrites with:

...
genfun <- get(S3[i, 1L][[1]], mode = "function", envir = parent.frame())
...

Or at least the error does. Im not keen on hacking away at this because im pretty much a newb (i've no idea how S3 or namespaces actually work), but I think this is either a freakish mismanagement of my base packages (e.g. i carry a bug in utils::assignInNamespace), or a particular use of it that got mangled somewhere.

I LOVE the thematic idea. I want to use it! Let me know if I can help out.

[cpsievert]

Interesting, thanks for the report. Is your package publicly available?

[cpsievert]

Looks like the problem derives from the zoo package (a dependency of these packages):

> library(zoo); thematic::thematic_on()
Error in get(S3[i, 1L], mode = "function", envir = parent.frame()) : 
  invalid first argument

[cpsievert]

Turns out that library(zoo) causes this problem since it's calling registerS3method() in an .onLoad() hook, which unfortunately causes assignInNamespace() to no longer work (this seems like a bug in R itself). A minimal example:

library(ggplot2)
# works
ggplotBuild <- getFromNamespace("ggplot_build.ggplot", "ggplot2")
assignInNamespace("ggplot_build.ggplot", function(x) { warning("owned"); ggplotBuild(x) }, "ggplot2")
qplot(1:10)

# doesn't work
library(zoo)
assignInNamespace("ggplot_build.ggplot", function(x) { warning("owned"); ggplotBuild(x) }, "ggplot2")
#> Error in get(S3[i, 1L], mode = "function", envir = parent.frame()) : 
#>   invalid first argument

And this happens because the S3 lookup matrix turns into a list when registerS3method() happens:

is.matrix(.getNamespaceInfo(asNamespace("ggplot2"), "S3methods"))
#> TRUE
library(zoo)
is.matrix(.getNamespaceInfo(asNamespace("ggplot2"), "S3methods"))
#> FALSE

I may submit a bug to R core for this, but in the meantime, I think I can have thematic workaround this

[elfatherbrown]

Tested s3methods-matrix branch. My problem has gone away. Thanks!

[ghost]

Turns out that library(zoo) causes this problem since it's calling registerS3method() in an .onLoad() hook, which unfortunately causes assignInNamespace() to no longer work (this seems like a bug in R itself). A minimal example:

library(ggplot2)
# works
ggplotBuild <- getFromNamespace("ggplot_build.ggplot", "ggplot2")
assignInNamespace("ggplot_build.ggplot", function(x) { warning("owned"); ggplotBuild(x) }, "ggplot2")
qplot(1:10)

# doesn't work
library(zoo)
assignInNamespace("ggplot_build.ggplot", function(x) { warning("owned"); ggplotBuild(x) }, "ggplot2")
#> Error in get(S3[i, 1L], mode = "function", envir = parent.frame()) : 
#>   invalid first argument

And this happens because the S3 lookup matrix turns into a list when registerS3method() happens:

is.matrix(.getNamespaceInfo(asNamespace("ggplot2"), "S3methods"))
#> TRUE
library(zoo)
is.matrix(.getNamespaceInfo(asNamespace("ggplot2"), "S3methods"))
#> FALSE

I may submit a bug to R core for this, but in the meantime, I think I can have thematic workaround this

Hi. I still face the same problem

#> Error in get(S3[i, 1L], mode = "function", envir = parent.frame()) : 
#>   invalid first argument

Here is my sessionInfo

R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Greek_Greece.1253 
[2] LC_CTYPE=Greek_Greece.1253   
[3] LC_MONETARY=Greek_Greece.1253
[4] LC_NUMERIC=C                 
[5] LC_TIME=Greek_Greece.1253    

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

other attached packages:
[1] zoo_1.8-8     ggplot2_3.3.3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        bslib_0.2.4       compiler_4.0.4   
 [4] pillar_1.5.1      jquerylib_0.1.3   tools_4.0.4      
 [7] odbc_1.3.0        digest_0.6.27     bit_4.0.4        
[10] lattice_0.20-41   gtable_0.3.0      evaluate_0.14    
[13] jsonlite_1.7.2    lifecycle_1.0.0   tibble_3.1.0     
[16] debugme_1.1.0     pkgconfig_2.0.3   rlang_0.4.10     
[19] DBI_1.1.1         rstudioapi_0.13   yaml_2.2.1       
[22] xfun_0.21         withr_2.4.1       dplyr_1.0.5      
[25] knitr_1.31        htmlwidgets_1.5.3 generics_0.1.0   
[28] vctrs_0.3.6       sass_0.3.1        hms_1.0.0        
[31] thematic_0.1.1    bit64_4.0.5       grid_4.0.4       
[34] tidyselect_1.1.0  glue_1.4.2        R6_2.5.0         
[37] fansi_0.4.2       rmarkdown_2.7     librarian_1.7.0  
[40] farver_2.1.0      purrr_0.3.4       blob_1.2.1       
[43] magrittr_2.0.1    scales_1.1.1      ellipsis_0.3.1   
[46] htmltools_0.5.1.1 rsconnect_0.8.16  assertthat_0.2.1 
[49] colorspace_2.0-0  labeling_0.4.2    utf8_1.1.4       
[52] munsell_0.5.0     crayon_1.4.1     

[cpsievert]

You need the development version remotes::install_github('rstudio/thematic')

[michaelgaunt404]

Hi, I'm still receiving this error as well.
This is my yaml and first code chunk:

---
title: "ETAN Database Exploration Tool"
output:
  html_document:
    theme:
      bg: "#002b36"
      fg: "#eee8d5"
      primary: "#2aa198"
      font: "auto"

# runtime: shiny
---

'''{r setup, include=FALSE}
knitr::opts_chunk$set(
  cache = FALSE, cache.lazy = FALSE, autodep = TRUE, warning = FALSE, 
  message = FALSE, echo = TRUE, dpi = 180,
  fig.width = 8, fig.height = 5, echo = FALSE
  )
thematic::thematic_rmd(font = "auto")

'''

I'm receiving the following error both in isolated code chunks that generate ggplot visuals and during markdown knit.

> > sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] shiny_1.6.0          gridExtra_2.3        scales_1.1.1         ggraph_2.0.5        
 [5] tidygraph_1.2.0      networkD3_0.4        thematic_0.1.2.1     ggridges_0.5.3      
 [9] here_1.0.1           data.validator_0.1.5 skimr_2.1.2          DT_0.17             
[13] lubridate_1.7.9.2    data.table_1.13.2    janitor_2.1.0        readxl_1.3.1        
[17] magrittr_2.0.1       forcats_0.5.1        stringr_1.4.0        dplyr_1.0.4         
[21] purrr_0.3.4          readr_1.4.0          tidyr_1.1.3          tibble_3.1.0        
[25] ggplot2_3.3.3        tidyverse_1.3.0     

loaded via a namespace (and not attached):
 [1] colorspace_2.0-0     ellipsis_0.3.1       rsconnect_0.8.16     rprojroot_2.0.2     
 [5] snakecase_0.11.0     base64enc_0.1-3      fs_1.5.0             rstudioapi_0.13     
 [9] farver_2.0.3         rstan_2.21.2         graphlayouts_0.7.1   ggrepel_0.9.1       
[13] fansi_0.4.2          xml2_1.3.2           codetools_0.2-16     knitr_1.31          
[17] polyclip_1.10-0      jsonlite_1.7.2       packrat_0.5.0        broom_0.7.5         
[21] gganimate_1.0.7      dbplyr_2.1.0         ggforce_0.3.2        compiler_3.6.2      
[25] httr_1.4.2           backports_1.2.1      assertthat_0.2.1     fastmap_1.0.1       
[29] cli_2.3.1            later_1.1.0.1        tweenr_1.0.1         htmltools_0.5.1.1   
[33] prettyunits_1.1.1    tools_3.6.2          igraph_1.2.6         gtable_0.3.0        
[37] glue_1.4.2           V8_3.4.0             Rcpp_1.0.6           jquerylib_0.1.3     
[41] cellranger_1.1.0     vctrs_0.3.6          crosstalk_1.1.1      xfun_0.19           
[45] ps_1.3.2             rvest_0.3.6          mime_0.9             lifecycle_1.0.0     
[49] MASS_7.3-51.4        hms_1.0.0            promises_1.1.1       parallel_3.6.2      
[53] inline_0.3.17        yaml_2.2.1           curl_4.3             sass_0.3.1          
[57] loo_2.4.1            StanHeaders_2.21.0-6 stringi_1.5.3        gifski_0.8.6        
[61] pkgbuild_1.2.0       repr_1.1.3           matrixStats_0.57.0   rlang_0.4.10        
[65] pkgconfig_2.0.3      evaluate_0.14        lattice_0.20-38      htmlwidgets_1.5.3   
[69] labeling_0.4.2       tidyselect_1.1.0     processx_3.4.4       plyr_1.8.6          
[73] R6_2.5.0             generics_0.1.0       DBI_1.1.1            pillar_1.6.0        
[77] haven_2.3.1          withr_2.4.1          modelr_0.1.8         crayon_1.4.1        
[81] utf8_1.1.4           rmarkdown_2.7        viridis_0.5.1        progress_1.2.2      
[85] grid_3.6.2           callr_3.5.1          reprex_1.0.0         digest_0.6.27       
[89] xtable_1.8-4         httpuv_1.5.4         RcppParallel_5.0.2   stats4_3.6.2        
[93] munsell_0.5.0        viridisLite_0.3.0    bslib_0.2.4 

[cpsievert]

@michaelgaunt404 your theme definition is off. You probably want base_font (not font) set to a Google Font? https://rstudio.github.io/bslib/articles/bslib.html#custom-themes

[cpsievert]

If that doesn't fix your issues, you might need to update to a more recent version of R